Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
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cln_sentence
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is_cap
bool
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cit_qc
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lgtm
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__index_level_0__
int64
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Figure 1.Structural transitions involving SL1.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
46
9,400
0
false
Figure 1.Structural transitions involving SL1.
[]
Figure 1.Structural transitions involving SL1.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
(A) The 5′-leader in the HIV-1 RNA genome.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
42
9,401
0
false
(A) The 5′-leader in the HIV-1 RNA genome.
[]
(A) The 5′-leader in the HIV-1 RNA genome.
false
false
true
true
false
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
180
9,402
0
false
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
[]
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
102
9,403
0
false
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
[]
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
false
false
true
true
false
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Base-pairs added to stem I are shown in italic.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
47
9,404
0
false
Base-pairs added to stem I are shown in italic.
[]
Base-pairs added to stem I are shown in italic.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
116
9,405
0
false
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
[]
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
171
9,406
0
false
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
[]
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
146
9,407
0
false
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
[]
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Guanine imino signals that could not be assigned are labeled with a question mark.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
82
9,408
0
false
Guanine imino signals that could not be assigned are labeled with a question mark.
[]
Guanine imino signals that could not be assigned are labeled with a question mark.
true
true
true
true
true
1,494
1
INTRODUCTION
1
41
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1 (41).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
93
9,409
1
false
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1.
[ "41" ]
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
85
9,410
0
false
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
[]
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
167
9,411
0
false
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
[]
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
134
9,412
0
false
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
[]
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
true
true
true
true
true
1,494
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Structural transitions involving SL1.
[ "41" ]
37
9,413
0
false
Structural transitions involving SL1.
[]
Structural transitions involving SL1.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
(A) The 5′-leader in the HIV-1 RNA genome.
[ "41" ]
42
9,414
0
false
(A) The 5′-leader in the HIV-1 RNA genome.
[]
(A) The 5′-leader in the HIV-1 RNA genome.
false
false
true
true
false
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
[ "41" ]
180
9,415
0
false
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
[]
Dynamical transitions between (B) metastable kissing and stable duplex SL1 dimers and (C) ‘long distance interaction’ (LDI) and ‘branched multiple hairpin’ (BMH) leader conformers.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
[ "41" ]
102
9,416
0
false
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
[]
(D) Spectroscopic comparison of the SL1m mutant used in the NMR study and the wild-type kissing dimer.
false
false
true
true
false
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Base-pairs added to stem I are shown in italic.
[ "41" ]
47
9,417
0
false
Base-pairs added to stem I are shown in italic.
[]
Base-pairs added to stem I are shown in italic.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
[ "41" ]
116
9,418
0
false
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
[]
Residues exhibiting significant chemical shift differences relative to the wild-type kissing dimer are shown in red.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
[ "41" ]
171
9,419
0
false
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
[]
Overlays of 2D 1H–15N and 1H–13C and HSQC spectra of SL1m (in black) on corresponding spectra of the wild-type SL1 kissing dimer (in red) in the absence of Mg2+ are shown.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
[ "41" ]
146
9,420
0
false
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
[]
Peaks from the GC-rich loop in the kissing dimer are indicated using an asterisk and those belonging to the GAGA SL1m tetraloop labeled in italic.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Guanine imino signals that could not be assigned are labeled with a question mark.
[ "41" ]
82
9,421
0
false
Guanine imino signals that could not be assigned are labeled with a question mark.
[]
Guanine imino signals that could not be assigned are labeled with a question mark.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1 (41).
[ "41" ]
93
9,422
1
false
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1.
[ "41" ]
Similar unaccounted for guanine peaks have been reported in previous NMR studies of SL1.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
[ "41" ]
85
9,423
0
false
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
[]
One of those peaks has a weak NOESY cross peak to G2 consistent with a G1 assignment.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
[ "41" ]
167
9,424
0
false
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
[]
Through comparison with spectra of elongated SL1m, one uridine and two guanine signals could also be assigned to alternative forms of terminal residues G1, G2 and U34.
true
true
true
true
true
1,495
2
INTRODUCTION
1
41
[ "B41" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
[ "41" ]
134
9,425
0
false
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
[]
In the absence of Mg2+, the U10 imino signal could not be observed while that of U11 could only be observed at low temperatures (5°C).
true
true
true
true
true
1,495
3
INTRODUCTION
1
17
[ "B17", "B18", "B19 B20 B21 B22 B23 B24 B25", "B26" ]
17,311,812
pmid-8969239|pmid-8755517|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-11702070
In vitro studies show that treatment of kissing SL1 dimers with the NCp7 protein (the maturated form of the Gag NC domain) results in the formation of a more stable duplex dimer in which two SL1 molecules are held together by extensive inter-strand base-pairing (Figure 1B) (17,18).
[ "17", "18", "19–25", "26" ]
282
9,426
0
false
In vitro studies show that treatment of kissing SL1 dimers with the NCp7 protein (the maturated form of the Gag NC domain) results in the formation of a more stable duplex dimer in which two SL1 molecules are held together by extensive inter-strand base-pairing (Figure 1B).
[ "17,18" ]
In vitro studies show that treatment of kissing SL1 dimers with the NCp7 protein (the maturated form of the Gag NC domain) results in the formation of a more stable duplex dimer in which two SL1 molecules are held together by extensive inter-strand base-pairing.
true
true
true
true
true
1,496
3
INTRODUCTION
1
17
[ "B17", "B18", "B19 B20 B21 B22 B23 B24 B25", "B26" ]
17,311,812
pmid-8969239|pmid-8755517|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-11702070
This duplex dimer is believed to be a key component of the in vivo maturated heat-stable dimer.
[ "17", "18", "19–25", "26" ]
95
9,427
0
false
This duplex dimer is believed to be a key component of the in vivo maturated heat-stable dimer.
[]
This duplex dimer is believed to be a key component of the in vivo maturated heat-stable dimer.
true
true
true
true
true
1,496
3
INTRODUCTION
1
19–25
[ "B17", "B18", "B19 B20 B21 B22 B23 B24 B25", "B26" ]
17,311,812
pmid-8969239|pmid-8755517|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-11702070
The conformational pathway between the kissing and duplex SL1 dimer is thought to involve the melting and reannealing of strands without disrupting the loop–loop interaction (19–25) though an alternative mechanism involving a transesterification mechanism has also been proposed (26).
