Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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3
INTRODUCTION
1
22
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Adenine quartets (22), uracil quartets (23) and bulges may also be accommodated in RNA quadruplexes (24), expanding the structural repertoire of quadruplexes.
[ "18", "19", "20", "21", "22", "23", "24" ]
158
4,600
1
false
Adenine quartets, uracil quartets and bulges may also be accommodated in RNA quadruplexes, expanding the structural repertoire of quadruplexes.
[ "22", "23", "24" ]
Adenine quartets, uracil quartets and bulges may also be accommodated in RNA quadruplexes, expanding the structural repertoire of quadruplexes.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
However, the contributions of these non-G quartets to the kinetics and energetics of the quadruplex are poorly understood, and structural methods provide only clues to the effects of these modifications.
[ "18", "19", "20", "21", "22", "23", "24" ]
203
4,601
0
false
However, the contributions of these non-G quartets to the kinetics and energetics of the quadruplex are poorly understood, and structural methods provide only clues to the effects of these modifications.
[]
However, the contributions of these non-G quartets to the kinetics and energetics of the quadruplex are poorly understood, and structural methods provide only clues to the effects of these modifications.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Little data is available for sequences in which the G-tract is interrupted by a ‘mismatch,’ i.e.
[ "18", "19", "20", "21", "22", "23", "24" ]
96
4,602
0
false
Little data is available for sequences in which the G-tract is interrupted by a ‘mismatch,’ i.e.
[]
Little data is available for sequences in which the G-tract is interrupted by a ‘mismatch,’ i.e.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
any base (natural or synthetic) different from a guanine.
[ "18", "19", "20", "21", "22", "23", "24" ]
57
4,603
0
false
any base (natural or synthetic) different from a guanine.
[]
any base (natural or synthetic) different from a guanine.
false
true
true
true
false
777
4
INTRODUCTION
0
null
null
17,452,368
pmid-11159416
Using the canonical tetramolecular quadruplexes formed by TG4T and TG5T, we substituted each of the four or five guanines, respectively, with a variety of bases (the natural bases A, T, C and U, and the non-natural bases represented in Figure 1) and analyzed the impacts of these modifications on the kinetics of formati...
null
364
4,604
0
false
null
null
Using the canonical tetramolecular quadruplexes formed by TG4T and TG5T, we substituted each of the four or five guanines, respectively, with a variety of bases (the natural bases A, T, C and U, and the non-natural bases represented in Figure 1) and analyzed the impacts of these modifications on the kinetics of formati...
true
true
true
true
true
778
4
INTRODUCTION
0
null
null
17,452,368
pmid-11159416
We demonstrate that, in most cases, the incorporation of a single modified quartet not only leads to decreased melting temperature but also to a decreased association rate.
null
172
4,605
0
false
null
null
We demonstrate that, in most cases, the incorporation of a single modified quartet not only leads to decreased melting temperature but also to a decreased association rate.
true
true
true
true
true
778
4
INTRODUCTION
0
null
null
17,452,368
pmid-11159416
Non-guanine base quartets are, at best, tolerated in a parallel quadruplex and generally do not contribute to the stability of the structure, two exceptions being the 8-bromo-guanine (X) and 6-methyl-isoxanthopterin (P) substitutions.
null
234
4,606
0
false
null
null
Non-guanine base quartets are, at best, tolerated in a parallel quadruplex and generally do not contribute to the stability of the structure, two exceptions being the 8-bromo-guanine (X) and 6-methyl-isoxanthopterin (P) substitutions.
true
true
true
true
true
778
0
DISCUSSION
1
17
[ "B17" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
In the present study, we analyzed the effects of 12 different base substitutions on the kinetics and thermodynamics of parallel tetramolecular quadruplexes.
[ "17" ]
156
4,607
0
false
In the present study, we analyzed the effects of 12 different base substitutions on the kinetics and thermodynamics of parallel tetramolecular quadruplexes.
[]
In the present study, we analyzed the effects of 12 different base substitutions on the kinetics and thermodynamics of parallel tetramolecular quadruplexes.
true
true
true
true
true
779
0
DISCUSSION
1
17
[ "B17" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
The data were compared with the parallel-stranded tetramolecular quadruplexes formed by TG4T and TG5T.
[ "17" ]
102
4,608
0
false
The data were compared with the parallel-stranded tetramolecular quadruplexes formed by TG4T and TG5T.
[]
The data were compared with the parallel-stranded tetramolecular quadruplexes formed by TG4T and TG5T.
true
true
true
true
true
779
0
DISCUSSION
1
17
[ "B17" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Most isothermal and melting experiments could be analyzed in the framework of an all-or-none process, in agreement with Petraccone et al., who demonstrated that the quadruplex-to-single strand transition of TG4T involved only two significant spectral species, suggesting a simple dissociation pathway (17).
[ "17" ]
306
4,609
1
false
Most isothermal and melting experiments could be analyzed in the framework of an all-or-none process, in agreement with Petraccone et al., who demonstrated that the quadruplex-to-single strand transition of TG4T involved only two significant spectral species, suggesting a simple dissociation pathway.
[ "17" ]
Most isothermal and melting experiments could be analyzed in the framework of an all-or-none process, in agreement with Petraccone et al., who demonstrated that the quadruplex-to-single strand transition of TG4T involved only two significant spectral species, suggesting a simple dissociation pathway.
true
true
true
true
true
779
0
DISCUSSION
1
17
[ "B17" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
To our knowledge, the present work is the first experimental attempt to quantify and compare a variety of modified quadruplex sequences.
[ "17" ]
136
4,610
0
false
To our knowledge, the present work is the first experimental attempt to quantify and compare a variety of modified quadruplex sequences.
[]
To our knowledge, the present work is the first experimental attempt to quantify and compare a variety of modified quadruplex sequences.
true
true
true
true
true
779
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
Although many oligomers adopt relatively similar conformations, the kinetics of these complexes may vary greatly.
[ "37", "38" ]
113
4,611
0
false
Although many oligomers adopt relatively similar conformations, the kinetics of these complexes may vary greatly.
[]
Although many oligomers adopt relatively similar conformations, the kinetics of these complexes may vary greatly.
true
true
true
true
true
780
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
We showed that the consideration of Tm (or T1/2) as the sole indicator of quadruplex thermodynamics may lead to a profound underestimation of the energetic penalty imposed by a single guanine replacement.
