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
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ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
13
DISCUSSION
0
null
null
17,594,150
null
For unruptured aneurysms, a follow-up angiography is necessary to detect formation or growth of aneurysm.
null
105
42,319
0
false
null
null
For unruptured aneurysms, a follow-up angiography is necessary to detect formation or growth of aneurysm.
true
true
true
true
true
7,337
13
DISCUSSION
0
null
null
17,594,150
null
The treatment modality of dissecting aneurysm of the VA should be selected according to the clinical characteristics of each patient and close collaboration between neurosurgeons and neurointerventionists is essential to improve the management outcome.
null
252
42,320
0
false
null
null
The treatment modality of dissecting aneurysm of the VA should be selected according to the clinical characteristics of each patient and close collaboration between neurosurgeons and neurointerventionists is essential to improve the management outcome.
true
true
true
true
true
7,337
0
DISCUSSION
0
null
null
18,632,663
null
In this work, we report the results of structure-activity analysis of MccJ25 using a comprehensive panel of MccJ25 point mutants obtained from saturation mutagenesis.
null
168
42,321
0
false
null
null
In this work, we report the results of structure-activity analysis of MccJ25 using a comprehensive panel of MccJ25 point mutants obtained from saturation mutagenesis.
true
true
true
true
true
7,338
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
Of the 381 single-amino acid substitutions analyzed, 242 were shown to be compatible with production of MccJ25 (comprising synthesis of MccJ25 precursor, processing of MccJ25 precursor, export of mature MccJ25, and stability of mature MccJ25) (Fig.
[ "5", "7", "9", "11" ]
251
42,322
0
false
Of the 381 single-amino acid substitutions analyzed, 242 were shown to be compatible with production of MccJ25 (Fig.
[ "comprising synthesis of MccJ25\n precursor, processing of MccJ25 precursor, export of mature MccJ25, and\n stability of mature MccJ25" ]
Of the 381 single-amino acid substitutions analyzed, 242 were shown to be compatible with production of MccJ25 (Fig.
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
Inspection of the lariat-protoknot (threaded lasso) covalent structure of MccJ25 suggests that the residues that form the lactam linkage of the MccJ25 cycle and at least one of the two aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle may be critical for production of MccJ25, whereas resi...
[ "5", "7", "9", "11" ]
386
42,323
0
false
Inspection of the lariat-protoknot (threaded lasso) covalent structure of MccJ25 suggests that the residues that form the lactam linkage of the MccJ25 cycle and at least one of the two aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle may be critical for production of MccJ25, whereas residues...
[]
Inspection of the lariat-protoknot (threaded lasso) covalent structure of MccJ25 suggests that the residues that form the lactam linkage of the MccJ25 cycle and at least one of the two aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle may be critical for production of MccJ25, whereas residues...
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
Our findings support these expectations.
[ "5", "7", "9", "11" ]
40
42,324
0
false
Our findings support these expectations.
[]
Our findings support these expectations.
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
The residues that form the lactam linkage (Gly1 and Glu8) and one immediately adjacent residue (Gly2) are the sole residues for which no non-wild-type side chains are tolerated in production of MccJ25, and the distal aromatic residue of the pair of aromatic residues that lock the threaded MccJ25 tail within the Mc...
[ "5", "7", "9", "11" ]
432
42,325
0
false
The residues that form the lactam linkage (Gly1 and Glu8) and one immediately adjacent residue (Gly2) are the sole residues for which no non-wild-type side chains are tolerated in production of MccJ25, and the distal aromatic residue of the pair of aromatic residues that lock the threaded MccJ25 tail within the MccJ25 ...
[]
The residues that form the lactam linkage (Gly1 and Glu8) and one immediately adjacent residue (Gly2) are the sole residues for which no non-wild-type side chains are tolerated in production of MccJ25, and the distal aromatic residue of the pair of aromatic residues that lock the threaded MccJ25 tail within the MccJ25 ...
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
In the three-dimensional structure of MccJ25 (5-7), these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
[ "5", "7", "9", "11" ]
145
42,326
0
false
In the three-dimensional structure of MccJ25, these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
[ "5-7" ]
In the three-dimensional structure of MccJ25, these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
4, black residues).
[ "5", "7", "9", "11" ]
20
42,327
0
false
4, black residues).
[]
4, black residues).
false
false
true
true
false
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
We propose that the MccJ25 maturation machinery (McjB and McjC; see Refs.
[ "5", "7", "9", "11" ]
74
42,328
0
false
We propose that the MccJ25 maturation machinery (McjB and McjC; see Refs.
[]
We propose that the MccJ25 maturation machinery (McjB and McjC; see Refs.
true
true
true
true
true
7,339
1
DISCUSSION
1
5
[ "ref5", "ref7", "ref9", "ref11" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-8655570|pmid-17656316
9 and 11) recognizes and interacts with this surface determinant during processing of MccJ25 precursor.
[ "5", "7", "9", "11" ]
105
42,329
0
false
9 and 11) recognizes and interacts with this surface determinant during processing of MccJ25 precursor.
[]
9 and 11) recognizes and interacts with this surface determinant during processing of MccJ25 precursor.
false
false
true
true
false
7,339
2
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
FIGURE 4.Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
[ "5", "3", "4" ]
133
42,330
0
false
FIGURE 4.Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
[]
FIGURE 4.Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
true
true
true
true
true
7,340
2
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 (residues 4, 7, 9, 10, 17, and 19; red) on the three-dimensional structure of MccJ25 (see Ref.
[ "5", "3", "4" ]
281
42,331
0
false
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 on the three-dimensional structure of MccJ25 (see Ref.
[ "residues 4, 7, 9, 10,\n 17, and 19; red" ]
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 on the three-dimensional structure of MccJ25 (see Ref.
true
true
true
true
true
7,340
2
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
5; see also Refs.
[ "5", "3", "4" ]
17
42,332
0
false
5; see also Refs.
[]
5; see also Refs.
false
false
true
true
false
7,340
2
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
A, stereoviews in solvent-accessible surface representation.
[ "5", "3", "4" ]
61
42,333
0
false
A, stereoviews in solvent-accessible surface representation.
[]
A, stereoviews in solvent-accessible surface representation.
true
true
true
true
true
7,340
2
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
B, stereoviews in stick representation.
