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
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
0
DISCUSSION
0
null
null
16,923,775
pmid-10908658|pmid-11134333|pmid-7556079|pmid-7588618|pmid-3032448|pmid-1322248|pmid-7556079|pmid-10964560|pmid-12093750|pmid-9761671|pmid-10838584|NA
The method is simple and should be applicable to the study of other transposable elements.
null
90
2,100
0
false
null
null
The method is simple and should be applicable to the study of other transposable elements.
true
true
true
true
true
361
1
DISCUSSION
1
10
[ "b10", "b29" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
We have used OrfAB[149], a transposase derivative that was chosen as a technical compromise since it was found to bind more readily to the terminal IRs than does the full-length OrfAB protein (10).
[ "10", "29" ]
197
2,101
1
false
We have used OrfAB[149], a transposase derivative that was chosen as a technical compromise since it was found to bind more readily to the terminal IRs than does the full-length OrfAB protein.
[ "10" ]
We have used OrfAB, a transposase derivative that was chosen as a technical compromise since it was found to bind more readily to the terminal IRs than does the full-length OrfAB protein.
true
true
true
true
true
362
1
DISCUSSION
1
10
[ "b10", "b29" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
Although we believe that its binding approximates that of OrfAB, it is possible that it is not identical and that the presence of the C-terminal domain changes the kinetics of binding and PEC formation.
[ "10", "29" ]
202
2,102
0
false
Although we believe that its binding approximates that of OrfAB, it is possible that it is not identical and that the presence of the C-terminal domain changes the kinetics of binding and PEC formation.
[]
Although we believe that its binding approximates that of OrfAB, it is possible that it is not identical and that the presence of the C-terminal domain changes the kinetics of binding and PEC formation.
true
true
true
true
true
362
1
DISCUSSION
1
29
[ "b10", "b29" ]
16,923,775
NA|pmid-10320583|pmid-15359283|pmid-9761671|pmid-15102449
Further studies will be needed to improve OrfAB binding either by changes in binding conditions or by generating full-length mutant derivatives with increased binding capacity as has been done in the case of Tn5 (29).
[ "10", "29" ]
217
2,103
1
false
Further studies will be needed to improve OrfAB binding either by changes in binding conditions or by generating full-length mutant derivatives with increased binding capacity as has been done in the case of Tn5.
[ "29" ]
Further studies will be needed to improve OrfAB binding either by changes in binding conditions or by generating full-length mutant derivatives with increased binding capacity as has been done in the case of Tn5.
true
true
true
true
true
362
2
DISCUSSION
1
30
[ "b30", "b31", "b32" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
DNA compaction by the DNA bending protein IHF has been previously observed using a similar TPM approach (30).
[ "30", "31", "32" ]
109
2,104
1
false
DNA compaction by the DNA bending protein IHF has been previously observed using a similar TPM approach.
[ "30" ]
DNA compaction by the DNA bending protein IHF has been previously observed using a similar TPM approach.
true
true
true
true
true
363
2
DISCUSSION
1
30
[ "b30", "b31", "b32" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
In this case, however, the non-specific binding contribution of IHF appeared to mask the bend introduced by a single IHF dimer on its specific target sequence.
[ "30", "31", "32" ]
159
2,105
0
false
In this case, however, the non-specific binding contribution of IHF appeared to mask the bend introduced by a single IHF dimer on its specific target sequence.
[]
In this case, however, the non-specific binding contribution of IHF appeared to mask the bend introduced by a single IHF dimer on its specific target sequence.
true
true
true
true
true
363
2
DISCUSSION
1
31
[ "b30", "b31", "b32" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
However, it was postulated that detection of single binding events requires the use of a short (∼10–20 nm) DNA fragment for sufficient resolution (31).
[ "30", "31", "32" ]
151
2,106
1
false
However, it was postulated that detection of single binding events requires the use of a short (∼10–20 nm) DNA fragment for sufficient resolution.
[ "31" ]
However, it was postulated that detection of single binding events requires the use of a short DNA fragment for sufficient resolution.
true
true
true
true
true
363
2
DISCUSSION
1
30
[ "b30", "b31", "b32" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
Indeed, using a more sophisticated TPM approach these authors revealed that IHF shortened a small DNA fragment carrying a single IHF binding site, consistent with DNA bending.
[ "30", "31", "32" ]
175
2,107
0
false
Indeed, using a more sophisticated TPM approach these authors revealed that IHF shortened a small DNA fragment carrying a single IHF binding site, consistent with DNA bending.
[]
Indeed, using a more sophisticated TPM approach these authors revealed that IHF shortened a small DNA fragment carrying a single IHF binding site, consistent with DNA bending.
true
true
true
true
true
363
2
DISCUSSION
1
30
[ "b30", "b31", "b32" ]
16,923,775
pmid-7590258|pmid-11535804|pmid-15903892|pmid-8980235
In view of the difficulties experienced in demonstrating IHF-induced bending [known to be >160° (32)], it was therefore unexpected that the simple TPM system with long DNA molecules used in the present study would be sufficiently sensitive to detect small protein-induced DNA bends introduced by OrfAB[149] binding to a ...
[ "30", "31", "32" ]
341
2,108
0
false
In view of the difficulties experienced in demonstrating IHF-induced bending, it was therefore unexpected that the simple TPM system with long DNA molecules used in the present study would be sufficiently sensitive to detect small protein-induced DNA bends introduced by OrfAB[149] binding to a single specific site.
[ "known to be >160° (32)" ]
In view of the difficulties experienced in demonstrating IHF-induced bending, it was therefore unexpected that the simple TPM system with long DNA molecules used in the present study would be sufficiently sensitive to detect small protein-induced DNA bends introduced by OrfAB[149] binding to a single specific site.
true
true
true
true
true
363
3
DISCUSSION
0
null
null
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
The single IR in the fragment (Figure 3) was essential to obtain the small but consistent decrease in apparent length of a DNA fragment in the presence of OrfAB[149].
null
166
2,109
0
false
null
null
The single IR in the fragment (Figure 3) was essential to obtain the small but consistent decrease in apparent length of a DNA fragment in the presence of OrfAB[149].
true
true
true
true
true
364
3
DISCUSSION
0
null
null
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Results from population-based experiments using EMSA and a set of four circularly permutated DNA fragments in which an IRR copy is located at different distances from the end (Figure 4) support the view that this shortening is due to DNA bending.
null
246
2,110
0
false
null
null
Results from population-based experiments using EMSA and a set of four circularly permutated DNA fragments in which an IRR copy is located at different distances from the end (Figure 4) support the view that this shortening is due to DNA bending.