[ "37", "38" ]
204
4,612
0
false
We showed that the consideration of Tm (or T1/2) as the sole indicator of quadruplex thermodynamics may lead to a profound underestimation of the energetic penalty imposed by a single guanine replacement.
[]
We showed that the consideration of Tm (or T1/2) as the sole indicator of quadruplex thermodynamics may lead to a profound underestimation of the energetic penalty imposed by a single guanine replacement.
true
true
true
true
true
780
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
It is essential to evaluate the kinetics of both dissociation and association to obtain a reliable estimate of the thermodynamic penalty imposed by the sequence modification.
[ "37", "38" ]
174
4,613
0
false
It is essential to evaluate the kinetics of both dissociation and association to obtain a reliable estimate of the thermodynamic penalty imposed by the sequence modification.
[]
It is essential to evaluate the kinetics of both dissociation and association to obtain a reliable estimate of the thermodynamic penalty imposed by the sequence modification.
true
true
true
true
true
780
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
It is striking that for quadruplexes, a ‘mismatch’ has a deleterious impact on both the association and dissociation processes, whereas for duplexes and triplexes, a mismatched base-pair or base-triplet affects the dissociation process (37,38).
[ "37", "38" ]
244
4,614
0
false
It is striking that for quadruplexes, a ‘mismatch’ has a deleterious impact on both the association and dissociation processes, whereas for duplexes and triplexes, a mismatched base-pair or base-triplet affects the dissociation process.
[ "37,38" ]
It is striking that for quadruplexes, a ‘mismatch’ has a deleterious impact on both the association and dissociation processes, whereas for duplexes and triplexes, a mismatched base-pair or base-triplet affects the dissociation process.
true
true
true
true
true
780
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
A possible explanation for this behavior comes from the differences in length among these motifs.
[ "37", "38" ]
97
4,615
0
false
A possible explanation for this behavior comes from the differences in length among these motifs.
[]
A possible explanation for this behavior comes from the differences in length among these motifs.
true
true
true
true
true
780
1
DISCUSSION
1
37
[ "B37", "B38" ]
17,452,368
pmid-5138337|pmid-1390713
Only four to five base quartets are formed in quadruplexes, and a mismatch is more likely to affect the nucleation event for initial quadruplex association.
[ "37", "38" ]
156
4,616
0
false
Only four to five base quartets are formed in quadruplexes, and a mismatch is more likely to affect the nucleation event for initial quadruplex association.
[]
Only four to five base quartets are formed in quadruplexes, and a mismatch is more likely to affect the nucleation event for initial quadruplex association.
true
true
true
true
true
780
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The 5′/3′ asymmetry observed in the influence of stabilizing modifications also gives interesting insights into the nucleation process.
[ "39", "40", "41–46" ]
135
4,617
0
false
The 5′/3′ asymmetry observed in the influence of stabilizing modifications also gives interesting insights into the nucleation process.
[]
The 5′/3′ asymmetry observed in the influence of stabilizing modifications also gives interesting insights into the nucleation process.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
One may therefore be tempted to propose that the rate-limiting step involves the 5′ side of the strands.
[ "39", "40", "41–46" ]
104
4,618
0
false
One may therefore be tempted to propose that the rate-limiting step involves the 5′ side of the strands.
[]
One may therefore be tempted to propose that the rate-limiting step involves the 5′ side of the strands.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
All three favorable modifications (8, X and P) accelerated formation or decelerated dissociation of quadruplexes only when located on the 5′ side.
[ "39", "40", "41–46" ]
146
4,619
0
false
All three favorable modifications (8, X and P) accelerated formation or decelerated dissociation of quadruplexes only when located on the 5′ side.
[]
All three favorable modifications (8, X and P) accelerated formation or decelerated dissociation of quadruplexes only when located on the 5′ side.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
In X and P modifications, the respective bromo- and methyl substituents may favor the initial hydrophobic collapse that brings strands together.
[ "39", "40", "41–46" ]
144
4,620
0
false
In X and P modifications, the respective bromo- and methyl substituents may favor the initial hydrophobic collapse that brings strands together.
[]
In X and P modifications, the respective bromo- and methyl substituents may favor the initial hydrophobic collapse that brings strands together.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
However, as this asymmetry is not observed for all substitutions, this putative directional nucleation-zipping mechanism for quadruplex formation is probably less pronounced than for triplexes (39).
[ "39", "40", "41–46" ]
198
4,621
1
false
However, as this asymmetry is not observed for all substitutions, this putative directional nucleation-zipping mechanism for quadruplex formation is probably less pronounced than for triplexes.
[ "39" ]
However, as this asymmetry is not observed for all substitutions, this putative directional nucleation-zipping mechanism for quadruplex formation is probably less pronounced than for triplexes.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The extremely deleterious impact of a central guanine substitution on association also indicates that the central guanines participate in the rate-limiting step.
[ "39", "40", "41–46" ]
161
4,622
0
false
The extremely deleterious impact of a central guanine substitution on association also indicates that the central guanines participate in the rate-limiting step.
[]
The extremely deleterious impact of a central guanine substitution on association also indicates that the central guanines participate in the rate-limiting step.
true
true
true
true
true
781
2
DISCUSSION
1
40
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
It is also worth noticing that with these three modifications (P, X and 8), the syn conformation is (or is likely to be) favored as compared to a regular guanine (40) suggesting the implication of the syn G at the 5′ end in the nucleation process.
[ "39", "40", "41–46" ]
247
4,623
1
false
It is also worth noticing that with these three modifications (P, X and 8), the syn conformation is (or is likely to be) favored as compared to a regular guanine suggesting the implication of the syn G at the 5′ end in the nucleation process.
[ "40" ]
It is also worth noticing that with these three modifications (P, X and 8), the syn conformation is (or is likely to be) favored as compared to a regular guanine suggesting the implication of the syn G at the 5′ end in the nucleation process.
true
true
true
true
true
781
2
DISCUSSION
1
41–46
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
In the publications reporting quadruplex structures based on the (3 + 1) or mixed parallel–antiparallel scaffold (41–46) the Gs on the 5′ part of the quadruplex are mostly syn.
[ "39", "40", "41–46" ]
176
4,624
1
false
In the publications reporting quadruplex structures based on the (3 + 1) or mixed parallel–antiparallel scaffold the Gs on the 5′ part of the quadruplex are mostly syn.