[ "17", "18", "19–25", "26" ]
284
9,428
1
false
The conformational pathway between the kissing and duplex SL1 dimer is thought to involve the melting and reannealing of strands without disrupting the loop–loop interaction though an alternative mechanism involving a transesterification mechanism has also been proposed.
[ "19–25", "26" ]
The conformational pathway between the kissing and duplex SL1 dimer is thought to involve the melting and reannealing of strands without disrupting the loop–loop interaction though an alternative mechanism involving a transesterification mechanism has also been proposed.
true
true
true
true
true
1,496
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
There is evidence that dimerization and packaging of the HIV-1 RNA genome is further regulated by another conformational switch involving SL1 and the poly(A) hairpin in the 5′-leader (Figure 1C).
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
195
9,429
0
false
There is evidence that dimerization and packaging of the HIV-1 RNA genome is further regulated by another conformational switch involving SL1 and the poly(A) hairpin in the 5′-leader (Figure 1C).
[]
There is evidence that dimerization and packaging of the HIV-1 RNA genome is further regulated by another conformational switch involving SL1 and the poly(A) hairpin in the 5′-leader (Figure 1C).
true
true
true
true
true
1,497
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
The 5′-leader RNA can adopt two distinct conformations that migrate at different rates on native polyacrylamide gels (27,28).
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
125
9,430
0
false
The 5′-leader RNA can adopt two distinct conformations that migrate at different rates on native polyacrylamide gels.
[ "27,28" ]
The 5′-leader RNA can adopt two distinct conformations that migrate at different rates on native polyacrylamide gels.
true
true
true
true
true
1,497
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
Secondary structure prediction and chemical probing suggest that the faster migrating species adopts an extended ‘long distance interaction’ (LDI) conformation that cannot be converted into dimers because the SL1 apical loop is masked by base-pairing with the poly(A) hairpin (Figure 1C)
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
287
9,431
0
false
Secondary structure prediction and chemical probing suggest that the faster migrating species adopts an extended ‘long distance interaction’ (LDI) conformation that cannot be converted into dimers because the SL1 apical loop is masked by base-pairing with the poly(A) hairpin (Figure 1C)
[]
Secondary structure prediction and chemical probing suggest that the faster migrating species adopts an extended ‘long distance interaction’ (LDI) conformation that cannot be converted into dimers because the SL1 apical loop is masked by base-pairing with the poly(A) hairpin (Figure 1C)
true
true
false
true
false
1,497
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
The slowly migrating species is believed to be the conventional ‘branched multiple hairpin’ (BMH) conformer which is capable of dimerizing since the SL1 apical loop is exposed and available for self-pairing (Figure 1C)
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
218
9,432
0
false
The slowly migrating species is believed to be the conventional ‘branched multiple hairpin’ (BMH) conformer which is capable of dimerizing since the SL1 apical loop is exposed and available for self-pairing (Figure 1C)
[]
The slowly migrating species is believed to be the conventional ‘branched multiple hairpin’ (BMH) conformer which is capable of dimerizing since the SL1 apical loop is exposed and available for self-pairing (Figure 1C)
true
true
false
true
false
1,497
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
Chemical probing experiments show that LDI can be converted into BMH by addition of NCp7 and that Mg2+ stabilizes BMH over LDI (9,27,28).
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
137
9,433
0
false
Chemical probing experiments show that LDI can be converted into BMH by addition of NCp7 and that Mg2+ stabilizes BMH over LDI.
[ "9,27,28" ]
Chemical probing experiments show that LDI can be converted into BMH by addition of NCp7 and that Mg2+ stabilizes BMH over LDI.
true
true
true
true
true
1,497
4
INTRODUCTION
1
27
[ "B27", "B28", "B28", "B28", "B9", "B27", "B28", "B27", "B29" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
This conformational switch is proposed to regulate dimerization and possibly packaging of the HIV-1 genome (27,29).
[ "27", "28", "28", "28", "9", "27", "28", "27", "29" ]
115
9,434
0
false
This conformational switch is proposed to regulate dimerization and possibly packaging of the HIV-1 genome.
[ "27,29" ]
This conformational switch is proposed to regulate dimerization and possibly packaging of the HIV-1 genome.
true
true
true
true
true
1,497
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
NC is known to bind single-stranded RNA particularly regions that have exposed guanine residues (30,31).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
104
9,435
0
false
NC is known to bind single-stranded RNA particularly regions that have exposed guanine residues.
[ "30,31" ]
NC is known to bind single-stranded RNA particularly regions that have exposed guanine residues.
true
true
true
true
true
1,498
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
In addition to the GC-rich apical loop, a candidate site in SL1 for NC binding is the highly conserved A271G272G273 × G247 internal loop (Figure 1A and B).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
155
9,436
0
false
In addition to the GC-rich apical loop, a candidate site in SL1 for NC binding is the highly conserved A271G272G273 × G247 internal loop (Figure 1A and B).
[]
In addition to the GC-rich apical loop, a candidate site in SL1 for NC binding is the highly conserved A271G272G273 × G247 internal loop (Figure 1A and B).
true
true
true
true
true
1,498
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
The internal loop has been shown to be essential for the kissing–duplex transition and for proper packaging of the HIV-1 genome (22,32).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
136
9,437
0
false
The internal loop has been shown to be essential for the kissing–duplex transition and for proper packaging of the HIV-1 genome.
[ "22,32" ]
The internal loop has been shown to be essential for the kissing–duplex transition and for proper packaging of the HIV-1 genome.
true
true
true
true
true
1,498
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Chemical probing experiments show that guanine residues G272 and G273 in the internal loop are accessible in the context of the 206 nt Ψ
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
136
9,438
0
false
Chemical probing experiments show that guanine residues G272 and G273 in the internal loop are accessible in the context of the 206 nt Ψ
[]
Chemical probing experiments show that guanine residues G272 and G273 in the internal loop are accessible in the context of the 206 nt Ψ
true
true
false
true
false
1,498
5
INTRODUCTION
1
33
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
HIV-1 RNA (33).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
15
9,439
1
false
HIV-1 RNA.
[ "33" ]
HIV-1 RNA.
true
true
true
true
true
1,498
5
INTRODUCTION
1
34
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Footprinting data on a 401-nt fragment of the HIV-1 RNA leader shows that G272 and G273 are both strongly accessible in the free RNA and strongly protected upon binding to GST-tagged Gag or NC (34).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
198
9,440
1
false
Footprinting data on a 401-nt fragment of the HIV-1 RNA leader shows that G272 and G273 are both strongly accessible in the free RNA and strongly protected upon binding to GST-tagged Gag or NC.