[ "5", "3", "4" ]
40
42,334
0
false
B, stereoviews in stick representation.
[]
B, stereoviews in stick representation.
true
true
true
true
true
7,340
3
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
[ "5", "3", "4" ]
124
42,335
0
false
Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
[]
Locations of residues important for production/maturation/export/stability of MccJ25 and for inhibition of RNAP by MccJ25.
true
true
true
true
true
7,341
3
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 (residues 4, 7, 9, 10, 17, and 19; red) on the three-dimensional structure of MccJ25 (see Ref.
[ "5", "3", "4" ]
281
42,336
0
false
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 on the three-dimensional structure of MccJ25 (see Ref.
[ "residues 4, 7, 9, 10,\n 17, and 19; red" ]
Shown are locations of residues shown here to be important for production/maturation/export/stability of MccJ25 (residues 1, 2, 8, and 20; black) and for inhibition of RNAP by MccJ25 on the three-dimensional structure of MccJ25 (see Ref.
true
true
true
true
true
7,341
3
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
5; see also Refs.
[ "5", "3", "4" ]
17
42,337
0
false
5; see also Refs.
[]
5; see also Refs.
false
false
true
true
false
7,341
3
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
A, stereoviews in solvent-accessible surface representation.
[ "5", "3", "4" ]
61
42,338
0
false
A, stereoviews in solvent-accessible surface representation.
[]
A, stereoviews in solvent-accessible surface representation.
true
true
true
true
true
7,341
3
DISCUSSION
1
5
[ "ref5", "ref3", "ref4" ]
18,632,663
pmid-14531691|pmid-1429464|pmid-10092860
B, stereoviews in stick representation.
[ "5", "3", "4" ]
40
42,339
0
false
B, stereoviews in stick representation.
[]
B, stereoviews in stick representation.
true
true
true
true
true
7,341
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
Of the 242 substituted MccJ25 derivatives competent for production of MccJ25, 155 substituted MccJ25 derivatives also are competent for inhibition of RNAP in vitro (Fig.
[ "5", "7", "13" ]
171
42,340
0
false
Of the 242 substituted MccJ25 derivatives competent for production of MccJ25, 155 substituted MccJ25 derivatives also are competent for inhibition of RNAP in vitro (Fig.
[]
Of the 242 substituted MccJ25 derivatives competent for production of MccJ25, 155 substituted MccJ25 derivatives also are competent for inhibition of RNAP in vitro (Fig.
true
true
true
true
true
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
The residue immediately following the MccJ25 cycle (Tyr9) is the sole residue for which no non-wild-type side chain is tolerated in inhibition of RNAP; two residues of the MccJ25 cycle (Gly4 and Pro7), one residue nearly immediately following the MccJ25 cycle (Phe10), and the proximal aromatic residue of the pair ...
[ "5", "7", "13" ]
501
42,341
0
false
The residue immediately following the MccJ25 cycle (Tyr9) is the sole residue for which no non-wild-type side chain is tolerated in inhibition of RNAP; two residues of the MccJ25 cycle, one residue nearly immediately following the MccJ25 cycle (Phe10), and the proximal aromatic residue of the pair of aromatic residues ...
[ "Gly4 and Pro7" ]
The residue immediately following the MccJ25 cycle (Tyr9) is the sole residue for which no non-wild-type side chain is tolerated in inhibition of RNAP; two residues of the MccJ25 cycle, one residue nearly immediately following the MccJ25 cycle (Phe10), and the proximal aromatic residue of the pair of aromatic residues ...
true
true
true
true
true
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
In the three-dimensional structure of MccJ25 (5-7), these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
[ "5", "7", "13" ]
146
42,342
0
false
In the three-dimensional structure of MccJ25, these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
[ "5-7" ]
In the three-dimensional structure of MccJ25, these residues form a discrete, continuous surface determinant on one face of MccJ25 (Fig.
true
true
true
true
true
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
4, red residues), the face opposite the face with the determinant for production of MccJ25 (Fig.
[ "5", "7", "13" ]
98
42,343
0
false
4, red residues), the face opposite the face with the determinant for production of MccJ25 (Fig.
[]
4, red residues), the face opposite the face with the determinant for production of MccJ25 (Fig.
false
false
true
true
false
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
4, red residues and black residues).
[ "5", "7", "13" ]
37
42,344
0
false
4, red residues and black residues).
[]
4, red residues and black residues).
false
false
true
true
false
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
We propose that the surface determinant comprising Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 makes direct interactions with RNAP in the RNAP-MccJ25 complex (a proposal consistent with the provisional model for the structure of the RNAP-MccJ25 complex in Ref.
[ "5", "7", "13" ]
265
42,345
0
false
We propose that the surface determinant comprising Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 makes direct interactions with RNAP in the RNAP-MccJ25 complex (a proposal consistent with the provisional model for the structure of the RNAP-MccJ25 complex in Ref.
[]
We propose that the surface determinant comprising Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 makes direct interactions with RNAP in the RNAP-MccJ25 complex (a proposal consistent with the provisional model for the structure of the RNAP-MccJ25 complex in Ref.
true
true
true
true
true
7,342
4
DISCUSSION
1
5
[ "ref5", "ref7", "ref13" ]
18,632,663
pmid-14531691|pmid-14531661|pmid-15200952
We note that the wild-type side chains of Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 all are hydrophobic and in three cases are aromatic, and we suggest that RNAP-MccJ25 interactions involve predominantly hydrophobic interactions.
[ "5", "7", "13" ]
236
42,346
0
false
We note that the wild-type side chains of Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 all are hydrophobic and in three cases are aromatic, and we suggest that RNAP-MccJ25 interactions involve predominantly hydrophobic interactions.