true
true
true
true
true
364
3
DISCUSSION
0
null
null
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
However, we do not think that we have sufficient data to draw quantitative conclusions about the bend angle.
null
108
2,111
0
false
null
null
However, we do not think that we have sufficient data to draw quantitative conclusions about the bend angle.
true
true
true
true
true
364
3
DISCUSSION
0
null
null
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Note that with a single IRR, two molecules with different lengths (DNAR798 and DNAR2083) give different amplitude reductions.
null
125
2,112
0
false
null
null
Note that with a single IRR, two molecules with different lengths (DNAR798 and DNAR2083) give different amplitude reductions.
true
true
true
true
true
364
3
DISCUSSION
0
null
null
16,923,775
pmid-9761671|pmid-10677279|pmid-11352577|pmid-10677279|pmid-11352577|pmid-11352577
Therefore within the limits of experimental error, protein binding to a single site can be considered to reduce the amplitude by about 30 nm with an uncertainty of 10 mn.
null
170
2,113
0
false
null
null
Therefore within the limits of experimental error, protein binding to a single site can be considered to reduce the amplitude by about 30 nm with an uncertainty of 10 mn.
true
true
true
true
true
364
4
DISCUSSION
0
null
null
16,923,775
pmid-11352577
It will be important to investigate and generalize the experimental relation between DNA amplitude and protein-induced bending using a more defined protein–DNA binding system for which detailed structural and thermodynamic information is available.
null
248
2,114
0
false
null
null
It will be important to investigate and generalize the experimental relation between DNA amplitude and protein-induced bending using a more defined protein–DNA binding system for which detailed structural and thermodynamic information is available.
true
true
true
true
true
365
5
DISCUSSION
0
null
null
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
An additional OrfAB[149]-dependent species was observed if two IR copies were present on the same DNA molecule in an inverted configuration (Figure 5).
null
151
2,115
0
false
null
null
An additional OrfAB[149]-dependent species was observed if two IR copies were present on the same DNA molecule in an inverted configuration (Figure 5).
true
true
true
true
true
366
5
DISCUSSION
0
null
null
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
Its apparent length was consistent with the formation of an IR–IR synapse.
null
74
2,116
0
false
null
null
Its apparent length was consistent with the formation of an IR–IR synapse.
true
true
true
true
true
366
5
DISCUSSION
0
null
null
16,923,775
pmid-15155821|pmid-1861724|pmid-7824935|pmid-16407332
Once formed, this appeared quite stable over periods of at least 30 min even if excess protein was removed by flushing the chamber (data not shown).
null
148
2,117
0
false
null
null
Once formed, this appeared quite stable over periods of at least 30 min even if excess protein was removed by flushing the chamber (data not shown).
true
true
true
true
true
366
6
DISCUSSION
0
null
null
16,923,775
null
Kinetic analysis showed that loop formation occurred relatively rapidly (Figure 6): most of the complexes had been formed within the first 15 min.
null
146
2,118
0
false
null
null
Kinetic analysis showed that loop formation occurred relatively rapidly (Figure 6): most of the complexes had been formed within the first 15 min.
true
true
true
true
true
367
6
DISCUSSION
0
null
null
16,923,775
null
Moreover, results obtained from visualization of molecules undergoing transitions following injection of OrfAB[149] into the chamber (Figure 7a) indicated that assembly of the nascent complexes did not necessarily occur in a single step.
null
237
2,119
0
false
null
null
Moreover, results obtained from visualization of molecules undergoing transitions following injection of OrfAB[149] into the chamber (Figure 7a) indicated that assembly of the nascent complexes did not necessarily occur in a single step.
true
true
true
true
true
367
6
DISCUSSION
0
null
null
16,923,775
null
Before such complexes were established, steps of assembly and disassembly could be observed.
null
92
2,120
0
false
null
null
Before such complexes were established, steps of assembly and disassembly could be observed.
true
true
true
true
true
367
6
DISCUSSION
0
null
null
16,923,775
null
These were often accompanied by the formation of molecules of intermediate length (Figure 7a and b).
null
100
2,121
0
false
null
null
These were often accompanied by the formation of molecules of intermediate length (Figure 7a and b).
true
true
true
true
true
367
6
DISCUSSION
0
null
null
16,923,775
null
These observations suggest that complexes pass through a metastable state.
null
74
2,122
0
false
null
null
These observations suggest that complexes pass through a metastable state.
true
true
true
true
true
367
6
DISCUSSION
0
null
null
16,923,775
null
The nature of these metastable complexes remains to be determined.
null
66
2,123
0
false
null
null
The nature of these metastable complexes remains to be determined.
true
true
true
true
true
367
7
DISCUSSION
1
33
[ "b33" ]
16,923,775
pmid-10760133
To address some of these questions, we analysed the behaviour of DNA molecules with directly repeated IRs.
[ "33" ]
106
2,124
0
false
To address some of these questions, we analysed the behaviour of DNA molecules with directly repeated IRs.
[]
To address some of these questions, we analysed the behaviour of DNA molecules with directly repeated IRs.
true
true
true
true
true
368
7
DISCUSSION
1
33
[ "b33" ]
16,923,775
pmid-10760133
In previous analyses (33) where reactions between both inverted and directly repeated IRs were in competition, we were unable to detect cleavage or strand transfer reactions between the directly repeated IRs.
[ "33" ]
208
2,125
1
false
In previous analyses where reactions between both inverted and directly repeated IRs were in competition, we were unable to detect cleavage or strand transfer reactions between the directly repeated IRs.
[ "33" ]
In previous analyses where reactions between both inverted and directly repeated IRs were in competition, we were unable to detect cleavage or strand transfer reactions between the directly repeated IRs.
true
true
true
true
true
368
7
DISCUSSION
1
33
[ "b33" ]
16,923,775
pmid-10760133
This presumably resulted from inherently less favourable PEC formation between such ends due to an energetic cost of, e.g.
[ "33" ]
122
2,126
0
false
This presumably resulted from inherently less favourable PEC formation between such ends due to an energetic cost of, e.g.
[]
This presumably resulted from inherently less favourable PEC formation between such ends due to an energetic cost of, e.g.
true
true
true
true
true
368
7
DISCUSSION
1
33
[ "b33" ]
16,923,775
pmid-10760133
introducing an additional twist when forming a loop.
[ "33" ]
52
2,127
0
false
introducing an additional twist when forming a loop.
[]
introducing an additional twist when forming a loop.
false
true
true
true
false
368
7
DISCUSSION
1
33
[ "b33" ]
16,923,775
pmid-10760133
Consistent with this, PEC formation was indeed observed with directly repeated IRs using the TPM approach but with lower efficiency than when using a substrate with inverted IRs (Figure 8).