[ "41–46" ]
In the publications reporting quadruplex structures based on the or mixed parallel–antiparallel scaffold the Gs on the 5′ part of the quadruplex are mostly syn.
true
true
true
true
true
781
2
DISCUSSION
1
39
[ "B39", "B40", "B41 B42 B43 B44 B45 B46" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
These 5′ syn bases might also participate in the stability of the quadruplex (for X and 8).
[ "39", "40", "41–46" ]
91
4,625
0
false
These 5′ syn bases might also participate in the stability of the quadruplex (for X and 8).
[]
These 5′ syn bases might also participate in the stability of the quadruplex (for X and 8).
true
true
true
true
true
781
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
The structure of this kinetic intermediate remains elusive but some observations help to eliminate some possibilities: (i) a Hoogsteen duplex or triplex is an extremely unstable, and therefore unlikely, intermediate (13), (ii) transient strand dimers and trimers have been evidenced by mass spectrometry (47), (iii) mono...
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
575
4,626
1
false
The structure of this kinetic intermediate remains elusive but some observations help to eliminate some possibilities: (i) a Hoogsteen duplex or triplex is an extremely unstable, and therefore unlikely, intermediate, (ii) transient strand dimers and trimers have been evidenced by mass spectrometry, (iii) monocations pa...
[ "13", "47", "15,16", "15", "14–17" ]
The structure of this kinetic intermediate remains elusive but some observations help to eliminate some possibilities: (i) a Hoogsteen duplex or triplex is an extremely unstable, and therefore unlikely, intermediate, (ii) transient strand dimers and trimers have been evidenced by mass spectrometry, (iii) monocations pa...
true
true
true
true
true
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Starting from the double-dimer to tetramer pathway proposed by Wyatt et al.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
75
4,627
0
false
Starting from the double-dimer to tetramer pathway proposed by Wyatt et al.
[]
Starting from the double-dimer to tetramer pathway proposed by Wyatt et al.
true
true
true
true
true
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
and the ‘cross-like’ two-stranded assemblies proposed by Stefl et al.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
69
4,628
0
false
and the ‘cross-like’ two-stranded assemblies proposed by Stefl et al.
[]
and the ‘cross-like’ two-stranded assemblies proposed by Stefl et al.
false
true
true
true
false
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
(13), one may envision that the rate-limiting step is the formation of ‘nucleation’ quartets, with four guanines unlikely to originate from four different strands.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
163
4,629
1
false
, one may envision that the rate-limiting step is the formation of ‘nucleation’ quartets, with four guanines unlikely to originate from four different strands.
[ "13" ]
, one may envision that the rate-limiting step is the formation of ‘nucleation’ quartets, with four guanines unlikely to originate from four different strands.
false
false
true
true
false
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Two of these guanines must then originate from the same strand (for example, one ‘central’ and the other towards the 5′ end, thereby explaining a certain asymmetry) and some of these bases transiently adopt a syn conformation.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
226
4,630
0
false
Two of these guanines must then originate from the same strand (for example, one ‘central’ and the other towards the 5′ end, thereby explaining a certain asymmetry) and some of these bases transiently adopt a syn conformation.
[]
Two of these guanines must then originate from the same strand (for example, one ‘central’ and the other towards the 5′ end, thereby explaining a certain asymmetry) and some of these bases transiently adopt a syn conformation.
true
true
true
true
true
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
This transient geometry could be facilitated by the presence of some modifications, (X or P for example), for which the syn conformation is preferred.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
150
4,631
0
false
This transient geometry could be facilitated by the presence of some modifications, (X or P for example), for which the syn conformation is preferred.
[]
This transient geometry could be facilitated by the presence of some modifications, (X or P for example), for which the syn conformation is preferred.
true
true
true
true
true
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
A long guanine tract facilitates the formation of two (and perhaps three) stacked quartet, which captures one to two monocations and defines the nucleation event.
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
162
4,632
0
false
A long guanine tract facilitates the formation of two (and perhaps three) stacked quartet, which captures one to two monocations and defines the nucleation event.
[]
A long guanine tract facilitates the formation of two (and perhaps three) stacked quartet, which captures one to two monocations and defines the nucleation event.
true
true
true
true
true
782
3
DISCUSSION
1
15
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
This could explain the puzzling observation that the longer the guanine tract, the faster the association and this is in agreement with the negative activation energy of association (Eon = −29 kcal/mol for TG4T) found for tetramolecular quadruplexes (15).
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
255
4,633
1
false
This could explain the puzzling observation that the longer the guanine tract, the faster the association and this is in agreement with the negative activation energy of association (Eon = −29 kcal/mol for TG4T) found for tetramolecular quadruplexes.
[ "15" ]
This could explain the puzzling observation that the longer the guanine tract, the faster the association and this is in agreement with the negative activation energy of association (Eon = −29 kcal/mol for TG4T) found for tetramolecular quadruplexes.
true
true
true
true
true
782
3
DISCUSSION
1
13
[ "B13", "B47", "B15", "B16", "B15", "B14 B15 B16 B17", "B14", "B13", "B15" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
These initial quartet(s) are embedded in a two-stranded dimer, rather than a Hoogsteen duplex, and will then undergo a series of rearrangements involving the association of additional strands, possible formation of a trimer, syn to anti conversion (again, the presence of syn bases in the final structure may be proposed...
[ "13", "47", "15", "16", "15", "14–17", "14", "13", "15" ]
572
4,634
0
false
These initial quartet(s) are embedded in a two-stranded dimer, rather than a Hoogsteen duplex, and will then undergo a series of rearrangements involving the association of additional strands, possible formation of a trimer, syn to anti conversion (again, the presence of syn bases in the final structure may be proposed...
[]
These initial quartet(s) are embedded in a two-stranded dimer, rather than a Hoogsteen duplex, and will then undergo a series of rearrangements involving the association of additional strands, possible formation of a trimer, syn to anti conversion (again, the presence of syn bases in the final structure may be proposed...
true
true
true
true
true
782
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
The wealth of data compiled here can serve as a basis for future structural interpretation.
[ "48" ]
91
4,635
0
false
The wealth of data compiled here can serve as a basis for future structural interpretation.
[]
The wealth of data compiled here can serve as a basis for future structural interpretation.
true
true
true
true
true
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
Interestingly, Stefl et al.
[ "48" ]
27
4,636
0
false
Interestingly, Stefl et al.