[]
We note that the wild-type side chains of Gly4, Pro7, Tyr9, Phe10, and Phe19 of MccJ25 all are hydrophobic and in three cases are aromatic, and we suggest that RNAP-MccJ25 interactions involve predominantly hydrophobic interactions.
true
true
true
true
true
7,342
5
DISCUSSION
0
null
null
18,632,663
null
Of the 155 substituted MccJ25 derivatives competent for production of MccJ25 and competent for inhibition of RNAP by MccJ25 in vitro, 70 substituted MccJ25 derivatives also are competent for inhibition of bacterial growth by MccJ25 in culture and thus apparently are competent to permeate bacterial cells in order to...
null
363
42,347
0
false
null
null
Of the 155 substituted MccJ25 derivatives competent for production of MccJ25 and competent for inhibition of RNAP by MccJ25 in vitro, 70 substituted MccJ25 derivatives also are competent for inhibition of bacterial growth by MccJ25 in culture and thus apparently are competent to permeate bacterial cells in order to...
true
true
true
true
true
7,343
6
DISCUSSION
1
19
[ "ref19", "ref20" ]
18,632,663
pmid-8244949|NA
Two residues of the MccJ25 cycle (Gly4 and Pro7), one residue nearly immediately following the MccJ25 cycle (Phe10), and the pair of aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle (Phe19 and Tyr20) are the sole residues for which no non-wild-type side chains are tolerated in permeation...
[ "19", "20" ]
343
42,348
0
false
Two residues of the MccJ25 cycle (Gly4 and Pro7), one residue nearly immediately following the MccJ25 cycle (Phe10), and the pair of aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle are the sole residues for which no non-wild-type side chains are tolerated in permeation into bacterial cells.
[ "Phe19 and Tyr20" ]
Two residues of the MccJ25 cycle (Gly4 and Pro7), one residue nearly immediately following the MccJ25 cycle, and the pair of aromatic residues that lock the threaded MccJ25 tail within the MccJ25 cycle are the sole residues for which no non-wild-type side chains are tolerated in permeation into bacterial cells.
true
true
true
true
true
7,344
6
DISCUSSION
1
19
[ "ref19", "ref20" ]
18,632,663
pmid-8244949|NA
Three residues of the MccJ25 cycle (Ala3, His5, and Val6), and three residues of the MccJ25 tail (Gly14, Ser18, and Gly21) are the sole additional residues at which <40% or fewer of tested substitutions are compatible with permeation into bacterial cells (Fig.
[ "19", "20" ]
264
42,349
0
false
Three residues of the MccJ25 cycle (Ala3, His5, and Val6), and three residues of the MccJ25 tail (Gly14, Ser18, and Gly21) are the sole additional residues at which <40% or fewer of tested substitutions are compatible with permeation into bacterial cells (Fig.
[]
Three residues of the MccJ25 cycle (Ala3, His5, and Val6), and three residues of the MccJ25 tail are the sole additional residues at which <40% or fewer of tested substitutions are compatible with permeation into bacterial cells (Fig.
true
true
true
true
true
7,344
6
DISCUSSION
1
19
[ "ref19", "ref20" ]
18,632,663
pmid-8244949|NA
The residues at which substitutions affect the ability to permeate bacterial cells do not form a single surface determinant (possibly reflecting the fact that, during permeation of MccJ25 into bacterial cells, MccJ25 makes successive interactions with import complexes in the cell outer membrane and with import comp...
[ "19", "20" ]
363
42,350
0
false
The residues at which substitutions affect the ability to permeate bacterial cells do not form a single surface determinant (possibly reflecting the fact that, during permeation of MccJ25 into bacterial cells, MccJ25 makes successive interactions with import complexes in the cell outer membrane and with import complexe...
[]
The residues at which substitutions affect the ability to permeate bacterial cells do not form a single surface determinant (possibly reflecting the fact that, during permeation of MccJ25 into bacterial cells, MccJ25 makes successive interactions with import complexes in the cell outer membrane and with import complexe...
true
true
true
true
true
7,344
6
DISCUSSION
1
19
[ "ref19", "ref20" ]
18,632,663
pmid-8244949|NA
19 and 20).
[ "19", "20" ]
12
42,351
0
false
19 and 20).
[]
19 and 20).
false
false
true
true
false
7,344
7
DISCUSSION
0
null
null
18,632,663
null
In summary, our results show that only a small number of wild-type side chains of MccJ25 are strictly essential for MccJ25 production and function.
null
148
42,352
0
false
null
null
In summary, our results show that only a small number of wild-type side chains of MccJ25 are strictly essential for MccJ25 production and function.
true
true
true
true
true
7,345
7
DISCUSSION
0
null
null
18,632,663
null
Therefore, despite its small size and complex structure, MccJ25 can be regarded as an attractive platform for engineering antibacterials with higher potencies and/or broadened specificities by further rounds of mutagenesis.
null
225
42,353
0
false
null
null
Therefore, despite its small size and complex structure, MccJ25 can be regarded as an attractive platform for engineering antibacterials with higher potencies and/or broadened specificities by further rounds of mutagenesis.
true
true
true
true
true
7,345
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
Sequence-specific DNA-binding agents have been regarded as a great promise toward the development of new therapeutic strategies based on gene regulation or modification.
[ "1", "2", "3", "4", "5", "6", "7" ]
169
42,354
0
false
Sequence-specific DNA-binding agents have been regarded as a great promise toward the development of new therapeutic strategies based on gene regulation or modification.
[]
Sequence-specific DNA-binding agents have been regarded as a great promise toward the development of new therapeutic strategies based on gene regulation or modification.
true
true
true
true
true
7,346
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
Synthetic molecules that can recognize specific DNA sequences include triplex-forming oligonucleotides (TFOs), peptide nucleic acids and minor-groove binding agents.
[ "1", "2", "3", "4", "5", "6", "7" ]
165
42,355
0
false
Synthetic molecules that can recognize specific DNA sequences include triplex-forming oligonucleotides (TFOs), peptide nucleic acids and minor-groove binding agents.
[]
Synthetic molecules that can recognize specific DNA sequences include triplex-forming oligonucleotides (TFOs), peptide nucleic acids and minor-groove binding agents.
true
true
true
true
true
7,346
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
TFOs were developed in order to modulate the transcription of specific genes, in the so-called antigene strategy, but their affinity and specificity have been exploited for many other purposes, for example to target cleaving or cross-linking agents, transcription factors, or nucleases to a specific site [see refs (1,2)...
[ "1", "2", "3", "4", "5", "6", "7" ]
333
42,356
0
false
TFOs were developed in order to modulate the transcription of specific genes, in the so-called antigene strategy, but their affinity and specificity have been exploited for many other purposes, for example to target cleaving or cross-linking agents, transcription factors, or nucleases to a specific site.