[ "33" ]
189
2,128
0
false
Consistent with this, PEC formation was indeed observed with directly repeated IRs using the TPM approach but with lower efficiency than when using a substrate with inverted IRs (Figure 8).
[]
Consistent with this, PEC formation was indeed observed with directly repeated IRs using the TPM approach but with lower efficiency than when using a substrate with inverted IRs (Figure 8).
true
true
true
true
true
368
8
DISCUSSION
0
null
null
16,923,775
null
In addition to the looped and unlooped molecules observed with the substrate carrying directly repeated IRR copies, a pronounced peak of intermediate length was observed (Figure 8b).
null
182
2,129
0
false
null
null
In addition to the looped and unlooped molecules observed with the substrate carrying directly repeated IRR copies, a pronounced peak of intermediate length was observed (Figure 8b).
true
true
true
true
true
369
8
DISCUSSION
0
null
null
16,923,775
null
A species with similar amplitude was observed for the substrate with inverted IRRs (Figure 8a) as a shoulder to the right of the looped DNA population.
null
151
2,130
0
false
null
null
A species with similar amplitude was observed for the substrate with inverted IRRs (Figure 8a) as a shoulder to the right of the looped DNA population.
true
true
true
true
true
369
8
DISCUSSION
0
null
null
16,923,775
null
These may correspond to the transitory intermediate state observed during looping of a substrate with inverted IRs (Figure 7).
null
126
2,131
0
false
null
null
These may correspond to the transitory intermediate state observed during looping of a substrate with inverted IRs (Figure 7).
true
true
true
true
true
369
9
DISCUSSION
1
18
[ "b18" ]
16,923,775
pmid-11352577
The intermediate species seen in Figure 7b and those observed in equilibrium conditions (Figure 8 and Table 1) are probably the same type of complex.
[ "18" ]
149
2,132
0
false
The intermediate species seen in Figure 7b and those observed in equilibrium conditions (Figure 8 and Table 1) are probably the same type of complex.
[]
The intermediate species seen in Figure 7b and those observed in equilibrium conditions are probably the same type of complex.
true
true
true
true
true
370
9
DISCUSSION
1
18
[ "b18" ]
16,923,775
pmid-11352577
These could reflect the formation of loops of intermediate length by an OrfAB[149] complex bound to one end while searching for the other.
[ "18" ]
138
2,133
0
false
These could reflect the formation of loops of intermediate length by an OrfAB[149] complex bound to one end while searching for the other.
[]
These could reflect the formation of loops of intermediate length by an OrfAB complex bound to one end while searching for the other.
true
true
true
true
true
370
9
DISCUSSION
1
18
[ "b18" ]
16,923,775
pmid-11352577
It is possible that additional weak OrfAB[149] binding sites are present between the IRs.
[ "18" ]
89
2,134
0
false
It is possible that additional weak OrfAB[149] binding sites are present between the IRs.
[]
It is possible that additional weak OrfAB binding sites are present between the IRs.
true
true
true
true
true
370
9
DISCUSSION
1
18
[ "b18" ]
16,923,775
pmid-11352577
However, we were unable to identify sequences with significant similarities to the defined OrfAB[149] binding sites [data not shown, (18)].
[ "18" ]
139
2,135
0
false
However, we were unable to identify sequences with significant similarities to the defined OrfAB[149] binding sites.
[ "data not shown, (18)" ]
However, we were unable to identify sequences with significant similarities to the defined OrfAB binding sites.
true
true
true
true
true
370
9
DISCUSSION
1
18
[ "b18" ]
16,923,775
pmid-11352577
In addition, such intermediate states were not observed using substrates with a single IR.
[ "18" ]
90
2,136
0
false
In addition, such intermediate states were not observed using substrates with a single IR.
[]
In addition, such intermediate states were not observed using substrates with a single IR.
true
true
true
true
true
370
10
DISCUSSION
1
27
[ "b27", "b28" ]
16,923,775
pmid-1480106|pmid-8404817
A second and simpler explanation is that these species represent DNA molecules with OrfAB[149] bound to both IRs.
[ "27", "28" ]
113
2,137
0
false
A second and simpler explanation is that these species represent DNA molecules with OrfAB[149] bound to both IRs.
[]
A second and simpler explanation is that these species represent DNA molecules with OrfAB[149] bound to both IRs.
true
true
true
true
true
371
10
DISCUSSION
1
27
[ "b27", "b28" ]
16,923,775
pmid-1480106|pmid-8404817
This interpretation stems from the DNA length reduction provoked by OrfAB[149] binding to the IRs (Figure 3).
[ "27", "28" ]
109
2,138
0
false
This interpretation stems from the DNA length reduction provoked by OrfAB[149] binding to the IRs (Figure 3).
[]
This interpretation stems from the DNA length reduction provoked by OrfAB[149] binding to the IRs (Figure 3).
true
true
true
true
true
371
10
DISCUSSION
1
27
[ "b27", "b28" ]
16,923,775
pmid-1480106|pmid-8404817
In contrast to EMSA, in which one bend can cancel the effect of another depending on relative position and geometry (27,28), in TPM (a situation where one end of the DNA molecule is anchored), bends should have a cumulative effect.
[ "27", "28" ]
231
2,139
0
false
In contrast to EMSA, in which one bend can cancel the effect of another depending on relative position and geometry, in TPM (a situation where one end of the DNA molecule is anchored), bends should have a cumulative effect.
[ "27,28" ]
In contrast to EMSA, in which one bend can cancel the effect of another depending on relative position and geometry, in TPM (a situation where one end of the DNA molecule is anchored), bends should have a cumulative effect.
true
true
true
true
true
371
10
DISCUSSION
1
27
[ "b27", "b28" ]
16,923,775
pmid-1480106|pmid-8404817
Doubly bound DNA would therefore be expected to undergo a larger reduction in amplitude than that observed for binding to a single IR.
[ "27", "28" ]
134
2,140
0
false
Doubly bound DNA would therefore be expected to undergo a larger reduction in amplitude than that observed for binding to a single IR.