[]
Interestingly, Stefl et al.
true
true
true
true
true
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
already performed molecular dynamics simulations of DNA quadruplex molecules containing modified bases (48).
[ "48" ]
108
4,637
1
false
already performed molecular dynamics simulations of DNA quadruplex molecules containing modified bases.
[ "48" ]
already performed molecular dynamics simulations of DNA quadruplex molecules containing modified bases.
false
true
true
true
false
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
The incorporation of 6-thioguanine (6) or 6-methylguanine (M) sharply destabilized four-stranded G-DNA structures, whereas inosine (I) had a limited effect.
[ "48" ]
156
4,638
0
false
The incorporation of 6-thioguanine (6) or 6-methylguanine (M) sharply destabilized four-stranded G-DNA structures, whereas inosine (I) had a limited effect.
[]
The incorporation of 6-thioguanine (6) or 6-methylguanine (M) sharply destabilized four-stranded G-DNA structures, whereas inosine (I) had a limited effect.
true
true
true
true
true
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
The first two modifications prevented proper cation coordination and created a steric clash in the central part of the quartet, whereas inosine could still form a quartet, even though the external ring of H-bonds is lost.
[ "48" ]
221
4,639
0
false
The first two modifications prevented proper cation coordination and created a steric clash in the central part of the quartet, whereas inosine could still form a quartet, even though the external ring of H-bonds is lost.
[]
The first two modifications prevented proper cation coordination and created a steric clash in the central part of the quartet, whereas inosine could still form a quartet, even though the external ring of H-bonds is lost.
true
true
true
true
true
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
All these predictions are verified in our experiments.
[ "48" ]
54
4,640
0
false
All these predictions are verified in our experiments.
[]
All these predictions are verified in our experiments.
true
true
true
true
true
783
4
DISCUSSION
1
48
[ "B48" ]
17,452,368
pmid-11159416
Also, the higher destabilization observed with central modifications, together with the mass spectrometry measurements of the number of coordinated cations, suggest that the stability should be interpreted in terms of nearest neighbors (two neighboring quartets and the associated cations) instead of quartets only.
[ "48" ]
315
4,641
0
false
Also, the higher destabilization observed with central modifications, together with the mass spectrometry measurements of the number of coordinated cations, suggest that the stability should be interpreted in terms of nearest neighbors (two neighboring quartets and the associated cations) instead of quartets only.
[]
Also, the higher destabilization observed with central modifications, together with the mass spectrometry measurements of the number of coordinated cations, suggest that the stability should be interpreted in terms of nearest neighbors (two neighboring quartets and the associated cations) instead of quartets only.
true
true
true
true
true
783
5
DISCUSSION
0
null
null
17,452,368
null
One of the major findings of our study is that most substitutions are extremely detrimental to quadruplex stability, as shown by substantial decreases in both the association rate and the thermal stability of the complex.
null
221
4,642
0
false
null
null
One of the major findings of our study is that most substitutions are extremely detrimental to quadruplex stability, as shown by substantial decreases in both the association rate and the thermal stability of the complex.
true
true
true
true
true
784
5
DISCUSSION
0
null
null
17,452,368
null
In particular, all natural bases (A, C, T and U) fall in this category.
null
71
4,643
0
false
null
null
In particular, all natural bases (A, C, T and U) fall in this category.
true
true
true
true
true
784
5
DISCUSSION
0
null
null
17,452,368
null
Non-G quartets in genomic DNA are therefore clearly not favorable to the energetics of the quadruplexes: they are tolerated at best.
null
132
4,644
0
false
null
null
Non-G quartets in genomic DNA are therefore clearly not favorable to the energetics of the quadruplexes: they are tolerated at best.
true
true
true
true
true
784
5
DISCUSSION
0
null
null
17,452,368
null
This is independent of the nature of the monocation: with a few exceptions, an unfavorable substitution in K+ remains unfavorable in Na+ and .
null
142
4,645
0
false
null
null
This is independent of the nature of the monocation: with a few exceptions, an unfavorable substitution in K+ remains unfavorable in Na+ and .
true
true
true
true
true
784
5
DISCUSSION
0
null
null
17,452,368
null
Despite the presence of well-defined non-guanine base quartets in a number of NMR and X-ray structures, our data suggest that these quartets do not participate favorably in structural stability and are formed only by virtue of the docking platform provided by neighboring G-quartets.
null
283
4,646
0
false
null
null
Despite the presence of well-defined non-guanine base quartets in a number of NMR and X-ray structures, our data suggest that these quartets do not participate favorably in structural stability and are formed only by virtue of the docking platform provided by neighboring G-quartets.
true
true
true
true
true
784
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
Our study also provides useful guidelines for the future conception of synthetic DNA assemblies based on quadruplex formation.
[ "49" ]
126
4,647
0
false
Our study also provides useful guidelines for the future conception of synthetic DNA assemblies based on quadruplex formation.
[]
Our study also provides useful guidelines for the future conception of synthetic DNA assemblies based on quadruplex formation.
true
true
true
true
true
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
Comparing the association constants found for a variety of substitutions led us to propose the following conclusions: (i) the central part of the quartet (the central ring of H-bonds and O6 carbonyl groups) is vital to its stability: altering this part not only leads to the loss of one H-bond, but may also hamper coord...
[ "49" ]
350
4,648
0
false
Comparing the association constants found for a variety of substitutions led us to propose the following conclusions: (i) the central part of the quartet (the central ring of H-bonds and O6 carbonyl groups) is vital to its stability: altering this part not only leads to the loss of one H-bond, but may also hamper coord...
[]
Comparing the association constants found for a variety of substitutions led us to propose the following conclusions: (i) the central part of the quartet (the central ring of H-bonds and O6 carbonyl groups) is vital to its stability: altering this part not only leads to the loss of one H-bond, but may also hamper coord...
true
true
true
true
true
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
(ii) Removal of the external ring of H-bonds leads to a moderate decrease in the association rate (ex: inosine).
[ "49" ]
112
4,649
0
false
(ii) Removal of the external ring of H-bonds leads to a moderate decrease in the association rate (ex: inosine).
[]
(ii) Removal of the external ring of H-bonds leads to a moderate decrease in the association rate (ex: inosine).
false
false
true
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
However, if one not only remove these H-bonds but perturbs the geometry/planarity of the quartet as a result of a steric clash, as for 7-deazaguanine, the penalty is more severe.