[ "see refs (1,2) for review" ]
TFOs were developed in order to modulate the transcription of specific genes, in the so-called antigene strategy, but their affinity and specificity have been exploited for many other purposes, for example to target cleaving or cross-linking agents, transcription factors, or nucleases to a specific site.
true
true
true
true
true
7,346
0
INTRODUCTION
1
7
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
Moreover, they have been used as tools to induce DNA sequence modifications in live cells (3,4), as well as in various assays aimed at purifying or labelling DNA (5,6) or at investigating DNA–protein interactions (7).
[ "1", "2", "3", "4", "5", "6", "7" ]
217
42,357
1
false
Moreover, they have been used as tools to induce DNA sequence modifications in live cells, as well as in various assays aimed at purifying or labelling DNA or at investigating DNA–protein interactions.
[ "3,4", "5,6", "7" ]
Moreover, they have been used as tools to induce DNA sequence modifications in live cells, as well as in various assays aimed at purifying or labelling DNA or at investigating DNA–protein interactions.
true
true
true
true
true
7,346
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Triple-helix formation is based on sequence-specific recognition of oligopyrimidine–oligopurine sequence by a third nucleic-acid strand.
[ "8", "9", "10", "11", "12" ]
136
42,358
0
false
Triple-helix formation is based on sequence-specific recognition of oligopyrimidine–oligopurine sequence by a third nucleic-acid strand.
[]
Triple-helix formation is based on sequence-specific recognition of oligopyrimidine–oligopurine sequence by a third nucleic-acid strand.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
This third-strand binds in the major groove and recognizes the oligopurine strand by establishing a pair of hydrogen bonds with purine bases that remain involved in Watson–Crick base pairing.
[ "8", "9", "10", "11", "12" ]
191
42,359
0
false
This third-strand binds in the major groove and recognizes the oligopurine strand by establishing a pair of hydrogen bonds with purine bases that remain involved in Watson–Crick base pairing.
[]
This third-strand binds in the major groove and recognizes the oligopurine strand by establishing a pair of hydrogen bonds with purine bases that remain involved in Watson–Crick base pairing.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Different types of triple helices, which contain different types of base triplets, can be formed.
[ "8", "9", "10", "11", "12" ]
97
42,360
0
false
Different types of triple helices, which contain different types of base triplets, can be formed.
[]
Different types of triple helices, which contain different types of base triplets, can be formed.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
The first discovered triple helices, which were formed with third strands containing only pyrimidines, relied on the formation of T.AxT and C.GxC+ base triplets.
[ "8", "9", "10", "11", "12" ]
161
42,361
0
false
The first discovered triple helices, which were formed with third strands containing only pyrimidines, relied on the formation of T.AxT and C.GxC+ base triplets.
[]
The first discovered triple helices, which were formed with third strands containing only pyrimidines, relied on the formation of T.AxT and C.GxC+ base triplets.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
In this so-called pyrimidine or parallel motif, the third-strand binds in a parallel orientation with respect to the oligopurine strand.
[ "8", "9", "10", "11", "12" ]
136
42,362
0
false
In this so-called pyrimidine or parallel motif, the third-strand binds in a parallel orientation with respect to the oligopurine strand.
[]
In this so-called pyrimidine or parallel motif, the third-strand binds in a parallel orientation with respect to the oligopurine strand.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Purine-containing oligonucleotides can also bind double-helical DNA, thanks to the formation of C.GxG and T.AxA base triplets.
[ "8", "9", "10", "11", "12" ]
126
42,363
0
false
Purine-containing oligonucleotides can also bind double-helical DNA, thanks to the formation of C.GxG and T.AxA base triplets.
[]
Purine-containing oligonucleotides can also bind double-helical DNA, thanks to the formation of C.GxG and T.AxA base triplets.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
In this case, the third-strand binds in an antiparallel orientation.
[ "8", "9", "10", "11", "12" ]
68
42,364
0
false
In this case, the third-strand binds in an antiparallel orientation.
[]
In this case, the third-strand binds in an antiparallel orientation.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Recognition of T.A base pairs can be achieved by adenines, but also by thymines.
[ "8", "9", "10", "11", "12" ]
80
42,365
0
false
Recognition of T.A base pairs can be achieved by adenines, but also by thymines.
[]
Recognition of T.A base pairs can be achieved by adenines, but also by thymines.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Therefore this recognition scheme has been named the ‘antiparallel’ motif.
[ "8", "9", "10", "11", "12" ]
74
42,366
0
false
Therefore this recognition scheme has been named the ‘antiparallel’ motif.
[]
Therefore this recognition scheme has been named the ‘antiparallel’ motif.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
The stability of triple helices depends on the recognition scheme, on the sequences and on experimental conditions.
[ "8", "9", "10", "11", "12" ]
115
42,367
0
false
The stability of triple helices depends on the recognition scheme, on the sequences and on experimental conditions.
[]
The stability of triple helices depends on the recognition scheme, on the sequences and on experimental conditions.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Whereas the parallel motif is favoured by an acidic pH and a low GC content within the target sequence, the antiparallel motif can be formed at neutral pH but preferentially in the presence of divalent cations and on target sequences with a very high GC content.
[ "8", "9", "10", "11", "12" ]
262
42,368
0
false
Whereas the parallel motif is favoured by an acidic pH and a low GC content within the target sequence, the antiparallel motif can be formed at neutral pH but preferentially in the presence of divalent cations and on target sequences with a very high GC content.
[]
Whereas the parallel motif is favoured by an acidic pH and a low GC content within the target sequence, the antiparallel motif can be formed at neutral pH but preferentially in the presence of divalent cations and on target sequences with a very high GC content.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
The design and experimental study of TFOs binding in the antiparallel motif can be complicated by the fact that purine-rich oligonucleotides can self-associate into G-quadruplex containing structures or GA duplexes that can compete with triple-helix formation (8,9).
[ "8", "9", "10", "11", "12" ]
266
42,369
0
false
The design and experimental study of TFOs binding in the antiparallel motif can be complicated by the fact that purine-rich oligonucleotides can self-associate into G-quadruplex containing structures or GA duplexes that can compete with triple-helix formation.
[ "8,9" ]
The design and experimental study of TFOs binding in the antiparallel motif can be complicated by the fact that purine-rich oligonucleotides can self-associate into G-quadruplex containing structures or GA duplexes that can compete with triple-helix formation.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
A systematic comparison of the use of A or T to recognize AT base pairs in the antiparallel motif has never been undertaken.