[]
Doubly bound DNA would therefore be expected to undergo a larger reduction in amplitude than that observed for binding to a single IR.
true
true
true
true
true
371
11
DISCUSSION
0
null
null
16,923,775
null
Such doubly bound species might represent complexes on the pathway to synapse formation or non-productive complexes unable to undergo synapsis.
null
143
2,141
0
false
null
null
Such doubly bound species might represent complexes on the pathway to synapse formation or non-productive complexes unable to undergo synapsis.
true
true
true
true
true
372
11
DISCUSSION
0
null
null
16,923,775
null
We do not yet know how both ends of IS911 find each other to form the synaptic complex: whether OrfAB[149] binds to a single end as a multimer, which must then find and bind the second end, or whether it binds both ends and synapsis is driven by protein–protein interactions.
null
275
2,142
0
false
null
null
We do not yet know how both ends of IS911 find each other to form the synaptic complex: whether OrfAB[149] binds to a single end as a multimer, which must then find and bind the second end, or whether it binds both ends and synapsis is driven by protein–protein interactions.
true
true
true
true
true
372
12
DISCUSSION
0
null
null
16,923,775
null
In the experiments shown in Figure 7, only molecules actually undergoing transitions were analysed.
null
99
2,143
0
false
null
null
In the experiments shown in Figure 7, only molecules actually undergoing transitions were analysed.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
These should therefore have protein already bound.
null
50
2,144
0
false
null
null
These should therefore have protein already bound.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
This inference is supported by the observation that the ‘unlooped’ molecules were shorter than the protein-free DNA (Figure 7a).
null
128
2,145
0
false
null
null
This inference is supported by the observation that the ‘unlooped’ molecules were shorter than the protein-free DNA (Figure 7a).
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
It is probable that only a single IR is occupied in these molecules.
null
68
2,146
0
false
null
null
It is probable that only a single IR is occupied in these molecules.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
The further reduction in length which occurs in the intermediate states could represent occupation of the second IR.
null
116
2,147
0
false
null
null
The further reduction in length which occurs in the intermediate states could represent occupation of the second IR.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
If these are complexes on the pathway to synapsis, they might then rapidly evolve into the looped structure by interaction between the OrfAB[149] molecules bound to each end, or disassemble into the singly bound or unbound DNA molecule.
null
236
2,148
0
false
null
null
If these are complexes on the pathway to synapsis, they might then rapidly evolve into the looped structure by interaction between the OrfAB[149] molecules bound to each end, or disassemble into the singly bound or unbound DNA molecule.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
Although the molecules were observed for only a short period (mean period of 4 min), of the 17 analysed, 5 went on to form looped complexes from the intermediate state.
null
168
2,149
0
false
null
null
Although the molecules were observed for only a short period (mean period of 4 min), of the 17 analysed, 5 went on to form looped complexes from the intermediate state.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
The remaining 11 appeared to oscillate between the intermediate state and the singly bound state.
null
97
2,150
0
false
null
null
The remaining 11 appeared to oscillate between the intermediate state and the singly bound state.
true
true
true
true
true
373
12
DISCUSSION
0
null
null
16,923,775
null
Therefore while all molecules in an intermediate state do not necessarily give rise to looped molecules over our period of observation, all looped molecules identified had passed through the intermediate state.
null
210
2,151
0
false
null
null
Therefore while all molecules in an intermediate state do not necessarily give rise to looped molecules over our period of observation, all looped molecules identified had passed through the intermediate state.
true
true
true
true
true
373
13
DISCUSSION
1
10
[ "b10" ]
16,923,775
pmid-9761671
The presumed doubly bound molecules were not obvious in all equilibrium studies (see Figure 5).
[ "10" ]
95
2,152
0
false
The presumed doubly bound molecules were not obvious in all equilibrium studies (see Figure 5).
[]
The presumed doubly bound molecules were not obvious in all equilibrium studies (see Figure 5).
true
true
true
true
true
374
13
DISCUSSION
1
10
[ "b10" ]
16,923,775
pmid-9761671
This is either because they represent only a small fraction of bound molecules or because they are confounded with the looped population.
[ "10" ]
137
2,153
0
false
This is either because they represent only a small fraction of bound molecules or because they are confounded with the looped population.
[]
This is either because they represent only a small fraction of bound molecules or because they are confounded with the looped population.
true
true
true
true
true
374
13
DISCUSSION
1
10
[ "b10" ]
16,923,775
pmid-9761671
They have never been detected in EMSA studies where no pre-PEC intermediates have as yet been observed (10).
[ "10" ]
108
2,154
1
false
They have never been detected in EMSA studies where no pre-PEC intermediates have as yet been observed.
[ "10" ]
They have never been detected in EMSA studies where no pre-PEC intermediates have as yet been observed.
true
true
true
true
true
374
14
DISCUSSION
1
8
[ "b8", "b34", "b35", "b36" ]
16,923,775
pmid-10964560|pmid-15767689|pmid-15718297|pmid-15958388
These results are consistent with models, such as those proposed for Tn5 (8), mariner elements (34) and, with experimental support, for retroviral IN activity (35,36).
[ "8", "34", "35", "36" ]
167
2,155
1
false
These results are consistent with models, such as those proposed for Tn5, mariner elements and, with experimental support, for retroviral IN activity.
[ "8", "34", "35,36" ]
These results are consistent with models, such as those proposed for Tn5, mariner elements and, with experimental support, for retroviral IN activity.
true
true
true
true
true
375
14
DISCUSSION
1
8
[ "b8", "b34", "b35", "b36" ]
16,923,775
pmid-10964560|pmid-15767689|pmid-15718297|pmid-15958388
Here transposase molecules are proposed to bind to each end of the transposon separately and synapsis then occurs by interaction between these bound transposase molecules.
[ "8", "34", "35", "36" ]
171
2,156
0
false
Here transposase molecules are proposed to bind to each end of the transposon separately and synapsis then occurs by interaction between these bound transposase molecules.
[]
Here transposase molecules are proposed to bind to each end of the transposon separately and synapsis then occurs by interaction between these bound transposase molecules.
true
true
true
true
true
375
15
DISCUSSION
0
null
null
16,923,775
null
This model could also explain the results obtained with the pair of substrates carrying the inverted and directly repeated IRRs (Figure 8).
null
139
2,157
0
false
null
null
This model could also explain the results obtained with the pair of substrates carrying the inverted and directly repeated IRRs (Figure 8).
true
true
true
true
true
376
15
DISCUSSION
0
null
null
16,923,775
null
We assume that the shoulder observed on the right of the looped population peak (Figure 8a) with the inverted IR substrate and the pronounced additional peak found with the directly repeated IR substrates are both doubly bound complexes.
null
237
2,158
0
false
null
null
We assume that the shoulder observed on the right of the looped population peak (Figure 8a) with the inverted IR substrate and the pronounced additional peak found with the directly repeated IR substrates are both doubly bound complexes.