[ "49" ]
178
4,650
0
false
However, if one not only remove these H-bonds but perturbs the geometry/planarity of the quartet as a result of a steric clash, as for 7-deazaguanine, the penalty is more severe.
[]
However, if one not only remove these H-bonds but perturbs the geometry/planarity of the quartet as a result of a steric clash, as for 7-deazaguanine, the penalty is more severe.
true
true
true
true
true
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
(iii) One is left with a limited freedom to play with the 8-position and, in a few cases (8-bromo-guanine), substitutions may even become favorable.
[ "49" ]
148
4,651
0
false
(iii) One is left with a limited freedom to play with the 8-position and, in a few cases (8-bromo-guanine), substitutions may even become favorable.
[]
(iii) One is left with a limited freedom to play with the 8-position and, in a few cases (8-bromo-guanine), substitutions may even become favorable.
false
false
true
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
Modifications that do not affect the cyclic hydrogen bond pattern nor the central carbonyl groups are well tolerated and may effectively replace guanines, although syn/anti sugar configuration preferences play a role.
[ "49" ]
217
4,652
0
false
Modifications that do not affect the cyclic hydrogen bond pattern nor the central carbonyl groups are well tolerated and may effectively replace guanines, although syn/anti sugar configuration preferences play a role.
[]
Modifications that do not affect the cyclic hydrogen bond pattern nor the central carbonyl groups are well tolerated and may effectively replace guanines, although syn/anti sugar configuration preferences play a role.
true
true
true
true
true
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
(iv) Finally, the purine geometry is not an absolute requirement to form a stable quartet: isoxanthopterine is fully compatible with quadruplex formation, and other planar bicyclic groups may also form a quartet.
[ "49" ]
212
4,653
0
false
(iv) Finally, the purine geometry is not an absolute requirement to form a stable quartet: isoxanthopterine is fully compatible with quadruplex formation, and other planar bicyclic groups may also form a quartet.
[]
(iv) Finally, the purine geometry is not an absolute requirement to form a stable quartet: isoxanthopterine is fully compatible with quadruplex formation, and other planar bicyclic groups may also form a quartet.
false
false
true
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
In that case, we believe that the presence of a central carbonyl group is required (i.e.
[ "49" ]
88
4,654
0
false
In that case, we believe that the presence of a central carbonyl group is required (i.e.
[]
In that case, we believe that the presence of a central carbonyl group is required (i.e.
true
true
true
true
true
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
at a position equivalent to the O6 group of guanine) and should be H-bonded to a H-bond donor group (likely an amino group) from another base.
[ "49" ]
142
4,655
0
false
at a position equivalent to the O6 group of guanine) and should be H-bonded to a H-bond donor group (likely an amino group) from another base.
[]
at a position equivalent to the O6 group of guanine) and should be H-bonded to a H-bond donor group (likely an amino group) from another base.
false
true
true
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
(v) The conclusions reached here apply to base quartets in which, by virtue of the tetramolecular system, all four bases are substituted.
[ "49" ]
137
4,656
0
false
(v) The conclusions reached here apply to base quartets in which, by virtue of the tetramolecular system, all four bases are substituted.
[]
(v) The conclusions reached here apply to base quartets in which, by virtue of the tetramolecular system, all four bases are substituted.
false
false
true
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
It should be interesting to compare this system with intramolecular quadruplexes, in which a single base may be replaced in each quartet
[ "49" ]
136
4,657
0
false
It should be interesting to compare this system with intramolecular quadruplexes, in which a single base may be replaced in each quartet
[]
It should be interesting to compare this system with intramolecular quadruplexes, in which a single base may be replaced in each quartet
true
true
false
true
false
785
6
DISCUSSION
1
49
[ "B49" ]
17,452,368
pmid-16292787
[for example: (49)].
[ "49" ]
20
4,658
0
false
.
[ "for example: (49)" ]
.
false
false
true
true
false
785
7
DISCUSSION
0
null
null
17,452,368
null
The two ‘non-canonical’ modifications X and P even lead to faster quadruplex formations than the all-guanine reference sequences.
null
129
4,659
0
false
null
null
The two ‘non-canonical’ modifications X and P even lead to faster quadruplex formations than the all-guanine reference sequences.
true
true
true
true
true
786
7
DISCUSSION
0
null
null
17,452,368
null
The only substitution that leads to a stability improvement in both association and dissociation parameters (as compared to guanine) is 8-bromo-guanine (X), when inserted at the 5′ end (position 1).
null
198
4,660
0
false
null
null
The only substitution that leads to a stability improvement in both association and dissociation parameters (as compared to guanine) is 8-bromo-guanine (X), when inserted at the 5′ end (position 1).
true
true
true
true
true
786
7
DISCUSSION
0
null
null
17,452,368
null
However, the case of P substitution is also highly interesting on the application point of view, because this modification in the 5′ side leads to an increase of both the association and dissociation rates.
null
206
4,661
0
false
null
null
However, the case of P substitution is also highly interesting on the application point of view, because this modification in the 5′ side leads to an increase of both the association and dissociation rates.
true
true
true
true
true
786
7
DISCUSSION
0
null
null
17,452,368
null
Reversible devices based on P-modified quadruplexes could therefore have a higher turnover than the classical G-quadruplexes.
null
125
4,662
0
false
null
null
Reversible devices based on P-modified quadruplexes could therefore have a higher turnover than the classical G-quadruplexes.
true
true
true
true
true
786
7
DISCUSSION
0
null
null
17,452,368
null
The thermodynamic and kinetic data compiled here is highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties.
null
161
4,663
0
false
null
null
The thermodynamic and kinetic data compiled here is highly valuable for the design of DNA quadruplex assemblies with tunable association/dissociation properties.
true
true
true
true
true
786
7
DISCUSSION
0
null
null
17,452,368
null
So far, guanines are still a quartet′s best friends!
null
52
4,664
0
false
null
null
So far, guanines are still a quartet′s best friends!
true
true
true
true
true
786
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Small regulatory RNAs (sRNAs) are expressed in both prokaryotes and eukaryotes, primarily as posttranscriptional regulators.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
124
4,665
0
false
Small regulatory RNAs (sRNAs) are expressed in both prokaryotes and eukaryotes, primarily as posttranscriptional regulators.
[]
Small regulatory RNAs (sRNAs) are expressed in both prokaryotes and eukaryotes, primarily as posttranscriptional regulators.