[ "8", "9", "10", "11", "12" ]
124
42,370
0
false
A systematic comparison of the use of A or T to recognize AT base pairs in the antiparallel motif has never been undertaken.
[]
A systematic comparison of the use of A or T to recognize AT base pairs in the antiparallel motif has never been undertaken.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Alternative binding patterns have been observed in some instances.
[ "8", "9", "10", "11", "12" ]
66
42,371
0
false
Alternative binding patterns have been observed in some instances.
[]
Alternative binding patterns have been observed in some instances.
true
true
true
true
true
7,347
1
INTRODUCTION
1
10
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
For example, GT oligonucleotides have been reported to bind in a parallel orientation when the target sequence contains long runs of AT base pairs (10).
[ "8", "9", "10", "11", "12" ]
152
42,372
1
false
For example, GT oligonucleotides have been reported to bind in a parallel orientation when the target sequence contains long runs of AT base pairs.
[ "10" ]
For example, GT oligonucleotides have been reported to bind in a parallel orientation when the target sequence contains long runs of AT base pairs.
true
true
true
true
true
7,347
1
INTRODUCTION
1
11
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
The use of TFOs is also mostly limited to oligopyrimidine–oligopurine target sequences, although strategies have been proposed for the recognition of single or double inversions within the target or for recognizing alternated stretches of purines and pyrimidines (11).
[ "8", "9", "10", "11", "12" ]
268
42,373
1
false
The use of TFOs is also mostly limited to oligopyrimidine–oligopurine target sequences, although strategies have been proposed for the recognition of single or double inversions within the target or for recognizing alternated stretches of purines and pyrimidines.
[ "11" ]
The use of TFOs is also mostly limited to oligopyrimidine–oligopurine target sequences, although strategies have been proposed for the recognition of single or double inversions within the target or for recognizing alternated stretches of purines and pyrimidines.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
There is no convenient method for finding the best TFO for a given sequence.
[ "8", "9", "10", "11", "12" ]
76
42,374
0
false
There is no convenient method for finding the best TFO for a given sequence.
[]
There is no convenient method for finding the best TFO for a given sequence.
true
true
true
true
true
7,347
1
INTRODUCTION
1
8
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
There are some instances where both types of TFO can bind the same DNA target, but this is not typical.
[ "8", "9", "10", "11", "12" ]
103
42,375
0
false
There are some instances where both types of TFO can bind the same DNA target, but this is not typical.
[]
There are some instances where both types of TFO can bind the same DNA target, but this is not typical.
true
true
true
true
true
7,347
1
INTRODUCTION
1
12
[ "B8", "B9", "B10", "B11", "B12" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
TFO are generally chosen mostly on an empirical basis, using known rules for various triple helix motifs for the design followed by in vitro binding assays for validation (12).
[ "8", "9", "10", "11", "12" ]
176
42,376
1
false
TFO are generally chosen mostly on an empirical basis, using known rules for various triple helix motifs for the design followed by in vitro binding assays for validation.
[ "12" ]
TFO are generally chosen mostly on an empirical basis, using known rules for various triple helix motifs for the design followed by in vitro binding assays for validation.
true
true
true
true
true
7,347
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
Stability of triple helices formed by non-modified DNA oligonucleotides can be low at physiological pH and temperature.
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
119
42,377
0
false
Stability of triple helices formed by non-modified DNA oligonucleotides can be low at physiological pH and temperature.
[]
Stability of triple helices formed by non-modified DNA oligonucleotides can be low at physiological pH and temperature.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
This stability can be enhanced by using chemically modified oligonucleotides [see ref.
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
86
42,378
0
false
This stability can be enhanced by using chemically modified oligonucleotides [see ref.
[]
This stability can be enhanced by using chemically modified oligonucleotides [see ref.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
(2) for review].
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
16
42,379
1
false
for review].
[ "2" ]
for review].
false
true
true
true
false
7,348
2
INTRODUCTION
1
13
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
Another very efficient way of stabilizing triple helices is by using triplex-specific ligands (13).
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
99
42,380
1
false
Another very efficient way of stabilizing triple helices is by using triplex-specific ligands.
[ "13" ]
Another very efficient way of stabilizing triple helices is by using triplex-specific ligands.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
The most efficient triplex-stabilizing agents are polyaromatic compounds which bind duplex and triplex DNA by intercalation [see ref.
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
133
42,381
0
false
The most efficient triplex-stabilizing agents are polyaromatic compounds which bind duplex and triplex DNA by intercalation [see ref.
[]
The most efficient triplex-stabilizing agents are polyaromatic compounds which bind duplex and triplex DNA by intercalation [see ref.
true
true
true
true
true
7,348
2
INTRODUCTION
1
14
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
(14) for review].
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
17
42,382
1
false
for review].
[ "14" ]
for review].
false
true
true
true
false
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
Although there is no structural data regarding triplex-intercalator complexes, it has been demonstrated that increased stacking interactions obtained by additional cycles lead to more efficient triplex stabilizers (15,16).
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
222
42,383
0
false
Although there is no structural data regarding triplex-intercalator complexes, it has been demonstrated that increased stacking interactions obtained by additional cycles lead to more efficient triplex stabilizers.
[ "15,16" ]
Although there is no structural data regarding triplex-intercalator complexes, it has been demonstrated that increased stacking interactions obtained by additional cycles lead to more efficient triplex stabilizers.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
Most studies performed with such compounds have regarded the stabilization of triple helices with ‘canonical’ base triplets.
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
124
42,384
0
false
Most studies performed with such compounds have regarded the stabilization of triple helices with ‘canonical’ base triplets.
[]
Most studies performed with such compounds have regarded the stabilization of triple helices with ‘canonical’ base triplets.
true
true
true
true
true
7,348
2
INTRODUCTION
1
17
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
Some of these intercalators have been shown to bind to both parallel (with TC TFOs) and antiparallel (with GT TFOs) triple helices (17).
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
136
42,385
1
false
Some of these intercalators have been shown to bind to both parallel (with TC TFOs) and antiparallel (with GT TFOs) triple helices.
[ "17" ]
Some of these intercalators have been shown to bind to both parallel (with TC TFOs) and antiparallel (with GT TFOs) triple helices.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
However, there is no reason to exclude that the presence of some of these compounds intercalated between DNA bases may alter the recognition code and enhance the formation of structures that do not involve canonical base triplets.