true
true
true
true
true
376
15
DISCUSSION
0
null
null
16,923,775
null
Generating a PEC with directly repeated IRs might introduce specific constraints not present with the inverted IR substrate: e.g.
null
129
2,159
0
false
null
null
Generating a PEC with directly repeated IRs might introduce specific constraints not present with the inverted IR substrate: e.g.
true
true
true
true
true
376
15
DISCUSSION
0
null
null
16,923,775
null
the introduction of a crossing between the IRs to accommodate their docking.
null
76
2,160
0
false
null
null
the introduction of a crossing between the IRs to accommodate their docking.
false
true
true
true
false
376
15
DISCUSSION
0
null
null
16,923,775
null
Under these circumstances, a doubly bound DNA molecule with directly repeated IRs would face an energy barrier, not encountered by the inverted IR substrate, in forming a PEC.
null
175
2,161
0
false
null
null
Under these circumstances, a doubly bound DNA molecule with directly repeated IRs would face an energy barrier, not encountered by the inverted IR substrate, in forming a PEC.
true
true
true
true
true
376
15
DISCUSSION
0
null
null
16,923,775
null
This would be expected to be accompanied by an increase in the doubly bound intermediate as observed.
null
101
2,162
0
false
null
null
This would be expected to be accompanied by an increase in the doubly bound intermediate as observed.
true
true
true
true
true
376
16
DISCUSSION
0
null
null
16,923,775
null
The TPM technique is clearly applicable to fine scale analysis of synapsis during transposition.
null
96
2,163
0
false
null
null
The TPM technique is clearly applicable to fine scale analysis of synapsis during transposition.
true
true
true
true
true
377
16
DISCUSSION
0
null
null
16,923,775
null
It has revealed several properties of IS911 synaptic complex formation, which are not detectable by traditional procedures (complex formation in real-time; transient intermediates) and others which are (protein-induced DNA curvature).
null
234
2,164
0
false
null
null
It has revealed several properties of IS911 synaptic complex formation, which are not detectable by traditional procedures (complex formation in real-time; transient intermediates) and others which are (protein-induced DNA curvature).
true
true
true
true
true
377
16
DISCUSSION
0
null
null
16,923,775
null
TPM will be a powerful tool for investigating the importance of multimerization in complex formation by using available mutants defective in this process.
null
154
2,165
0
false
null
null
TPM will be a powerful tool for investigating the importance of multimerization in complex formation by using available mutants defective in this process.
true
true
true
true
true
377
16
DISCUSSION
0
null
null
16,923,775
null
The results obtained with OrfAB[149] have paved the way for analysis of PEC formation by the entire OrfAB transposase and, coupled with fluorescence detection, will be used to investigate steps downstream from synapse formation, such as cleavage and strand transfer reactions, and the role of the IS911 regulatory protei...
null
328
2,166
0
false
null
null
The results obtained with OrfAB[149] have paved the way for analysis of PEC formation by the entire OrfAB transposase and, coupled with fluorescence detection, will be used to investigate steps downstream from synapse formation, such as cleavage and strand transfer reactions, and the role of the IS911 regulatory protei...
true
true
true
true
true
377
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
The polypurine tract (PPT1) of retroviruses and long terminal repeat-containing retrotransposons is a short RNA sequence from which second or plus (+) strand DNA synthesis initiates (1).
[ "1", "2", "3", "13", "7", "14", "16" ]
186
2,167
1
false
The polypurine tract of retroviruses and long terminal repeat-containing retrotransposons is a short RNA sequence from which second or plus (+) strand DNA synthesis initiates.
[ "PPT1", "1" ]
The polypurine tract of retroviruses and long terminal repeat-containing retrotransposons is a short RNA sequence from which second or plus (+) strand DNA synthesis initiates.
true
true
true
true
true
378
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
Subsequent to this, the PPT primer must be accurately removed from nascent DNA to create a double-stranded, integration-competent DNA provirus.
[ "1", "2", "3", "13", "7", "14", "16" ]
143
2,168
0
false
Subsequent to this, the PPT primer must be accurately removed from nascent DNA to create a double-stranded, integration-competent DNA provirus.
[]
Subsequent to this, the PPT primer must be accurately removed from nascent DNA to create a double-stranded, integration-competent DNA provirus.
true
true
true
true
true
378
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
A stringent requirement is therefore that the PPT is precisely recognized by both the ribonuclease H (RNase H) and DNA polymerase domains of its cognate reverse transcriptase (RT).
[ "1", "2", "3", "13", "7", "14", "16" ]
180
2,169
0
false
A stringent requirement is therefore that the PPT is precisely recognized by both the ribonuclease H (RNase H) and DNA polymerase domains of its cognate reverse transcriptase (RT).
[]
A stringent requirement is therefore that the PPT is precisely recognized by both the ribonuclease H (RNase H) and DNA polymerase domains of its cognate reverse transcriptase (RT).
true
true
true
true
true
378
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
Using oligonucleotide-derived substrates, model systems accurately recapitulating (i) selection of the PPT 3′ terminus from within an RNA/DNA hybrid (ii) DNA-dependent DNA synthesis from the PPT 3′ terminus and (iii) removal from nascent DNA have been constructed.
[ "1", "2", "3", "13", "7", "14", "16" ]
264
2,170
0
false
Using oligonucleotide-derived substrates, model systems accurately recapitulating (i) selection of the PPT 3′ terminus from within an RNA/DNA hybrid (ii) DNA-dependent DNA synthesis from the PPT 3′ terminus and (iii) removal from nascent DNA have been constructed.
[]
Using oligonucleotide-derived substrates, model systems accurately recapitulating (i) selection of the PPT 3′ terminus from within an RNA/DNA hybrid (ii) DNA-dependent DNA synthesis from the PPT 3′ terminus and (iii) removal from nascent DNA have been constructed.
true
true
true
true
true
378
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
At the same time, several PPT mutations have now been studied in vivo, using recombinant viruses.
[ "1", "2", "3", "13", "7", "14", "16" ]
97
2,171
0
false
At the same time, several PPT mutations have now been studied in vivo, using recombinant viruses.
[]
At the same time, several PPT mutations have now been studied in vivo, using recombinant viruses.
true
true
true
true
true
378
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
Surprisingly, despite a wealth of crystallographic (2), biochemical (3–13) and cell culture data (7,14–16), the structural basis for PPT selection and utilization in (+)-strand
[ "1", "2", "3", "13", "7", "14", "16" ]
176
2,172
1
false
Surprisingly, despite a wealth of crystallographic, biochemical and cell culture data, the structural basis for PPT selection and utilization in (+)-strand
[ "2", "3–13", "7,14–16" ]
Surprisingly, despite a wealth of crystallographic, biochemical and cell culture data, the structural basis for PPT selection and utilization in (+)-strand
true
true
false
true
false
378
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b13", "b7", "b14", "b16" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
DNA synthesis remains elusive.