[ "34" ]
Footprinting data on a 401-nt fragment of the HIV-1 RNA leader shows that G272 and G273 are both strongly accessible in the free RNA and strongly protected upon binding to GST-tagged Gag or NC.
true
true
true
true
true
1,498
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Fluorescence experiments on isolated SL1 constructs show that NCp7 can bind to both the apical loop and internal loop (23,35).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
126
9,441
0
false
Fluorescence experiments on isolated SL1 constructs show that NCp7 can bind to both the apical loop and internal loop.
[ "23,35" ]
Fluorescence experiments on isolated SL1 constructs show that NCp7 can bind to both the apical loop and internal loop.
true
true
true
true
true
1,498
5
INTRODUCTION
1
36
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
More recent studies using electrospray ionization-Fourier transform mass spectrometry show that the interaction between NC and the internal loop is key for inducing the kissing–duplex structural transition whereas the interaction with the apical loop can inhibit dimer formation (36).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
284
9,442
1
false
More recent studies using electrospray ionization-Fourier transform mass spectrometry show that the interaction between NC and the internal loop is key for inducing the kissing–duplex structural transition whereas the interaction with the apical loop can inhibit dimer formation.
[ "36" ]
More recent studies using electrospray ionization-Fourier transform mass spectrometry show that the interaction between NC and the internal loop is key for inducing the kissing–duplex structural transition whereas the interaction with the apical loop can inhibit dimer formation.
true
true
true
true
true
1,498
5
INTRODUCTION
1
37–41
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Five NMR structures reported for various SL1 constructs containing the internal loop show different conformations and levels of accessibility for internal loop residues G272 and G273 making it difficult to assess if they are structurally available for NC recognition (37–41).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
275
9,443
1
false
Five NMR structures reported for various SL1 constructs containing the internal loop show different conformations and levels of accessibility for internal loop residues G272 and G273 making it difficult to assess if they are structurally available for NC recognition.
[ "37–41" ]
Five NMR structures reported for various SL1 constructs containing the internal loop show different conformations and levels of accessibility for internal loop residues G272 and G273 making it difficult to assess if they are structurally available for NC recognition.
true
true
true
true
true
1,498
5
INTRODUCTION
1
30
[ "B30", "B31", "B22", "B32", "B33", "B34", "B23", "B35", "B36", "B37 B38 B39 B40 B41", "B9", "B23", "B24" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
These NMR structures were all determined in the absence of divalent ions which are known to affect the SL1 structural transitions (9,23,24).
[ "30", "31", "22", "32", "33", "34", "23", "35", "36", "37–41", "9", "23", "24" ]
140
9,444
0
false
These NMR structures were all determined in the absence of divalent ions which are known to affect the SL1 structural transitions.
[ "9,23,24" ]
These NMR structures were all determined in the absence of divalent ions which are known to affect the SL1 structural transitions.
true
true
true
true
true
1,498
6
INTRODUCTION
1
42–44
[ "B42 B43 B44", "B23", "B45", "B46", "B22", "B37", "B38" ]
17,311,812
pmid-14627827|pmid-15025916|pmid-16403527|pmid-12475224|pmid-15150793|pmid-14734802|pmid-10668802|pmid-12225748|pmid-12559920
The involvement of SL1 in two distinct functionally important structural transitions raises the possibility that its structure codes for inherent plasticity that allows these conformational changes to take place in a specific and regulated manner.
[ "42–44", "23", "45", "46", "22", "37", "38" ]
247
9,445
0
false
The involvement of SL1 in two distinct functionally important structural transitions raises the possibility that its structure codes for inherent plasticity that allows these conformational changes to take place in a specific and regulated manner.
[]
The involvement of SL1 in two distinct functionally important structural transitions raises the possibility that its structure codes for inherent plasticity that allows these conformational changes to take place in a specific and regulated manner.
true
true
true
true
true
1,499
6
INTRODUCTION
1
42–44
[ "B42 B43 B44", "B23", "B45", "B46", "B22", "B37", "B38" ]
17,311,812
pmid-14627827|pmid-15025916|pmid-16403527|pmid-12475224|pmid-15150793|pmid-14734802|pmid-10668802|pmid-12225748|pmid-12559920
The kissing loop has been shown to be flexible particularly in the absence of Mg2+ (42–44) and this plasticity is believed to facilitate the exchange of strands during the kissing–duplex transition (23,45,46).
[ "42–44", "23", "45", "46", "22", "37", "38" ]
209
9,446
1
false
The kissing loop has been shown to be flexible particularly in the absence of Mg2+ and this plasticity is believed to facilitate the exchange of strands during the kissing–duplex transition.
[ "42–44", "23,45,46" ]
The kissing loop has been shown to be flexible particularly in the absence of Mg2+ and this plasticity is believed to facilitate the exchange of strands during the kissing–duplex transition.
true
true
true
true
true
1,499
6
INTRODUCTION
1
42–44
[ "B42 B43 B44", "B23", "B45", "B46", "B22", "B37", "B38" ]
17,311,812
pmid-14627827|pmid-15025916|pmid-16403527|pmid-12475224|pmid-15150793|pmid-14734802|pmid-10668802|pmid-12225748|pmid-12559920
There is also evidence that the internal loop introduces flexibility into SL1 that is essential for the kissing–duplex transition.
[ "42–44", "23", "45", "46", "22", "37", "38" ]
130
9,447
0
false
There is also evidence that the internal loop introduces flexibility into SL1 that is essential for the kissing–duplex transition.
[]
There is also evidence that the internal loop introduces flexibility into SL1 that is essential for the kissing–duplex transition.
true
true
true
true
true
1,499
6
INTRODUCTION
1
22
[ "B42 B43 B44", "B23", "B45", "B46", "B22", "B37", "B38" ]
17,311,812
pmid-14627827|pmid-15025916|pmid-16403527|pmid-12475224|pmid-15150793|pmid-14734802|pmid-10668802|pmid-12225748|pmid-12559920
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers in the absence of NCp7 when incubated at 55°C whereas corresponding constructs lacking the internal loop cannot even in the presence of NCp7 (22).