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Over the past six years, about 70 sRNAs have been discovered in E. coli, and about 20 of them have been assigned a function.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
124
4,666
0
false
Over the past six years, about 70 sRNAs have been discovered in E. coli, and about 20 of them have been assigned a function.
[]
Over the past six years, about 70 sRNAs have been discovered in E. coli, and about 20 of them have been assigned a function.
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Many of these trans-encoded RNAs are involved in metabolic processes [e.g.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
74
4,667
0
false
Many of these trans-encoded RNAs are involved in metabolic processes [e.g.
[]
Many of these trans-encoded RNAs are involved in metabolic processes [e.g.
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Spot42, DsrA, RprA, RyhB, SgrS, GadY, reviewed in (1)] and at least eight sRNAs regulate the expression of membrane proteins [reviewed in (2)].
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
143
4,668
1
false
Spot42, DsrA, RprA, RyhB, SgrS, GadY, reviewed in ] and at least eight sRNAs regulate the expression of membrane proteins.
[ "1", "reviewed in (2)" ]
Spot42, DsrA, RprA, RyhB, SgrS, GadY, reviewed in ] and at least eight sRNAs regulate the expression of membrane proteins.
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
To date, relatively few systematic searches have been performed in Gram-positive bacteria.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
90
4,669
0
false
To date, relatively few systematic searches have been performed in Gram-positive bacteria.
[]
To date, relatively few systematic searches have been performed in Gram-positive bacteria.
true
true
true
true
true
787
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Among the recently discovered sRNAs in Gram-positive hosts are RatA from the Bacillus subtilis chromosome (3), which came up in a systematic search (4) together with 12 other sRNAs that proved to be sporulation-controlled, but still await the identification of their targets (5).
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
279
4,670
1
false
Among the recently discovered sRNAs in Gram-positive hosts are RatA from the Bacillus subtilis chromosome, which came up in a systematic search together with 12 other sRNAs that proved to be sporulation-controlled, but still await the identification of their targets.
[ "3", "4", "5" ]
Among the recently discovered sRNAs in Gram-positive hosts are RatA from the Bacillus subtilis chromosome, which came up in a systematic search together with 12 other sRNAs that proved to be sporulation-controlled, but still await the identification of their targets.
true
true
true
true
true
787
0
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Furthermore, in addition to the well-studied RNAIII from Staphylococcus aureus (6), 12 novel sRNAs from Staphylococcus aureus pathogenicity islands have been detected (7) as well as three Hfq-binding sRNAs of Listeria monocytogenes with still unknown function (8), and nine novel sRNAs from Listeria monocytogenes within...
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
380
4,671
1
false
Furthermore, in addition to the well-studied RNAIII from Staphylococcus aureus, 12 novel sRNAs from Staphylococcus aureus pathogenicity islands have been detected as well as three Hfq-binding sRNAs of Listeria monocytogenes with still unknown function, and nine novel sRNAs from Listeria monocytogenes within intergenic ...
[ "6", "7", "8", "9" ]
Furthermore, in addition to the well-studied RNAIII from Staphylococcus aureus, 12 novel sRNAs from Staphylococcus aureus pathogenicity islands have been detected as well as three Hfq-binding sRNAs of Listeria monocytogenes with still unknown function, and nine novel sRNAs from Listeria monocytogenes within intergenic ...
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Additionally, more than 100 potential 6S RNA species have been identified by bioinformatics approaches, and many of them were verified experimentally, among them two 6S RNA species in B. subtilis (10,11).
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
204
4,672
0
false
Additionally, more than 100 potential 6S RNA species have been identified by bioinformatics approaches, and many of them were verified experimentally, among them two 6S RNA species in B. subtilis.
[ "10,11" ]
Additionally, more than 100 potential 6S RNA species have been identified by bioinformatics approaches, and many of them were verified experimentally, among them two 6S RNA species in B. subtilis.
true
true
true
true
true
787
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Still, the identification of mRNA targets of the recently discovered sRNAs is a challenging issue, and has been successful only in less than one-third of all cases.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
164
4,673
0
false
Still, the identification of mRNA targets of the recently discovered sRNAs is a challenging issue, and has been successful only in less than one-third of all cases.
[]
Still, the identification of mRNA targets of the recently discovered sRNAs is a challenging issue, and has been successful only in less than one-third of all cases.
true
true
true
true
true
787
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16" ]
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
One important hallmark of many trans-encoded regulatory RNAs from E. coli is their ability to bind the Sm-like abundant RNA chaperone Hfq (12).
[ "12", "13", "14", "15", "16" ]
143
4,674
1
false
One important hallmark of many trans-encoded regulatory RNAs from E. coli is their ability to bind the Sm-like abundant RNA chaperone Hfq.
[ "12" ]
One important hallmark of many trans-encoded regulatory RNAs from E. coli is their ability to bind the Sm-like abundant RNA chaperone Hfq.
true
true
true
true
true
788
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16" ]
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
While several sRNAs have been found to require Hfq for their stability, some were shown to need Hfq for efficient complex formation with their target RNA (13,14).
[ "12", "13", "14", "15", "16" ]
162
4,675
0
false
While several sRNAs have been found to require Hfq for their stability, some were shown to need Hfq for efficient complex formation with their target RNA.
[ "13,14" ]
While several sRNAs have been found to require Hfq for their stability, some were shown to need Hfq for efficient complex formation with their target RNA.
true
true
true
true
true
788
1
INTRODUCTION
1
15
[ "B12", "B13", "B14", "B15", "B16" ]
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
For DsrA/rpoS/Hfq, the pathway of complex formation has been investigated by biophysical techniques (15).
[ "12", "13", "14", "15", "16" ]
105
4,676
1
false
For DsrA/rpoS/Hfq, the pathway of complex formation has been investigated by biophysical techniques.
[ "15" ]
For DsrA/rpoS/Hfq, the pathway of complex formation has been investigated by biophysical techniques.
true
true
true
true
true
788
1
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16" ]
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
However, for sRNAs from Gram-positive bacteria, the putative function of Hfq is still elusive.
[ "12", "13", "14", "15", "16" ]
94
4,677
0
false
However, for sRNAs from Gram-positive bacteria, the putative function of Hfq is still elusive.