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
230
42,386
0
false
However, there is no reason to exclude that the presence of some of these compounds intercalated between DNA bases may alter the recognition code and enhance the formation of structures that do not involve canonical base triplets.
[]
However, there is no reason to exclude that the presence of some of these compounds intercalated between DNA bases may alter the recognition code and enhance the formation of structures that do not involve canonical base triplets.
true
true
true
true
true
7,348
2
INTRODUCTION
1
2
[ "B2", "B13", "B14", "B15", "B16", "B17", "B18", "B19" ]
20,007,154
pmid-10637355|pmid-1609278|NA|pmid-9520410|NA|pmid-8639533|pmid-8604349|pmid-9547278|pmid-10657289|pmid-16289104
In addition, it has been shown that triplex-specific intercalators can promote the formation of triple helices on target sequences that were not perfect oligopurine–oligopyrimidine stretches (18,19).
[ "2", "13", "14", "15", "16", "17", "18", "19" ]
199
42,387
0
false
In addition, it has been shown that triplex-specific intercalators can promote the formation of triple helices on target sequences that were not perfect oligopurine–oligopyrimidine stretches.
[ "18,19" ]
In addition, it has been shown that triplex-specific intercalators can promote the formation of triple helices on target sequences that were not perfect oligopurine–oligopyrimidine stretches.
true
true
true
true
true
7,348
3
INTRODUCTION
1
20
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
SELEX is an in vitro selection method for oligonucleotides (DNA or RNA) that bind very tightly to a chosen target.
[ "20", "21", "22–25", "26", "27–29" ]
114
42,388
0
false
SELEX is an in vitro selection method for oligonucleotides (DNA or RNA) that bind very tightly to a chosen target.
[]
SELEX is an in vitro selection method for oligonucleotides (DNA or RNA) that bind very tightly to a chosen target.
true
true
true
true
true
7,349
3
INTRODUCTION
1
20
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
It is based on the iterative repetition of cycles that include a binding step, an elution step and an amplification by PCR.
[ "20", "21", "22–25", "26", "27–29" ]
123
42,389
0
false
It is based on the iterative repetition of cycles that include a binding step, an elution step and an amplification by PCR.
[]
It is based on the iterative repetition of cycles that include a binding step, an elution step and an amplification by PCR.
true
true
true
true
true
7,349
3
INTRODUCTION
1
20
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
Selected oligonucleotide sequences are called aptamers.
[ "20", "21", "22–25", "26", "27–29" ]
55
42,390
0
false
Selected oligonucleotide sequences are called aptamers.
[]
Selected oligonucleotide sequences are called aptamers.
true
true
true
true
true
7,349
3
INTRODUCTION
1
20
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
The process was first described in 1990 using proteins (20) and small molecules (21) as targets.
[ "20", "21", "22–25", "26", "27–29" ]
96
42,391
1
false
The process was first described in 1990 using proteins and small molecules as targets.
[ "20", "21" ]
The process was first described in 1990 using proteins and small molecules as targets.
true
true
true
true
true
7,349
3
INTRODUCTION
1
22–25
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
Since then, numerous variants of the original process have been described, and the SELEX technology has been successfully applied for numerous applications on a large variety of targets (22–25), including whole cells and nucleic acids.
[ "20", "21", "22–25", "26", "27–29" ]
235
42,392
1
false
Since then, numerous variants of the original process have been described, and the SELEX technology has been successfully applied for numerous applications on a large variety of targets, including whole cells and nucleic acids.
[ "22–25" ]
Since then, numerous variants of the original process have been described, and the SELEX technology has been successfully applied for numerous applications on a large variety of targets, including whole cells and nucleic acids.
true
true
true
true
true
7,349
3
INTRODUCTION
1
26
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
For example, it has been demonstrated that DNA oligonucleotides selected against DNA secondary structures were able to recognize their target through base pair formation and additional interactions (26).
[ "20", "21", "22–25", "26", "27–29" ]
203
42,393
1
false
For example, it has been demonstrated that DNA oligonucleotides selected against DNA secondary structures were able to recognize their target through base pair formation and additional interactions.
[ "26" ]
For example, it has been demonstrated that DNA oligonucleotides selected against DNA secondary structures were able to recognize their target through base pair formation and additional interactions.
true
true
true
true
true
7,349
3
INTRODUCTION
1
27–29
[ "B20", "B21", "B22 B23 B24 B25", "B26", "B27 B28 B29" ]
20,007,154
pmid-2200121|pmid-1697402|pmid-10995196|pmid-10960261|pmid-17634987|pmid-17627883|pmid-8855239|pmid-10449422|pmid-12867086|pmid-15681618|pmid-7506827|pmid-7529405
SELEX experiments have also helped in the design of antisense oligonucleotides with the ability to bind specific structures (27–29).
[ "20", "21", "22–25", "26", "27–29" ]
132
42,394
1
false
SELEX experiments have also helped in the design of antisense oligonucleotides with the ability to bind specific structures.
[ "27–29" ]
SELEX experiments have also helped in the design of antisense oligonucleotides with the ability to bind specific structures.
true
true
true
true
true
7,349
4
INTRODUCTION
1
30
[ "B30", "B31" ]
20,007,154
pmid-1716784|pmid-8656424|pmid-19153138
Because of the limitations regarding the potential target sequences and as there is no systematic rule for designing the best TFO for a defined target sequence, the SELEX method represents an interesting tool for identifying nucleic acids sequences that bind double-stranded DNA.
[ "30", "31" ]
279
42,395
0
false
Because of the limitations regarding the potential target sequences and as there is no systematic rule for designing the best TFO for a defined target sequence, the SELEX method represents an interesting tool for identifying nucleic acids sequences that bind double-stranded DNA.
[]
Because of the limitations regarding the potential target sequences and as there is no systematic rule for designing the best TFO for a defined target sequence, the SELEX method represents an interesting tool for identifying nucleic acids sequences that bind double-stranded DNA.
true
true
true
true
true
7,350
4
INTRODUCTION
1
30
[ "B30", "B31" ]
20,007,154
pmid-1716784|pmid-8656424|pmid-19153138
Two studies have tried to identify RNA molecules binding to double-stranded DNA using a SELEX approach (30,31).