[ "42–44", "23", "45", "46", "22", "37", "38" ]
239
9,448
1
false
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers in the absence of NCp7 when incubated at 55°C whereas corresponding constructs lacking the internal loop cannot even in the presence of NCp7.
[ "22" ]
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers in the absence of NCp7 when incubated at 55°C whereas corresponding constructs lacking the internal loop cannot even in the presence of NCp7.
true
true
true
true
true
1,499
6
INTRODUCTION
1
42–44
[ "B42 B43 B44", "B23", "B45", "B46", "B22", "B37", "B38" ]
17,311,812
pmid-14627827|pmid-15025916|pmid-16403527|pmid-12475224|pmid-15150793|pmid-14734802|pmid-10668802|pmid-12225748|pmid-12559920
Thus far, two NMR studies of SL1 monomers in the absence of Mg2+ provide conflicting views regarding the presence/absence of flexibility at the internal loop (37,38).
[ "42–44", "23", "45", "46", "22", "37", "38" ]
166
9,449
0
false
Thus far, two NMR studies of SL1 monomers in the absence of Mg2+ provide conflicting views regarding the presence/absence of flexibility at the internal loop.
[ "37,38" ]
Thus far, two NMR studies of SL1 monomers in the absence of Mg2+ provide conflicting views regarding the presence/absence of flexibility at the internal loop.
true
true
true
true
true
1,499
7
INTRODUCTION
1
49
[ "B47", "B48", "B49" ]
17,311,812
pmid-7568117|pmid-9353189|pmid-16456078
In this study, we used a combination of NMR techniques, including residual dipolar couplings (RDCs) (47,48), dynamically decoupled spin relaxation (49) and chemical shift mapping to quantitatively characterize the internal flexibility of an SL1 monomer containing the internal loop and how it varies upon Mg2+ binding.
[ "47", "48", "49" ]
318
9,450
1
false
In this study, we used a combination of NMR techniques, including residual dipolar couplings (RDCs), dynamically decoupled spin relaxation and chemical shift mapping to quantitatively characterize the internal flexibility of an SL1 monomer containing the internal loop and how it varies upon Mg2+ binding.
[ "47,48", "49" ]
In this study, we used a combination of NMR techniques, including residual dipolar couplings (RDCs), dynamically decoupled spin relaxation and chemical shift mapping to quantitatively characterize the internal flexibility of an SL1 monomer containing the internal loop and how it varies upon Mg2+ binding.
true
true
true
true
true
1,500
7
INTRODUCTION
1
47
[ "B47", "B48", "B49" ]
17,311,812
pmid-7568117|pmid-9353189|pmid-16456078
Our results suggest that the SL1 internal loop codes for internal flexibility that renders the upper stem a dynamical nucleation site for strand exchange during the kissing–duplex transition.
[ "47", "48", "49" ]
191
9,451
0
false
Our results suggest that the SL1 internal loop codes for internal flexibility that renders the upper stem a dynamical nucleation site for strand exchange during the kissing–duplex transition.
[]
Our results suggest that the SL1 internal loop codes for internal flexibility that renders the upper stem a dynamical nucleation site for strand exchange during the kissing–duplex transition.
true
true
true
true
true
1,500
7
INTRODUCTION
1
47
[ "B47", "B48", "B49" ]
17,311,812
pmid-7568117|pmid-9353189|pmid-16456078
We show that Mg2+ specifically binds to the internal loop stabilizing the overall SL1 structure while maintaining high local mobility in internal loop residues G272 and G273 making them available for NC binding.
[ "47", "48", "49" ]
211
9,452
0
false
We show that Mg2+ specifically binds to the internal loop stabilizing the overall SL1 structure while maintaining high local mobility in internal loop residues G272 and G273 making them available for NC binding.
[]
We show that Mg2+ specifically binds to the internal loop stabilizing the overall SL1 structure while maintaining high local mobility in internal loop residues G272 and G273 making them available for NC binding.
true
true
true
true
true
1,500
7
INTRODUCTION
1
47
[ "B47", "B48", "B49" ]
17,311,812
pmid-7568117|pmid-9353189|pmid-16456078
We suggest that by stabilizing SL1, Mg2+ deters spontaneous kissing–duplex transitions from taking place making the process more dependent on NC binding and thus ensuring that RNA and protein maturation occur in concert.
[ "47", "48", "49" ]
220
9,453
0
false
We suggest that by stabilizing SL1, Mg2+ deters spontaneous kissing–duplex transitions from taking place making the process more dependent on NC binding and thus ensuring that RNA and protein maturation occur in concert.
[]
We suggest that by stabilizing SL1, Mg2+ deters spontaneous kissing–duplex transitions from taking place making the process more dependent on NC binding and thus ensuring that RNA and protein maturation occur in concert.
true
true
true
true
true
1,500
0
DISCUSSION
0
null
null
17,311,812
pmid-2124274|pmid-1645868|pmid-15152202|pmid-16064056|pmid-9217051|pmid-7947755|pmid-8197162|pmid-8768071|pmid-10688366|pmid-15152202|pmid-16064056
SL1 is a highly conserved stem-loop in the HIV-1 leader RNA that is believed to be involved in functionally important structural transitions that are modulated by Mg2+ binding and that are catalyzed by NC.
null
205
9,454
0
false
null
null
SL1 is a highly conserved stem-loop in the HIV-1 leader RNA that is believed to be involved in functionally important structural transitions that are modulated by Mg2+ binding and that are catalyzed by NC.
true
true
true
true
true
1,501
0
DISCUSSION
0
null
null
17,311,812
pmid-2124274|pmid-1645868|pmid-15152202|pmid-16064056|pmid-9217051|pmid-7947755|pmid-8197162|pmid-8768071|pmid-10688366|pmid-15152202|pmid-16064056
In our study, we examined the dynamical and Mg2+-binding properties of the SL1 structure with the goal of obtaining new insight into the molecular basis of its structural transitions.
null
183
9,455
0
false
null
null
In our study, we examined the dynamical and Mg2+-binding properties of the SL1 structure with the goal of obtaining new insight into the molecular basis of its structural transitions.
true
true
true
true
true
1,501
1
DISCUSSION
1
37
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Our study suggests that the highly conserved SL1 internal loop sequence specifically destabilizes the upper stem by allowing formation of two (or possibly more) competing secondary structures (Figure 2C).
[ "37", "37", "86" ]
204
9,456
0
false
Our study suggests that the highly conserved SL1 internal loop sequence specifically destabilizes the upper stem by allowing formation of two (or possibly more) competing secondary structures (Figure 2C).