[ "1", "2", "3", "13", "7", "14", "16" ]
30
2,173
0
false
DNA synthesis remains elusive.
[]
DNA synthesis remains elusive.
true
true
true
true
true
378
1
INTRODUCTION
1
2
[ "b2", "b12", "b17", "b18", "b19", "b20", "b17", "b20", "b18" ]
17,164,285
pmid-11250910|pmid-12730227|pmid-12972638|pmid-15778225|pmid-16306041|pmid-15004241|pmid-12972638|pmid-15004241|pmid-15778225|pmid-9649446|pmid-11250910|pmid-11875059|pmid-14512562|pmid-7681062|pmid-8764039|pmid-3040055
The unusual pattern of base pairing observed in a co-crystal of HIV-1 RT and a PPT-containing RNA/DNA hybrid (2) suggested that local flexibility might promote sequestering and orienting of the retroviral polymerase.
[ "2", "12", "17", "18", "19", "20", "17", "20", "18" ]
216
2,174
1
false
The unusual pattern of base pairing observed in a co-crystal of HIV-1 RT and a PPT-containing RNA/DNA hybrid suggested that local flexibility might promote sequestering and orienting of the retroviral polymerase.
[ "2" ]
The unusual pattern of base pairing observed in a co-crystal of HIV-1 RT and a PPT-containing RNA/DNA hybrid suggested that local flexibility might promote sequestering and orienting of the retroviral polymerase.
true
true
true
true
true
379
1
INTRODUCTION
1
2
[ "b2", "b12", "b17", "b18", "b19", "b20", "b17", "b20", "b18" ]
17,164,285
pmid-11250910|pmid-12730227|pmid-12972638|pmid-15778225|pmid-16306041|pmid-15004241|pmid-12972638|pmid-15004241|pmid-15778225|pmid-9649446|pmid-11250910|pmid-11875059|pmid-14512562|pmid-7681062|pmid-8764039|pmid-3040055
To explore this notion, we have inserted a variety of nucleoside analogs into PPT-containing RNA/DNA hybrids to alter their structure in a manner that minimally alters sequence context.
[ "2", "12", "17", "18", "19", "20", "17", "20", "18" ]
185
2,175
0
false
To explore this notion, we have inserted a variety of nucleoside analogs into PPT-containing RNA/DNA hybrids to alter their structure in a manner that minimally alters sequence context.
[]
To explore this notion, we have inserted a variety of nucleoside analogs into PPT-containing RNA/DNA hybrids to alter their structure in a manner that minimally alters sequence context.
true
true
true
true
true
379
1
INTRODUCTION
1
20
[ "b2", "b12", "b17", "b18", "b19", "b20", "b17", "b20", "b18" ]
17,164,285
pmid-11250910|pmid-12730227|pmid-12972638|pmid-15778225|pmid-16306041|pmid-15004241|pmid-12972638|pmid-15004241|pmid-15778225|pmid-9649446|pmid-11250910|pmid-11875059|pmid-14512562|pmid-7681062|pmid-8764039|pmid-3040055
Examples include pyrimidine isosteres, or shape mimics, which locally remove hydrogen bonding (12,17), abasic tetrahydrofuran linkages, which remove the nucleobase while preserving the sugar-phosphate backbone (18,19), pyrrolo-dC, a fluorescent cytosine analog providing information on local base pairing (20) and locked...
[ "2", "12", "17", "18", "19", "20", "17", "20", "18" ]
391
2,176
1
false
Examples include pyrimidine isosteres, or shape mimics, which locally remove hydrogen bonding, abasic tetrahydrofuran linkages, which remove the nucleobase while preserving the sugar-phosphate backbone, pyrrolo-dC, a fluorescent cytosine analog providing information on local base pairing and locked nucleic acid monomer...
[ "12,17", "18,19", "20" ]
Examples include pyrimidine isosteres, or shape mimics, which locally remove hydrogen bonding, abasic tetrahydrofuran linkages, which remove the nucleobase while preserving the sugar-phosphate backbone, pyrrolo-dC, a fluorescent cytosine analog providing information on local base pairing and locked nucleic acid monomer...
true
true
true
true
true
379
1
INTRODUCTION
1
17
[ "b2", "b12", "b17", "b18", "b19", "b20", "b17", "b20", "b18" ]
17,164,285
pmid-11250910|pmid-12730227|pmid-12972638|pmid-15778225|pmid-16306041|pmid-15004241|pmid-12972638|pmid-15004241|pmid-15778225|pmid-9649446|pmid-11250910|pmid-11875059|pmid-14512562|pmid-7681062|pmid-8764039|pmid-3040055
This strategy demonstrated (i) that the junction between the rG:dC and upstream rA:dT tract is particularly sensitive to altering hydrogen bonding (17) (ii) weakened base pairing at position −2 (20) and (iii) that DNA nucleobases on either side of the PPT-U3 junction are not required for accurate cleavage (18).
[ "2", "12", "17", "18", "19", "20", "17", "20", "18" ]
312
2,177
1
false
This strategy demonstrated (i) that the junction between the rG:dC and upstream rA:dT tract is particularly sensitive to altering hydrogen bonding (ii) weakened base pairing at position −2 and (iii) that DNA nucleobases on either side of the PPT-U3 junction are not required for accurate cleavage.
[ "17", "20", "18" ]
This strategy demonstrated (i) that the junction between the rG:dC and upstream rA:dT tract is particularly sensitive to altering hydrogen bonding (ii) weakened base pairing at position −2 and (iii) that DNA nucleobases on either side of the PPT-U3 junction are not required for accurate cleavage.
true
true
true
true
true
379
2
INTRODUCTION
1
7
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
Although our studies to date have focused primarily on individual bases of the PPT and its DNA complement, the modular architecture of the RNA/DNA hybrid may also be significant.
[ "7", "21", "21", "27", "28", "2" ]
178
2,178
0
false
Although our studies to date have focused primarily on individual bases of the PPT and its DNA complement, the modular architecture of the RNA/DNA hybrid may also be significant.
[]
Although our studies to date have focused primarily on individual bases of the PPT and its DNA complement, the modular architecture of the RNA/DNA hybrid may also be significant.
true
true
true
true
true
380
2
INTRODUCTION
1
7
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
A comparison of several retroviral (+)-strand primers (7,21) indicated a conserved rU:dA tract immediately 5′ to the PPT, an rA:dT-rich sequence constituting the upstream portion of the PPT, and a downstream rG:dC tract, the 3′ terminus of which is almost always flanked by from one to three A's.