[ "30", "31" ]
111
42,396
0
false
Two studies have tried to identify RNA molecules binding to double-stranded DNA using a SELEX approach.
[ "30,31" ]
Two studies have tried to identify RNA molecules binding to double-stranded DNA using a SELEX approach.
true
true
true
true
true
7,350
4
INTRODUCTION
1
30
[ "B30", "B31" ]
20,007,154
pmid-1716784|pmid-8656424|pmid-19153138
The selection process was carried out at acidic pH in the first study and at different pH values from 5.5 to 7 in the second one, using a target containing an oligopurine–oligopyrimidine sequence.
[ "30", "31" ]
196
42,397
0
false
The selection process was carried out at acidic pH in the first study and at different pH values from 5.5 to 7 in the second one, using a target containing an oligopurine–oligopyrimidine sequence.
[]
The selection process was carried out at acidic pH in the first study and at different pH values from 5.5 to 7 in the second one, using a target containing an oligopurine–oligopyrimidine sequence.
true
true
true
true
true
7,350
4
INTRODUCTION
1
30
[ "B30", "B31" ]
20,007,154
pmid-1716784|pmid-8656424|pmid-19153138
The selected RNAs consisted mostly in uraciles and cytosines that were able to form canonical T.AxU and C.GxC+ base triplets.
[ "30", "31" ]
125
42,398
0
false
The selected RNAs consisted mostly in uraciles and cytosines that were able to form canonical T.AxU and C.GxC+ base triplets.
[]
The selected RNAs consisted mostly in uraciles and cytosines that were able to form canonical T.AxU and C.GxC+ base triplets.
true
true
true
true
true
7,350
5
INTRODUCTION
0
null
null
20,007,154
pmid-15274215|pmid-15911633|pmid-9547278|pmid-9380499|pmid-9685475|pmid-9862797|NA|pmid-9862797|pmid-10454596
In the present study, we have selected DNA oligonucleotides for binding to a DNA target containing an oligopurine.oligopyrimidine sequence with a low GC content (35%) under neutral pH in the presence of a triplex-stabilizing agent.
null
231
42,399
0
false
null
null
In the present study, we have selected DNA oligonucleotides for binding to a DNA target containing an oligopurine.oligopyrimidine sequence with a low GC content (35%) under neutral pH in the presence of a triplex-stabilizing agent.
true
true
true
true
true
7,351
5
INTRODUCTION
0
null
null
20,007,154
pmid-15274215|pmid-15911633|pmid-9547278|pmid-9380499|pmid-9685475|pmid-9862797|NA|pmid-9862797|pmid-10454596
These selections were performed in order to determine what would be the best TFO for such a sequence in the presence of a triplex-binding agent and to investigate if the presence of intercalators may modify the ‘code’ for triple-helix formation by enhancing the formation of non-canonical base triplets.
null
303
42,400
0
false
null
null
These selections were performed in order to determine what would be the best TFO for such a sequence in the presence of a triplex-binding agent and to investigate if the presence of intercalators may modify the ‘code’ for triple-helix formation by enhancing the formation of non-canonical base triplets.
true
true
true
true
true
7,351
5
INTRODUCTION
0
null
null
20,007,154
pmid-15274215|pmid-15911633|pmid-9547278|pmid-9380499|pmid-9685475|pmid-9862797|NA|pmid-9862797|pmid-10454596
Our idea was also to implement a new approach for identifying new recognition schemes and maybe extend the range of sequences that can be recognized by oligonucleotides in a sequence-specific manner.
null
199
42,401
0
false
null
null
Our idea was also to implement a new approach for identifying new recognition schemes and maybe extend the range of sequences that can be recognized by oligonucleotides in a sequence-specific manner.
true
true
true
true
true
7,351
0
DISCUSSION
1
30
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
In vitro selection experiments have been applied to the recognition of double-stranded nucleic acid targets by only two different groups (30,31).
[ "30", "31", "36", "37" ]
145
42,402
0
false
In vitro selection experiments have been applied to the recognition of double-stranded nucleic acid targets by only two different groups.
[ "30,31" ]
In vitro selection experiments have been applied to the recognition of double-stranded nucleic acid targets by only two different groups.
true
true
true
true
true
7,352
0
DISCUSSION
1
30
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
These studies did not result in the discovery of new binding motifs, but identified pyrimidine-rich RNA oligonucleotides that were able to bind their target upon formation of canonical base-triplets within the parallel motif.
[ "30", "31", "36", "37" ]
225
42,403
0
false
These studies did not result in the discovery of new binding motifs, but identified pyrimidine-rich RNA oligonucleotides that were able to bind their target upon formation of canonical base-triplets within the parallel motif.
[]
These studies did not result in the discovery of new binding motifs, but identified pyrimidine-rich RNA oligonucleotides that were able to bind their target upon formation of canonical base-triplets within the parallel motif.
true
true
true
true
true
7,352
0
DISCUSSION
1
30
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
Two additional studies used a combinatorial approach in order to investigate the specificity of triple-helix formation.
[ "30", "31", "36", "37" ]
119
42,404
0
false
Two additional studies used a combinatorial approach in order to investigate the specificity of triple-helix formation.
[]
Two additional studies used a combinatorial approach in order to investigate the specificity of triple-helix formation.
true
true
true
true
true
7,352
0
DISCUSSION
1
36
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
In the first one (36), van Dyke and coworkers have selected the best double-stranded DNA substrate for a GT-rich TFO.
[ "30", "31", "36", "37" ]
117
42,405
1
false
In the first one, van Dyke and coworkers have selected the best double-stranded DNA substrate for a GT-rich TFO.
[ "36" ]
In the first one, van Dyke and coworkers have selected the best double-stranded DNA substrate for a GT-rich TFO.
true
true
true
true
true
7,352
0
DISCUSSION
1
37
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
In the second one (37), both the third strand and the target were randomized, which led to the selection of triple helices containing mostly C.GxG base triplets.
[ "30", "31", "36", "37" ]
161
42,406
1
false
In the second one, both the third strand and the target were randomized, which led to the selection of triple helices containing mostly C.GxG base triplets.
[ "37" ]
In the second one, both the third strand and the target were randomized, which led to the selection of triple helices containing mostly C.GxG base triplets.
true
true
true
true
true
7,352
0
DISCUSSION
1
30
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
None of these studies were able to identify TFOs that could bind a given target double-stranded DNA with an antiparallel configuration.