[]
Our study suggests that the highly conserved SL1 internal loop sequence specifically destabilizes the upper stem by allowing formation of two (or possibly more) competing secondary structures (Figure 2C).
true
true
true
true
true
1,502
1
DISCUSSION
1
37
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
This conformational equilibrium is intricately dependent on the sequence of the AGG internal loop and neighboring residues in stem II.
[ "37", "37", "86" ]
134
9,457
0
false
This conformational equilibrium is intricately dependent on the sequence of the AGG internal loop and neighboring residues in stem II.
[]
This conformational equilibrium is intricately dependent on the sequence of the AGG internal loop and neighboring residues in stem II.
true
true
true
true
true
1,502
1
DISCUSSION
1
37
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
For example, the reduced exchange broadening observed in the GGA internal loop mutant can be explained by its inability to slip into the B conformer (37).
[ "37", "37", "86" ]
154
9,458
1
false
For example, the reduced exchange broadening observed in the GGA internal loop mutant can be explained by its inability to slip into the B conformer.
[ "37" ]
For example, the reduced exchange broadening observed in the GGA internal loop mutant can be explained by its inability to slip into the B conformer.
true
true
true
true
true
1,502
1
DISCUSSION
1
37
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
A similar argument could be used to explain the higher stabilities of other SL1 internal loop mutants (37).
[ "37", "37", "86" ]
107
9,459
1
false
A similar argument could be used to explain the higher stabilities of other SL1 internal loop mutants.
[ "37" ]
A similar argument could be used to explain the higher stabilities of other SL1 internal loop mutants.
true
true
true
true
true
1,502
1
DISCUSSION
1
86
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Interestingly, a uridine-substituted SL1 internal loop does not disrupt dimer formation but results in a mutant virus with diminished genome packaging (86).
[ "37", "37", "86" ]
156
9,460
1
false
Interestingly, a uridine-substituted SL1 internal loop does not disrupt dimer formation but results in a mutant virus with diminished genome packaging.
[ "86" ]
Interestingly, a uridine-substituted SL1 internal loop does not disrupt dimer formation but results in a mutant virus with diminished genome packaging.
true
true
true
true
true
1,502
1
DISCUSSION
1
37
[ "B37", "B37", "B86" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
In addition to possibly interfering with NC binding, the uridine substitution is expected to impair formation of the B conformer and thus stabilize the internal loop and upper stem.
[ "37", "37", "86" ]
181
9,461
0
false
In addition to possibly interfering with NC binding, the uridine substitution is expected to impair formation of the B conformer and thus stabilize the internal loop and upper stem.
[]
In addition to possibly interfering with NC binding, the uridine substitution is expected to impair formation of the B conformer and thus stabilize the internal loop and upper stem.
true
true
true
true
true
1,502
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers at 55°C in the absence of Mg2+ whereas constructs lacking the internal loop cannot (22).
[ "22", "19–25", "23", "25", "22" ]
181
9,462
1
false
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers at 55°C in the absence of Mg2+ whereas constructs lacking the internal loop cannot.
[ "22" ]
SL1 kissing dimers containing the internal loop can spontaneously convert into duplex dimers at 55°C in the absence of Mg2+ whereas constructs lacking the internal loop cannot.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Our results show that the internal loop introduces internal flexibility into the SL1m structure that can promote the kissing–duplex transition.
[ "22", "19–25", "23", "25", "22" ]
143
9,463
0
false
Our results show that the internal loop introduces internal flexibility into the SL1m structure that can promote the kissing–duplex transition.
[]
Our results show that the internal loop introduces internal flexibility into the SL1m structure that can promote the kissing–duplex transition.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
The transition requires the exchange of strands between monomers in the kissing dimer which in turn requires that strands from the two monomers come into close proximity.
[ "22", "19–25", "23", "25", "22" ]
170
9,464
0
false
The transition requires the exchange of strands between monomers in the kissing dimer which in turn requires that strands from the two monomers come into close proximity.
[]
The transition requires the exchange of strands between monomers in the kissing dimer which in turn requires that strands from the two monomers come into close proximity.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
The two stems above the internal loop are likely candidates for initiating strand exchange since they are the most closely positioned in the kissing dimer (Figure 8).
[ "22", "19–25", "23", "25", "22" ]
166
9,465
0
false
The two stems above the internal loop are likely candidates for initiating strand exchange since they are the most closely positioned in the kissing dimer (Figure 8).
[]
The two stems above the internal loop are likely candidates for initiating strand exchange since they are the most closely positioned in the kissing dimer (Figure 8).
true
true
true
true
true
1,503
2
DISCUSSION
1
19–25
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Studies have shown that the kissing–duplex transition can occur without disrupting the loop–loop interaction (19–25).
[ "22", "19–25", "23", "25", "22" ]
117
9,466
1
false
Studies have shown that the kissing–duplex transition can occur without disrupting the loop–loop interaction.
[ "19–25" ]
Studies have shown that the kissing–duplex transition can occur without disrupting the loop–loop interaction.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
The two monomers can be brought into close proximity without disrupting the loop–loop interaction by rotating each monomer around a direction perpendicular to the C2 axis of symmetry.
[ "22", "19–25", "23", "25", "22" ]
183
9,467
0
false
The two monomers can be brought into close proximity without disrupting the loop–loop interaction by rotating each monomer around a direction perpendicular to the C2 axis of symmetry.
[]
The two monomers can be brought into close proximity without disrupting the loop–loop interaction by rotating each monomer around a direction perpendicular to the C2 axis of symmetry.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Such a rotation ensures that C2 symmetry is maintained in the dimer during the transition.
[ "22", "19–25", "23", "25", "22" ]
90
9,468
0
false
Such a rotation ensures that C2 symmetry is maintained in the dimer during the transition.
[]
Such a rotation ensures that C2 symmetry is maintained in the dimer during the transition.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
This leads to formation of an intermediate in which base-pairs in the upper stem are proximate and poised to form both inter- and intra-molecular hydrogen bonding.
[ "22", "19–25", "23", "25", "22" ]
163
9,469
0
false
This leads to formation of an intermediate in which base-pairs in the upper stem are proximate and poised to form both inter- and intra-molecular hydrogen bonding.