[]
However, for sRNAs from Gram-positive bacteria, the putative function of Hfq is still elusive.
true
true
true
true
true
788
1
INTRODUCTION
1
16
[ "B12", "B13", "B14", "B15", "B16" ]
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
At least in one case, staphylococcal RNAIII/spa interaction, no influence of Hfq has been found (16).
[ "12", "13", "14", "15", "16" ]
101
4,678
1
false
At least in one case, staphylococcal RNAIII/spa interaction, no influence of Hfq has been found.
[ "16" ]
At least in one case, staphylococcal RNAIII/spa interaction, no influence of Hfq has been found.
true
true
true
true
true
788
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20", "B14", "B21", "B22" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
In contrast to the cis-encoded sRNAs from accessory genetic elements like plasmids, phages, transposons that have been studied in detail over the past 25 years [reviewed in (17)], relatively little is known about structural requirements, binding kinetics and mechanisms or degradation pathways of these new trans-encoded...
[ "17", "18", "19", "20", "14", "21", "22" ]
338
4,679
0
false
In contrast to the cis-encoded sRNAs from accessory genetic elements like plasmids, phages, transposons that have been studied in detail over the past 25 years, relatively little is known about structural requirements, binding kinetics and mechanisms or degradation pathways of these new trans-encoded regulatory sRNAs.
[ "reviewed in (17)" ]
In contrast to the cis-encoded sRNAs from accessory genetic elements like plasmids, phages, transposons that have been studied in detail over the past 25 years, relatively little is known about structural requirements, binding kinetics and mechanisms or degradation pathways of these new trans-encoded regulatory sRNAs.
true
true
true
true
true
789
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20", "B14", "B21", "B22" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
Although complexes between sRNA and mRNA have been detected in vitro in some instances, only in five cases secondary structures of such complexes predicted by Mfold have been confirmed by experimental secondary structure probing.
[ "17", "18", "19", "20", "14", "21", "22" ]
229
4,680
0
false
Although complexes between sRNA and mRNA have been detected in vitro in some instances, only in five cases secondary structures of such complexes predicted by Mfold have been confirmed by experimental secondary structure probing.
[]
Although complexes between sRNA and mRNA have been detected in vitro in some instances, only in five cases secondary structures of such complexes predicted by Mfold have been confirmed by experimental secondary structure probing.
true
true
true
true
true
789
2
INTRODUCTION
1
18
[ "B17", "B18", "B19", "B20", "B14", "B21", "B22" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
These include MicF/ompF (18), Spot42/galK (19), RyhB/sodB (20), MicA/ompA (14,21) from E. coli and RNAIII/spa from Staphylococcus aureus (22).
[ "17", "18", "19", "20", "14", "21", "22" ]
142
4,681
1
false
These include MicF/ompF, Spot42/galK, RyhB/sodB, MicA/ompA from E. coli and RNAIII/spa from Staphylococcus aureus.
[ "18", "19", "20", "14,21", "22" ]
These include MicF/ompF, Spot42/galK, RyhB/sodB, MicA/ompA from E. coli and RNAIII/spa from Staphylococcus aureus.
true
true
true
true
true
789
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20", "B14", "B21", "B22" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
So far, the region of initial contact between a trans-encoded sRNA and a target RNA sharing more than one complementary region has not been narrowed down.
[ "17", "18", "19", "20", "14", "21", "22" ]
154
4,682
0
false
So far, the region of initial contact between a trans-encoded sRNA and a target RNA sharing more than one complementary region has not been narrowed down.
[]
So far, the region of initial contact between a trans-encoded sRNA and a target RNA sharing more than one complementary region has not been narrowed down.
true
true
true
true
true
789
2
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20", "B14", "B21", "B22" ]
17,576,690
NA|pmid-7534474|pmid-12101127|pmid-14739933|pmid-16313626|pmid-16204185|pmid-15678100|NA
The mechanism of action has been proposed in some cases, but not always corroborated by a combination of in vivo and in vitro experiments.
[ "17", "18", "19", "20", "14", "21", "22" ]
138
4,683
0
false
The mechanism of action has been proposed in some cases, but not always corroborated by a combination of in vivo and in vitro experiments.
[]
The mechanism of action has been proposed in some cases, but not always corroborated by a combination of in vivo and in vitro experiments.
true
true
true
true
true
789
3
INTRODUCTION
1
23
[ "B23", "B24" ]
17,576,690
pmid-16164558|pmid-17020585
The 205-nt untranslated RNA SR1 from the B. subtilis genome was found in our group by a combination of computer predictions and northern blotting (23).
[ "23", "24" ]
151
4,684
1
false
The 205-nt untranslated RNA SR1 from the B. subtilis genome was found in our group by a combination of computer predictions and northern blotting.
[ "23" ]
The 205-nt untranslated RNA SR1 from the B. subtilis genome was found in our group by a combination of computer predictions and northern blotting.
true
true
true
true
true
790
3
INTRODUCTION
1
24
[ "B23", "B24" ]
17,576,690
pmid-16164558|pmid-17020585
Recently, we have shown that SR1 is a bona fide antisense RNA that acts by basepairing with its primary target, ahrC mRNA, the transcriptional activator of the rocABC and rocDEF arginine catabolic operons (24).
[ "23", "24" ]
210
4,685
1
false
Recently, we have shown that SR1 is a bona fide antisense RNA that acts by basepairing with its primary target, ahrC mRNA, the transcriptional activator of the rocABC and rocDEF arginine catabolic operons.
[ "24" ]
Recently, we have shown that SR1 is a bona fide antisense RNA that acts by basepairing with its primary target, ahrC mRNA, the transcriptional activator of the rocABC and rocDEF arginine catabolic operons.
true
true
true
true
true
790
3
INTRODUCTION
1
23
[ "B23", "B24" ]
17,576,690
pmid-16164558|pmid-17020585
In vitro translation data and translational reporter gene fusions suggested that SR1 might inhibit ahrC translation at a post-initiation stage.
[ "23", "24" ]
143
4,686
0
false
In vitro translation data and translational reporter gene fusions suggested that SR1 might inhibit ahrC translation at a post-initiation stage.
[]
In vitro translation data and translational reporter gene fusions suggested that SR1 might inhibit ahrC translation at a post-initiation stage.
true
true
true
true
true
790
3
INTRODUCTION
1
23
[ "B23", "B24" ]
17,576,690
pmid-16164558|pmid-17020585
Hfq was shown to be dispensable for the stability of SR1.