[ "30", "31", "36", "37" ]
135
42,407
0
false
None of these studies were able to identify TFOs that could bind a given target double-stranded DNA with an antiparallel configuration.
[]
None of these studies were able to identify TFOs that could bind a given target double-stranded DNA with an antiparallel configuration.
true
true
true
true
true
7,352
0
DISCUSSION
1
30
[ "B30", "B31", "B36", "B37" ]
20,007,154
NA|pmid-10637355|pmid-11039937|pmid-18460344|pmid-12877387|pmid-17216036|pmid-10790375|pmid-1716784|pmid-8656424|pmid-8610123|pmid-10373587
The absence of further combinatorial investigations for the recognition of double-stranded DNA is likely due to the experimental challenge of forming stable triple helical structures at neutral pH, except for sequences that are rich in GC base pairs.
[ "30", "31", "36", "37" ]
250
42,408
0
false
The absence of further combinatorial investigations for the recognition of double-stranded DNA is likely due to the experimental challenge of forming stable triple helical structures at neutral pH, except for sequences that are rich in GC base pairs.
[]
The absence of further combinatorial investigations for the recognition of double-stranded DNA is likely due to the experimental challenge of forming stable triple helical structures at neutral pH, except for sequences that are rich in GC base pairs.
true
true
true
true
true
7,352
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
In the present study, we have implemented an in vitro selection scheme for the identification of oligonucleotides that bind duplex DNA in the presence of a triplex intercalator.
[ "16", "11" ]
177
42,409
0
false
In the present study, we have implemented an in vitro selection scheme for the identification of oligonucleotides that bind duplex DNA in the presence of a triplex intercalator.
[]
In the present study, we have implemented an in vitro selection scheme for the identification of oligonucleotides that bind duplex DNA in the presence of a triplex intercalator.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
We chose as triplex intercalator the BIQ compound, which has been shown to increase the melting temperature of a pyrimidine triple-helix by up to 40°C (16), and had also been shown to stabilize triple helices with purine containing third strands in our laboratory.
[ "16", "11" ]
264
42,410
1
false
We chose as triplex intercalator the BIQ compound, which has been shown to increase the melting temperature of a pyrimidine triple-helix by up to 40°C, and had also been shown to stabilize triple helices with purine containing third strands in our laboratory.
[ "16" ]
We chose as triplex intercalator the BIQ compound, which has been shown to increase the melting temperature of a pyrimidine triple-helix by up to 40°C, and had also been shown to stabilize triple helices with purine containing third strands in our laboratory.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Selection rounds were performed at neutral pH using as a target sequence a DNA fragment containing a 20 bp oligopurine–oligopyrimidine stretch, with 65% AT and 35% GC.
[ "16", "11" ]
167
42,411
0
false
Selection rounds were performed at neutral pH using as a target sequence a DNA fragment containing a 20 bp oligopurine–oligopyrimidine stretch, with 65% AT and 35% GC.
[]
Selection rounds were performed at neutral pH using as a target sequence a DNA fragment containing a 20 bp oligopurine–oligopyrimidine stretch, with 65% AT and 35% GC.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
The selection process was very convenient as each selection round could be performed in less than a day, and introduction of a fluorescent moiety at the end of a primer enabled the quantification of recovered DNA at each step in a convenient way.
[ "16", "11" ]
246
42,412
0
false
The selection process was very convenient as each selection round could be performed in less than a day, and introduction of a fluorescent moiety at the end of a primer enabled the quantification of recovered DNA at each step in a convenient way.
[]
The selection process was very convenient as each selection round could be performed in less than a day, and introduction of a fluorescent moiety at the end of a primer enabled the quantification of recovered DNA at each step in a convenient way.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
After only seven rounds of selection, a strong affinity of the oligonucleotide pool for the target sequence was evident from the amount of oligonucleotide recovered after elution.
[ "16", "11" ]
179
42,413
0
false
After only seven rounds of selection, a strong affinity of the oligonucleotide pool for the target sequence was evident from the amount of oligonucleotide recovered after elution.
[]
After only seven rounds of selection, a strong affinity of the oligonucleotide pool for the target sequence was evident from the amount of oligonucleotide recovered after elution.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Sequencing of the oligonucleotides revealed that most selected sequences were able to form antiparallel triple helices with the DNA target sequence through recognition of the oligopurine–oligopyrimidine stretch.
[ "16", "11" ]
211
42,414
0
false
Sequencing of the oligonucleotides revealed that most selected sequences were able to form antiparallel triple helices with the DNA target sequence through recognition of the oligopurine–oligopyrimidine stretch.
[]
Sequencing of the oligonucleotides revealed that most selected sequences were able to form antiparallel triple helices with the DNA target sequence through recognition of the oligopurine–oligopyrimidine stretch.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Importantly, GC base pairs were always recognized by guanines, whereas recognition of AT base pairs seemed to depend on the sequence context.
[ "16", "11" ]
141
42,415
0
false
Importantly, GC base pairs were always recognized by guanines, whereas recognition of AT base pairs seemed to depend on the sequence context.
[]
Importantly, GC base pairs were always recognized by guanines, whereas recognition of AT base pairs seemed to depend on the sequence context.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
For four positions, thymines were found exclusively, while others seemed to accommodate both adenine and thymine.
[ "16", "11" ]
113
42,416
0
false
For four positions, thymines were found exclusively, while others seemed to accommodate both adenine and thymine.
[]
For four positions, thymines were found exclusively, while others seemed to accommodate both adenine and thymine.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
Depending on the sequence context, adenine or thymine were found more or less frequently.
[ "16", "11" ]
89
42,417
0
false
Depending on the sequence context, adenine or thymine were found more or less frequently.
[]
Depending on the sequence context, adenine or thymine were found more or less frequently.
true
true
true
true
true
7,353
1
DISCUSSION
1
16
[ "B16", "B11" ]
20,007,154
pmid-7596824|pmid-7819208|pmid-9862797|NA|pmid-18954091|NA|NA
No clear rule can be established from the observation of this single target sequence.
[ "16", "11" ]
85
42,418
0
false
No clear rule can be established from the observation of this single target sequence.
[]
No clear rule can be established from the observation of this single target sequence.
true
true
true
true
true
7,353