[]
This leads to formation of an intermediate in which base-pairs in the upper stem are proximate and poised to form both inter- and intra-molecular hydrogen bonding.
true
true
true
true
true
1,503
2
DISCUSSION
1
23
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Such an intermediate has previously been proposed (23) and recently visualized by molecular dynamics simulations in the context of short kissing SL1 dimers lacking the internal loop (25).
[ "22", "19–25", "23", "25", "22" ]
187
9,470
1
false
Such an intermediate has previously been proposed and recently visualized by molecular dynamics simulations in the context of short kissing SL1 dimers lacking the internal loop.
[ "23", "25" ]
Such an intermediate has previously been proposed and recently visualized by molecular dynamics simulations in the context of short kissing SL1 dimers lacking the internal loop.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
The inclusion of the internal loop is expected to destabilize the upper stem making its base-pairs a key nucleation site for initiating the melting, exchange and reannealing of strands.
[ "22", "19–25", "23", "25", "22" ]
185
9,471
0
false
The inclusion of the internal loop is expected to destabilize the upper stem making its base-pairs a key nucleation site for initiating the melting, exchange and reannealing of strands.
[]
The inclusion of the internal loop is expected to destabilize the upper stem making its base-pairs a key nucleation site for initiating the melting, exchange and reannealing of strands.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
This would explain why constructs lacking the internal loop cannot undergo the kissing–duplex transition spontaneously (22).
[ "22", "19–25", "23", "25", "22" ]
124
9,472
1
false
This would explain why constructs lacking the internal loop cannot undergo the kissing–duplex transition spontaneously.
[ "22" ]
This would explain why constructs lacking the internal loop cannot undergo the kissing–duplex transition spontaneously.
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Due to inter-helical kinking, the lower stems are not expected to be in immediate register in the intermediate and inter-stem flexibility may play a role in bringing the lower stems into proper register for completing strand exchange (Figure 8).
[ "22", "19–25", "23", "25", "22" ]
245
9,473
0
false
Due to inter-helical kinking, the lower stems are not expected to be in immediate register in the intermediate and inter-stem flexibility may play a role in bringing the lower stems into proper register for completing strand exchange (Figure 8).
[]
Due to inter-helical kinking, the lower stems are not expected to be in immediate register in the intermediate and inter-stem flexibility may play a role in bringing the lower stems into proper register for completing strand exchange (Figure 8).
true
true
true
true
true
1,503
2
DISCUSSION
1
22
[ "B22", "B19 B20 B21 B22 B23 B24 B25", "B23", "B25", "B22" ]
17,311,812
pmid-16603544|pmid-10668802|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-12475224|pmid-16023135|pmid-10668802
Figure 8.Proposed role for internal loop-induced dynamics and Mg2+ binding in spontaneous and NC-dependent SL1 structural transition between kissing and duplex dimers.
[ "22", "19–25", "23", "25", "22" ]
167
9,474
0
false
Figure 8.Proposed role for internal loop-induced dynamics and Mg2+ binding in spontaneous and NC-dependent SL1 structural transition between kissing and duplex dimers.
[]
Figure 8.Proposed role for internal loop-induced dynamics and Mg2+ binding in spontaneous and NC-dependent SL1 structural transition between kissing and duplex dimers.
true
true
true
true
true
1,503
3
DISCUSSION
0
null
null
17,311,812
pmid-8969239|pmid-8755517|pmid-8987995|pmid-10785394|pmid-10739962|pmid-10668802|pmid-12475224|pmid-14602899|pmid-16023135|pmid-11702070
Proposed role for internal loop-induced dynamics and Mg2+ binding in spontaneous and NC-dependent SL1 structural transition between kissing and duplex dimers.
null
158
9,475
0
false
null
null
Proposed role for internal loop-induced dynamics and Mg2+ binding in spontaneous and NC-dependent SL1 structural transition between kissing and duplex dimers.
true
true
true
true
true
1,504
4
DISCUSSION
1
38
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
Our results show that Mg2+ binds to the SL1 internal loop region without significantly altering the average SL1 structure.
[ "38", "24", "23" ]
122
9,476
0
false
Our results show that Mg2+ binds to the SL1 internal loop region without significantly altering the average SL1 structure.
[]
Our results show that Mg2+ binds to the SL1 internal loop region without significantly altering the average SL1 structure.
true
true
true
true
true
1,505
4
DISCUSSION
1
38
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
Electrostatic calculations on the SL1m structure determined in the absence of Mg2+ (38) shows that residues that experience the largest Mg2+-induced chemical shift changes belong to regions with strong negative electrostatic potential (Figure S7).
[ "38", "24", "23" ]
247
9,477
1
false
Electrostatic calculations on the SL1m structure determined in the absence of Mg2+ shows that residues that experience the largest Mg2+-induced chemical shift changes belong to regions with strong negative electrostatic potential (Figure S7).
[ "38" ]
Electrostatic calculations on the SL1m structure determined in the absence of Mg2+ shows that residues that experience the largest Mg2+-induced chemical shift changes belong to regions with strong negative electrostatic potential (Figure S7).
true
true
true
true
true
1,505
4
DISCUSSION
1
38
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
The RDCs and relaxation data do however show that Mg2+ arrests the dynamical equilibrium stabilizing the hydrogen bond alignments in the upper stem while simultaneously reducing inter-stem motions.
[ "38", "24", "23" ]
197
9,478
0
false
The RDCs and relaxation data do however show that Mg2+ arrests the dynamical equilibrium stabilizing the hydrogen bond alignments in the upper stem while simultaneously reducing inter-stem motions.
[]
The RDCs and relaxation data do however show that Mg2+ arrests the dynamical equilibrium stabilizing the hydrogen bond alignments in the upper stem while simultaneously reducing inter-stem motions.
true
true
true
true
true
1,505
4
DISCUSSION
1
38
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
In this regard, Mg2+ binding is expected to reduce the likelihood for spontaneous kissing–duplex transitions in SL1 constructs containing the internal loop.
[ "38", "24", "23" ]
156
9,479
0
false
In this regard, Mg2+ binding is expected to reduce the likelihood for spontaneous kissing–duplex transitions in SL1 constructs containing the internal loop.
[]
In this regard, Mg2+ binding is expected to reduce the likelihood for spontaneous kissing–duplex transitions in SL1 constructs containing the internal loop.
true
true
true
true
true
1,505
4
DISCUSSION
1
38
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
So far, only one study has explored the effects of Mg2+ binding on the spontaneous transition in SL1 constructs containing the internal loop.