[ "23", "24" ]
57
4,687
0
false
Hfq was shown to be dispensable for the stability of SR1.
[]
Hfq was shown to be dispensable for the stability of SR1.
true
true
true
true
true
790
4
INTRODUCTION
0
null
null
17,576,690
pmid-11931231|pmid-17259613|NA
Here, we provide a detailed in vitro characterization of SR1 and the SR1/ahrC complex with and without Hfq.
null
107
4,688
0
false
null
null
Here, we provide a detailed in vitro characterization of SR1 and the SR1/ahrC complex with and without Hfq.
true
true
true
true
true
791
4
INTRODUCTION
0
null
null
17,576,690
pmid-11931231|pmid-17259613|NA
We determined the region of initial contact between SR1 and ahrC.
null
65
4,689
0
false
null
null
We determined the region of initial contact between SR1 and ahrC.
true
true
true
true
true
791
4
INTRODUCTION
0
null
null
17,576,690
pmid-11931231|pmid-17259613|NA
Furthermore, a combination of toeprinting and SR1/ahrC complex probing studies demonstrated that SR1 inhibits translation initiation of ahrC mRNA by inducing structural changes between the ahrC SD sequence and the first complementary region G.
null
243
4,690
0
false
null
null
Furthermore, a combination of toeprinting and SR1/ahrC complex probing studies demonstrated that SR1 inhibits translation initiation of ahrC mRNA by inducing structural changes between the ahrC SD sequence and the first complementary region G.
true
true
true
true
true
791
4
INTRODUCTION
0
null
null
17,576,690
pmid-11931231|pmid-17259613|NA
In contrast to many E. coli sense/antisense systems, Hfq was shown to be exclusively required for translation of ahrC RNA, but not for promoting the SR1/ahrC interaction.
null
170
4,691
0
false
null
null
In contrast to many E. coli sense/antisense systems, Hfq was shown to be exclusively required for translation of ahrC RNA, but not for promoting the SR1/ahrC interaction.
true
true
true
true
true
791
4
INTRODUCTION
0
null
null
17,576,690
pmid-11931231|pmid-17259613|NA
The intracellular concentration of SR1 in B. subtilis was calculated to be 30 nM in log phase and 315 nM in stationary phase in complex TY medium.
null
146
4,692
0
false
null
null
The intracellular concentration of SR1 in B. subtilis was calculated to be 30 nM in log phase and 315 nM in stationary phase in complex TY medium.
true
true
true
true
true
791
0
DISCUSSION
1
24
[ "B24" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
For all recently discovered trans-encoded sRNAs the targets of which have been identified, only one or two complementary regions were found.
[ "24" ]
140
4,693
0
false
For all recently discovered trans-encoded sRNAs the targets of which have been identified, only one or two complementary regions were found.
[]
For all recently discovered trans-encoded sRNAs the targets of which have been identified, only one or two complementary regions were found.
true
true
true
true
true
792
0
DISCUSSION
1
24
[ "B24" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
In the majority of cases, these regions covered the 5′ part of the target RNA, mostly including the SD sequence, and the mechanism of action was found to be inhibition or activation of translation initiation.
[ "24" ]
208
4,694
0
false
In the majority of cases, these regions covered the 5′ part of the target RNA, mostly including the SD sequence, and the mechanism of action was found to be inhibition or activation of translation initiation.
[]
In the majority of cases, these regions covered the 5′ part of the target RNA, mostly including the SD sequence, and the mechanism of action was found to be inhibition or activation of translation initiation.
true
true
true
true
true
792
0
DISCUSSION
1
24
[ "B24" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
Rather unusually, SR1 and ahrC mRNA contain seven regions of complementarity that comprise the 3′ half of SR1 and the central and 3′ portion of ahrC mRNA (24).
[ "24" ]
159
4,695
1
false
Rather unusually, SR1 and ahrC mRNA contain seven regions of complementarity that comprise the 3′ half of SR1 and the central and 3′ portion of ahrC mRNA.
[ "24" ]
Rather unusually, SR1 and ahrC mRNA contain seven regions of complementarity that comprise the 3′ half of SR1 and the central and 3′ portion of ahrC mRNA.
true
true
true
true
true
792
0
DISCUSSION
1
24
[ "B24" ]
17,576,690
pmid-15952886|pmid-17055775|pmid-16166525|pmid-11717296|pmid-16385044|pmid-7556100|pmid-16183745|pmid-16373489|pmid-17259222|pmid-15811922|pmid-15793584|pmid-17020585
This prompted us to determine the secondary structures of SR1 and the ahrC/SR1 complex and to investigate the structural requirements for efficient ahrC/SR1 pairing.
[ "24" ]
165
4,696
0
false
This prompted us to determine the secondary structures of SR1 and the ahrC/SR1 complex and to investigate the structural requirements for efficient ahrC/SR1 pairing.
[]
This prompted us to determine the secondary structures of SR1 and the ahrC/SR1 complex and to investigate the structural requirements for efficient ahrC/SR1 pairing.
true
true
true
true
true
792
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
Figure 1B shows that SR1 is composed of one large 5′ stem-loop (SL1) structure with a prominent bulge, a central small stem-loop SL2 and the terminator stem-loop SL3 separated by two single-stranded regions.
null
207
4,697
0
false
null
null
Figure 1B shows that SR1 is composed of one large 5′ stem-loop (SL1) structure with a prominent bulge, a central small stem-loop SL2 and the terminator stem-loop SL3 separated by two single-stranded regions.
true
true
true
true
true
793
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
Six out of seven regions of complementarity to ahrC RNA (B to G) are located in the 3′ 100 nt of SR1.
null
101
4,698
0
false
null
null
Six out of seven regions of complementarity to ahrC RNA (B to G) are located in the 3′ 100 nt of SR1.
true
true
true
true
true
793
1
DISCUSSION
0
null
null
17,576,690
pmid-15009882|pmid-11804582|pmid-16313626|pmid-17259214|pmid-17291347
Secondary structure probing of labelled SR1 in complex with increasing concentrations of unlabelled ahrC and vice versa (Figure 3A and B) revealed structural alterations in six of the seven complementary regions.
null
212
4,699
0
false
null
null
Secondary structure probing of labelled SR1 in complex with increasing concentrations of unlabelled ahrC and vice versa (Figure 3A and B) revealed structural alterations in six of the seven complementary regions.
true
true
true
true
true
793