[ "7", "21", "21", "27", "28", "2" ]
296
2,179
0
false
A comparison of several retroviral (+)-strand primers indicated a conserved rU:dA tract immediately 5′ to the PPT, an rA:dT-rich sequence constituting the upstream portion of the PPT, and a downstream rG:dC tract, the 3′ terminus of which is almost always flanked by from one to three A's.
[ "7,21" ]
A comparison of several retroviral (+)-strand primers indicated a conserved rU:dA tract immediately 5′ to the PPT, an rA:dT-rich sequence constituting the upstream portion of the PPT, and a downstream rG:dC tract, the 3′ terminus of which is almost always flanked by from one to three A's.
true
true
true
true
true
380
2
INTRODUCTION
1
28
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
Classically, rA:dT tracts have been associated with minor groove compression and DNA bending (21–27), while rG:dC tracts are reported to induce major groove compression (28).
[ "7", "21", "21", "27", "28", "2" ]
174
2,180
1
false
Classically, rA:dT tracts have been associated with minor groove compression and DNA bending, while rG:dC tracts are reported to induce major groove compression.
[ "21–27", "28" ]
Classically, rA:dT tracts have been associated with minor groove compression and DNA bending, while rG:dC tracts are reported to induce major groove compression.
true
true
true
true
true
380
2
INTRODUCTION
1
7
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
While the complete structure of the PPT-containing RNA/DNA hybrid was not solved by Sarafianos et al.
[ "7", "21", "21", "27", "28", "2" ]
101
2,181
0
false
While the complete structure of the PPT-containing RNA/DNA hybrid was not solved by Sarafianos et al.
[]
While the complete structure of the PPT-containing RNA/DNA hybrid was not solved by Sarafianos et al.
true
true
true
true
true
380
2
INTRODUCTION
1
2
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
(2) these authors did observe minor groove compression in one of the two rA:dT tracts within the HIV-1 PPT.
[ "7", "21", "21", "27", "28", "2" ]
107
2,182
1
false
these authors did observe minor groove compression in one of the two rA:dT tracts within the HIV-1 PPT.
[ "2" ]
these authors did observe minor groove compression in one of the two rA:dT tracts within the HIV-1 PPT.
false
true
true
true
false
380
2
INTRODUCTION
1
7
[ "b7", "b21", "b21", "b27", "b28", "b2" ]
17,164,285
pmid-9649446|pmid-15183342|pmid-15183342|pmid-15909999|pmid-1913209|pmid-11250910|pmid-1720554|pmid-1374166|pmid-8567660|pmid-11035788|pmid-10956669|pmid-7545436
Thus, we cannot rule out that alterations in groove width or malleability induced by juxtaposed homopolymer tracts may be exploited by the retroviral polymerase as a means of correctly ‘docking’ onto the PPT as either a DNA polymerase or RNase H. The goal of the present study was 2-fold, namely (i) to investigate the s...
[ "7", "21", "21", "27", "28", "2" ]
585
2,183
0
false
Thus, we cannot rule out that alterations in groove width or malleability induced by juxtaposed homopolymer tracts may be exploited by the retroviral polymerase as a means of correctly ‘docking’ onto the PPT as either a DNA polymerase or RNase H. The goal of the present study was 2-fold, namely (i) to investigate the s...
[]
Thus, we cannot rule out that alterations in groove width or malleability induced by juxtaposed homopolymer tracts may be exploited by the retroviral polymerase as a means of correctly ‘docking’ onto the PPT as either a DNA polymerase or RNase H. The goal of the present study was 2-fold, namely (i) to investigate the s...
true
true
true
true
true
380
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
Using a model system in which (+)-strand selection and initiation are recapitulated in vitro, we have determined that an important function of the rU:dA tract in HIV-1 is as a specificity determinant for 5′ terminal cleavage of the (+)-strand primer, which in turn assures that the primer is of a length sufficient for r...
[ "29", "2", "30" ]
358
2,184
0
false
Using a model system in which (+)-strand selection and initiation are recapitulated in vitro, we have determined that an important function of the rU:dA tract in HIV-1 is as a specificity determinant for 5′ terminal cleavage of the (+)-strand primer, which in turn assures that the primer is of a length sufficient for r...
[]
Using a model system in which (+)-strand selection and initiation are recapitulated in vitro, we have determined that an important function of the rU:dA tract in HIV-1 is as a specificity determinant for 5′ terminal cleavage of the (+)-strand primer, which in turn assures that the primer is of a length sufficient for r...
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
The rA:dT tracts likewise add length to the primer, and assures that only negligible internal cleavage of the PPT occurs.
[ "29", "2", "30" ]
121
2,185
0
false
The rA:dT tracts likewise add length to the primer, and assures that only negligible internal cleavage of the PPT occurs.
[]
The rA:dT tracts likewise add length to the primer, and assures that only negligible internal cleavage of the PPT occurs.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
However, the element most critical to PPT function is the rG:dC tract, which both resists internal hydrolysis and, more importantly, directs cleavage to the 5′-G-A-3′ PPT-U3 junction.
[ "29", "2", "30" ]
183
2,186
0
false
However, the element most critical to PPT function is the rG:dC tract, which both resists internal hydrolysis and, more importantly, directs cleavage to the 5′-G-A-3′ PPT-U3 junction.
[]
However, the element most critical to PPT function is the rG:dC tract, which both resists internal hydrolysis and, more importantly, directs cleavage to the 5′-G-A-3′ PPT-U3 junction.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
This occurs not only in the context of the wild-type PPT, but also when the rG:dC tract is relocated to alternative sites of the PPT.
[ "29", "2", "30" ]
133
2,187
0
false
This occurs not only in the context of the wild-type PPT, but also when the rG:dC tract is relocated to alternative sites of the PPT.
[]
This occurs not only in the context of the wild-type PPT, but also when the rG:dC tract is relocated to alternative sites of the PPT.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
In keeping with previous data (29), −2G and −4G (defining −1G as the base 5′ to the scissile bond) and +1A were found to be essential for directing HIV-1 RT to cleave precisely at the PPT-U3 junction.
[ "29", "2", "30" ]
200
2,188
1
false
In keeping with previous data, −2G and −4G (defining −1G as the base 5′ to the scissile bond) and +1A were found to be essential for directing HIV-1 RT to cleave precisely at the PPT-U3 junction.