[ "38", "24", "23" ]
141
9,480
0
false
So far, only one study has explored the effects of Mg2+ binding on the spontaneous transition in SL1 constructs containing the internal loop.
[]
So far, only one study has explored the effects of Mg2+ binding on the spontaneous transition in SL1 constructs containing the internal loop.
true
true
true
true
true
1,505
4
DISCUSSION
1
24
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
Using a ribozyme-based cleavage assay to monitor the kissing–duplex transition, this study showed that increasing the Mg2+ concentration (up to 100 mM) resulted in an increase in the probability for spontaneous kissing–duplex conversion (24).
[ "38", "24", "23" ]
242
9,481
1
false
Using a ribozyme-based cleavage assay to monitor the kissing–duplex transition, this study showed that increasing the Mg2+ concentration (up to 100 mM) resulted in an increase in the probability for spontaneous kissing–duplex conversion.
[ "24" ]
Using a ribozyme-based cleavage assay to monitor the kissing–duplex transition, this study showed that increasing the Mg2+ concentration (up to 100 mM) resulted in an increase in the probability for spontaneous kissing–duplex conversion.
true
true
true
true
true
1,505
4
DISCUSSION
1
23
[ "B38", "B24", "B23" ]
17,311,812
pmid-15367648|pmid-11214176|pmid-11214176|pmid-11214176|pmid-10688366|pmid-15367648|pmid-11214176|pmid-15367648|pmid-15966729|pmid-12559920|pmid-14602899|pmid-12475224
However at the low RNA concentrations used (∼0.01 mM compared to ∼1 mM used in other studies) the encounter of monomers may be rate-limiting and Mg2+ may increase the probability for encounter by stabilizing the loop–loop interaction (23).
[ "38", "24", "23" ]
239
9,482
1
false
However at the low RNA concentrations used (∼0.01 mM compared to ∼1 mM used in other studies) the encounter of monomers may be rate-limiting and Mg2+ may increase the probability for encounter by stabilizing the loop–loop interaction.
[ "23" ]
However at the low RNA concentrations used (∼0.01 mM compared to ∼1 mM used in other studies) the encounter of monomers may be rate-limiting and Mg2+ may increase the probability for encounter by stabilizing the loop–loop interaction.
true
true
true
true
true
1,505
5
DISCUSSION
1
30
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
In vivo, the transition between kissing and duplex dimers as well as between the LDI and BMH conformers is believed to be catalyzed by NC protein which is known to bind to exposed guanine residues (30,31).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
205
9,483
0
false
In vivo, the transition between kissing and duplex dimers as well as between the LDI and BMH conformers is believed to be catalyzed by NC protein which is known to bind to exposed guanine residues.
[ "30,31" ]
In vivo, the transition between kissing and duplex dimers as well as between the LDI and BMH conformers is believed to be catalyzed by NC protein which is known to bind to exposed guanine residues.
true
true
true
true
true
1,506
5
DISCUSSION
1
30
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Previous mapping studies have shown that G28 and G29 are accessible in the context of the 206 nt Ψ
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
98
9,484
0
false
Previous mapping studies have shown that G28 and G29 are accessible in the context of the 206 nt Ψ
[]
Previous mapping studies have shown that G28 and G29 are accessible in the context of the 206 nt Ψ
true
true
false
true
false
1,506
5
DISCUSSION
1
33
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
HIV-1 RNA (33).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
15
9,485
1
false
HIV-1 RNA.
[ "33" ]
HIV-1 RNA.
true
true
true
true
true
1,506
5
DISCUSSION
1
34
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Footprinting data on the 401-nt fragment of the RNA leader show that G28 and G29 are both strongly accessible in the free RNA and strongly protected upon binding to Gag and NC (34).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
181
9,486
1
false
Footprinting data on the 401-nt fragment of the RNA leader show that G28 and G29 are both strongly accessible in the free RNA and strongly protected upon binding to Gag and NC.
[ "34" ]
Footprinting data on the 401-nt fragment of the RNA leader show that G28 and G29 are both strongly accessible in the free RNA and strongly protected upon binding to Gag and NC.
true
true
true
true
true
1,506
5
DISCUSSION
1
36
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
A recent study suggests that NC binding to the SL1 internal loop is largely responsible for driving the kissing–duplex transition whereas binding at the apical loop inhibits dimer formation (36).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
195
9,487
1
false
A recent study suggests that NC binding to the SL1 internal loop is largely responsible for driving the kissing–duplex transition whereas binding at the apical loop inhibits dimer formation.
[ "36" ]
A recent study suggests that NC binding to the SL1 internal loop is largely responsible for driving the kissing–duplex transition whereas binding at the apical loop inhibits dimer formation.
true
true
true
true
true
1,506
5
DISCUSSION
1
36
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
The latter study also showed that NC binding to the SL1 internal loop is similar whether in the monomer or kissing dimer context further validating the relevance of our dynamical results on monomeric SL1m (36).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
210
9,488
1
false
The latter study also showed that NC binding to the SL1 internal loop is similar whether in the monomer or kissing dimer context further validating the relevance of our dynamical results on monomeric SL1m.
[ "36" ]
The latter study also showed that NC binding to the SL1 internal loop is similar whether in the monomer or kissing dimer context further validating the relevance of our dynamical results on monomeric SL1m.
true
true
true
true
true
1,506
5
DISCUSSION
1
30
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
Remarkably, our results show that while Mg2+ causes stabilization of the internal loop and upper stem, it increases or retains significant local flexibility in the base moieties of G28 and G29 likely making them available for NC binding.
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
237
9,489
0
false
Remarkably, our results show that while Mg2+ causes stabilization of the internal loop and upper stem, it increases or retains significant local flexibility in the base moieties of G28 and G29 likely making them available for NC binding.
[]
Remarkably, our results show that while Mg2+ causes stabilization of the internal loop and upper stem, it increases or retains significant local flexibility in the base moieties of G28 and G29 likely making them available for NC binding.
true
true
true
true
true
1,506
5
DISCUSSION
1
41
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
The RDCs measured in the presence and absence of Mg2+ are also consistent with an extra-helical conformation for G29 (Figure 8) (41).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
133
9,490
1
false
The RDCs measured in the presence and absence of Mg2+ are also consistent with an extra-helical conformation for G29 (Figure 8).
[ "41" ]
The RDCs measured in the presence and absence of Mg2+ are also consistent with an extra-helical conformation for G29 (Figure 8).
true
true
true
true
true
1,506
5
DISCUSSION
1
30
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
In this manner, Mg2+ binding may help ensure that the kissing–duplex conversion does not occur spontaneously and prematurely but rather only following NC binding (Figure 8).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
173
9,491
0
false
In this manner, Mg2+ binding may help ensure that the kissing–duplex conversion does not occur spontaneously and prematurely but rather only following NC binding (Figure 8).
[]
In this manner, Mg2+ binding may help ensure that the kissing–duplex conversion does not occur spontaneously and prematurely but rather only following NC binding (Figure 8).
true
true
true
true
true
1,506
5
DISCUSSION
1
88
[ "B30", "B31", "B33", "B34", "B36", "B36", "B41", "B88" ]
17,311,812
pmid-9430589|pmid-10926523|pmid-10668802|pmid-9094610|pmid-7884856|pmid-9685481|pmid-12475224|pmid-11955077|pmid-17020765|pmid-12225748|pmid-12559920|pmid-12731867|pmid-16272570|pmid-16603544|pmid-10688366|pmid-12475224|pmid-14602899|pmid-9430589|pmid-10926523|pmid-7884856|pmid-9685481|pmid-17020765|pmid-17020765|pmid-...
The conformational pathway may involve the ejection of stabilizing Mg2+ ions by the basic region of NC which has been shown to be sufficient for catalyzing the dynamical transition (88).
[ "30", "31", "33", "34", "36", "36", "41", "88" ]
186
9,492
1
false
The conformational pathway may involve the ejection of stabilizing Mg2+ ions by the basic region of NC which has been shown to be sufficient for catalyzing the dynamical transition.
[ "88" ]
The conformational pathway may involve the ejection of stabilizing Mg2+ ions by the basic region of NC which has been shown to be sufficient for catalyzing the dynamical transition.
true
true
true
true
true
1,506
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,090,584
pmid-16212497|pmid-16600909
RNA silencing in multicellular plants and animals is mediated by ∼21–24 nt small RNAs (sRNAs) that guide sequence-specific gene regulation, chromatin modification, and defense against viruses.
[ "1", "4" ]
192
9,493
0
false
RNA silencing in multicellular plants and animals is mediated by ∼21–24 nt small RNAs (sRNAs) that guide sequence-specific gene regulation, chromatin modification, and defense against viruses.
[]
RNA silencing in multicellular plants and animals is mediated by ∼21–24 nt small RNAs (sRNAs) that guide sequence-specific gene regulation, chromatin modification, and defense against viruses.
true
true
true
true
true
1,507
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,090,584
pmid-16212497|pmid-16600909
These sRNAs are broadly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs), which have similar chemical structures but differ in function and mode of biogenesis.
[ "1", "4" ]
181
9,494
0
false
These sRNAs are broadly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs), which have similar chemical structures but differ in function and mode of biogenesis.
[]
These sRNAs are broadly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs), which have similar chemical structures but differ in function and mode of biogenesis.
true
true
true
true
true
1,507
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,090,584
pmid-16212497|pmid-16600909
Production of both types of sRNAs depends on the activity of dicer proteins.
[ "1", "4" ]
76
9,495
0
false
Production of both types of sRNAs depends on the activity of dicer proteins.
[]
Production of both types of sRNAs depends on the activity of dicer proteins.
true
true
true
true
true
1,507
0
INTRODUCTION
1
1
[ "b1", "b4" ]
17,090,584
pmid-16212497|pmid-16600909
Plants such as Arabidopsis have evolved a diversity of RNA silencing pathways, sRNA classes and DICER-LIKE (DCL) genes that is unmatched in other eukaryotes (1–4).
[ "1", "4" ]
163
9,496
0
false
Plants such as Arabidopsis have evolved a diversity of RNA silencing pathways, sRNA classes and DICER-LIKE (DCL) genes that is unmatched in other eukaryotes.
[ "1–4" ]
Plants such as Arabidopsis have evolved a diversity of RNA silencing pathways, sRNA classes and DICER-LIKE (DCL) genes that is unmatched in other eukaryotes.
true
true
true
true
true
1,507
1
INTRODUCTION
1
5
[ "b5", "b6", "b7" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
Like their animal counterparts, plant miRNAs are excised from stem-loop structures of primary miRNA gene transcripts by DCL1 in cooperation with its binding partner HYL1 (5,6).
[ "5", "6", "7" ]
176
9,497
0
false
Like their animal counterparts, plant miRNAs are excised from stem-loop structures of primary miRNA gene transcripts by DCL1 in cooperation with its binding partner HYL1.
[ "5,6" ]
Like their animal counterparts, plant miRNAs are excised from stem-loop structures of primary miRNA gene transcripts by DCL1 in cooperation with its binding partner HYL1.
true
true
true
true
true
1,508
1
INTRODUCTION
1
7
[ "b5", "b6", "b7" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
The resulting miRNA/miRNA* duplex is loaded onto the argonaute family protein AGO1, the slicer component of the RNA-induced silencing complex (RISC) (7), which in turn is guided to the complementary target mRNAs by the miRNA strand.
[ "5", "6", "7" ]
232
9,498
1
false
The resulting miRNA/miRNA* duplex is loaded onto the argonaute family protein AGO1, the slicer component of the RNA-induced silencing complex (RISC), which in turn is guided to the complementary target mRNAs by the miRNA strand.
[ "7" ]
The resulting miRNA/miRNA* duplex is loaded onto the argonaute family protein AGO1, the slicer component of the RNA-induced silencing complex (RISC), which in turn is guided to the complementary target mRNAs by the miRNA strand.
true
true
true
true
true
1,508
2
INTRODUCTION
1
8
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
In contrast to miRNAs, endogenous siRNAs are cleaved from long perfect double-stranded (ds) RNAs, which are themselves products of specific RNA-dependent RNA polymerase (RDR) activities (8).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
190
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In contrast to miRNAs, endogenous siRNAs are cleaved from long perfect double-stranded (ds) RNAs, which are themselves products of specific RNA-dependent RNA polymerase (RDR) activities.
[ "8" ]
In contrast to miRNAs, endogenous siRNAs are cleaved from long perfect double-stranded (ds) RNAs, which are themselves products of specific RNA-dependent RNA polymerase (RDR) activities.
true
true
true
true
true
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