[ "29" ]
In keeping with previous data, −2G and −4G (defining −1G as the base 5′ to the scissile bond) and +1A were found to be essential for directing HIV-1 RT to cleave precisely at the PPT-U3 junction.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
The structural basis for these findings were investigated further using an oligonucleotide-based RNase H assay in which a variety of purine analogs were substituted for G or A at positions −4, −2 and +1.
[ "29", "2", "30" ]
203
2,189
0
false
The structural basis for these findings were investigated further using an oligonucleotide-based RNase H assay in which a variety of purine analogs were substituted for G or A at positions −4, −2 and +1.
[]
The structural basis for these findings were investigated further using an oligonucleotide-based RNase H assay in which a variety of purine analogs were substituted for G or A at positions −4, −2 and +1.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
Our results show a strong correlation between the efficiency and precision of RNase H-mediated hydrolysis and the identity of the chemical moieties at the 2- and 6-positions of the purine ring in nucleosides at PPT positions −4, −2 and +1.
[ "29", "2", "30" ]
239
2,190
0
false
Our results show a strong correlation between the efficiency and precision of RNase H-mediated hydrolysis and the identity of the chemical moieties at the 2- and 6-positions of the purine ring in nucleosides at PPT positions −4, −2 and +1.
[]
Our results show a strong correlation between the efficiency and precision of RNase H-mediated hydrolysis and the identity of the chemical moieties at the 2- and 6-positions of the purine ring in nucleosides at PPT positions −4, −2 and +1.
true
true
true
true
true
381
3
INTRODUCTION
1
29
[ "b29", "b2", "b30" ]
17,164,285
pmid-7681062|pmid-11250910|pmid-11939780|pmid-16306040|pmid-11250910|pmid-15004241|pmid-11875059|pmid-14636594
Potential explanations for these findings, especially the possible involvement of RNase H primer grip residues Q475 and R448 (2,30), are discussed.
[ "29", "2", "30" ]
147
2,191
0
false
Potential explanations for these findings, especially the possible involvement of RNase H primer grip residues Q475 and R448, are discussed.
[ "2,30" ]
Potential explanations for these findings, especially the possible involvement of RNase H primer grip residues Q475 and R448, are discussed.
true
true
true
true
true
381
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
In the present study, we have (i) assessed specificity determinants for cleavage at the 3′ and 5′ termini of the (+)-strand primer, (ii) determined the relationships among PPT sequence, (+)-strand primer length and primer function, and (iii) examined the functions of rG:dC-, rA:dT- and rU:dA-tracts within and immediate...
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
343
2,192
0
false
In the present study, we have (i) assessed specificity determinants for cleavage at the 3′ and 5′ termini of the (+)-strand primer, (ii) determined the relationships among PPT sequence, (+)-strand primer length and primer function, and (iii) examined the functions of rG:dC-, rA:dT- and rU:dA-tracts within and immediate...
[]
In the present study, we have (i) assessed specificity determinants for cleavage at the 3′ and 5′ termini of the (+)-strand primer, (ii) determined the relationships among PPT sequence, (+)-strand primer length and primer function, and (iii) examined the functions of rG:dC-, rA:dT- and rU:dA-tracts within and immediate...
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
Each of the homopolymeric tracts is highly conserved among retroviral PPTs (7,21).
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
82
2,193
0
false
Each of the homopolymeric tracts is highly conserved among retroviral PPTs.
[ "7,21" ]
Each of the homopolymeric tracts is highly conserved among retroviral PPTs.
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
In HIV, our data suggests the rU:dA tract helps define the 5′ terminus of the (+)-strand primer, thereby ensuring that it is the appropriate length for processing by RT (Figure 1a and b, cf.
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
190
2,194
0
false
In HIV, our data suggests the rU:dA tract helps define the 5′ terminus of the (+)-strand primer, thereby ensuring that it is the appropriate length for processing by RT (Figure 1a and b, cf.
[]
In HIV, our data suggests the rU:dA tract helps define the 5′ terminus of the (+)-strand primer, thereby ensuring that it is the appropriate length for processing by RT (Figure 1a and b, cf.
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
lanes W and 7).
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
15
2,195
0
false
lanes W and 7).
[]
lanes W and 7).
false
true
true
true
false
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
In vivo studies of simian immunodeficiency virus and Moloney murine leukemia virus have demonstrated this conserved sub-motif is critical for virus replication (7,14,35,36).
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
173
2,196
0
false
In vivo studies of simian immunodeficiency virus and Moloney murine leukemia virus have demonstrated this conserved sub-motif is critical for virus replication.
[ "7,14,35,36" ]
In vivo studies of simian immunodeficiency virus and Moloney murine leukemia virus have demonstrated this conserved sub-motif is critical for virus replication.
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
However, although removing the rU:dA tract drastically reduced the levels of reverse transcription in these studies, it is not clear that this effect was directly related to PPT-processing or initiation of (+)-strand DNA synthesis.
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
231
2,197
0
false
However, although removing the rU:dA tract drastically reduced the levels of reverse transcription in these studies, it is not clear that this effect was directly related to PPT-processing or initiation of (+)-strand DNA synthesis.
[]
However, although removing the rU:dA tract drastically reduced the levels of reverse transcription in these studies, it is not clear that this effect was directly related to PPT-processing or initiation of (+)-strand DNA synthesis.
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
It is interesting to note, however, that after extensive serial passaging of the defective virus, a number of viral variants emerged in which the deleted rU:dA tract was replaced by an extended rA:dT tract.
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
206
2,198
0
false
It is interesting to note, however, that after extensive serial passaging of the defective virus, a number of viral variants emerged in which the deleted rU:dA tract was replaced by an extended rA:dT tract.
[]
It is interesting to note, however, that after extensive serial passaging of the defective virus, a number of viral variants emerged in which the deleted rU:dA tract was replaced by an extended rA:dT tract.
true
true
true
true
true
382
0
DISCUSSION
1
7
[ "b7", "b21", "b7", "b14", "b35", "b36", "b7", "b32" ]
17,164,285
NA|pmid-11250910|pmid-2477553|pmid-12692229|pmid-9649446|pmid-11044073|pmid-15890925|pmid-9649446|pmid-15183342|pmid-9649446|pmid-11044073|pmid-10775614|pmid-9882295|pmid-9649446|pmid-8764039
The result, invariably, was 5′ terminal extension of the PPT.
[ "7", "21", "7", "14", "35", "36", "7", "32" ]
61
2,199
0
false
The result, invariably, was 5′ terminal extension of the PPT.
[]
The result, invariably, was 5′ terminal extension of the PPT.
true
true
true
true
true
382