Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
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citeids
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pmid
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sentences
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list
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lgtm
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__index_level_0__
int64
10
DISCUSSION
1
54
[ "b54", "b55" ]
16,835,309
pmid-8638105|pmid-12547794
(54), an extended conformation of the Lac repressor has been proposed (55).
[ "54", "55" ]
75
3,700
1
false
, an extended conformation of the Lac repressor has been proposed.
[ "54", "55" ]
, an extended conformation of the Lac repressor has been proposed.
false
false
true
true
false
617
10
DISCUSSION
1
54
[ "b54", "b55" ]
16,835,309
pmid-8638105|pmid-12547794
The rigidity of these conformations and the possibility for the protein to switch between these multiple structural states are fundamental in determining Jm for loop formation.
[ "54", "55" ]
176
3,701
0
false
The rigidity of these conformations and the possibility for the protein to switch between these multiple structural states are fundamental in determining Jm for loop formation.
[]
The rigidity of these conformations and the possibility for the protein to switch between these multiple structural states are fundamental in determining Jm for loop formation.
true
true
true
true
true
617
10
DISCUSSION
1
54
[ "b54", "b55" ]
16,835,309
pmid-8638105|pmid-12547794
Also, distance and phasing between the operators is a fundamental factor in determining the value of Jm, as already demonstrated for ligase-catalyzed circularization.
[ "54", "55" ]
166
3,702
0
false
Also, distance and phasing between the operators is a fundamental factor in determining the value of Jm, as already demonstrated for ligase-catalyzed circularization.
[]
Also, distance and phasing between the operators is a fundamental factor in determining the value of Jm, as already demonstrated for ligase-catalyzed circularization.
true
true
true
true
true
617
10
DISCUSSION
1
54
[ "b54", "b55" ]
16,835,309
pmid-8638105|pmid-12547794
The TPM method holds promise to allow a systematic characterization of the dependence of LacI regulation of the Lac operon on each of these components, providing in the near future, a complete picture of the orientation effects and of the protein and DNA mechanics involved in the process.
[ "54", "55" ]
289
3,703
0
false
The TPM method holds promise to allow a systematic characterization of the dependence of LacI regulation of the Lac operon on each of these components, providing in the near future, a complete picture of the orientation effects and of the protein and DNA mechanics involved in the process.
[]
The TPM method holds promise to allow a systematic characterization of the dependence of LacI regulation of the Lac operon on each of these components, providing in the near future, a complete picture of the orientation effects and of the protein and DNA mechanics involved in the process.
true
true
true
true
true
617
11
DISCUSSION
0
null
null
16,835,309
null
Our measurements on the mutants of the hinge region Q60G and Q60 + 1 indicate that alterations in the flexibility and geometry of the hinge lead to significant changes in the kinetics measurable with TPM.
null
204
3,704
0
false
null
null
Our measurements on the mutants of the hinge region Q60G and Q60 + 1 indicate that alterations in the flexibility and geometry of the hinge lead to significant changes in the kinetics measurable with TPM.
true
true
true
true
true
618
11
DISCUSSION
0
null
null
16,835,309
null
The association and dissociation rate constants for these mutants have not been measured in standard biochemical assays; however, the data shown in Figure 7b clearly demonstrate the large effects of these mutations on the looped lifetimes, with much smaller effects on the unlooped lifetimes.
null
292
3,705
0
false
null
null
The association and dissociation rate constants for these mutants have not been measured in standard biochemical assays; however, the data shown in Figure 7b clearly demonstrate the large effects of these mutations on the looped lifetimes, with much smaller effects on the unlooped lifetimes.
true
true
true
true
true
618
11
DISCUSSION
0
null
null
16,835,309
null
These results lead to the conclusion that the mutations studied cause changes predominantly in the value of the dissociation rate constant.
null
139
3,706
0
false
null
null
These results lead to the conclusion that the mutations studied cause changes predominantly in the value of the dissociation rate constant.
true
true
true
true
true
618
11
DISCUSSION
0
null
null
16,835,309
null
As expected, the mutant characterized by the lower equilibrium dissociation constant (Q60G) displays a longer looped average lifetime, whereas the mutant with the higher KD (Q60 + 1) displays a shorter looped average lifetime.
null
226
3,707
0
false
null
null
As expected, the mutant characterized by the lower equilibrium dissociation constant (Q60G) displays a longer looped average lifetime, whereas the mutant with the higher KD (Q60 + 1) displays a shorter looped average lifetime.
true
true
true
true
true
618
11
DISCUSSION
0
null
null
16,835,309
null
However, the sensitivity of the protein to DNA strain is not significantly affected by these mutations.
null
103
3,708
0
false
null
null
However, the sensitivity of the protein to DNA strain is not significantly affected by these mutations.
true
true
true
true
true
618
11
DISCUSSION
0
null
null
16,835,309
null
It is likely that a role of this kind may be more appropriate for the tetramerization domain, and for the regions of interaction between monomers in the tetramer, which affect the propensity of the protein to take a V-shape, an open shape or other possible conformations responsible for a different sensitivity to strain...
null
339
3,709
0
false
null
null
It is likely that a role of this kind may be more appropriate for the tetramerization domain, and for the regions of interaction between monomers in the tetramer, which affect the propensity of the protein to take a V-shape, an open shape or other possible conformations responsible for a different sensitivity to strain...
true
true
true
true
true
618
12
DISCUSSION
0
null
null
16,835,309
null
In conclusion, with regard to DNA bending, our work indicates that the rate of loop formation by Lac repressor depends more strongly than previously expected on the energetics of bending and twisting of DNA.
null
207
3,710
0
false
null
null
In conclusion, with regard to DNA bending, our work indicates that the rate of loop formation by Lac repressor depends more strongly than previously expected on the energetics of bending and twisting of DNA.
true
true
true
true
true
619
12
DISCUSSION
0
null
null
16,835,309
null
Therefore, the mechanical and biochemical factors that in vivo modulate these energetics can play a crucial role in the modulation of gene expression regulation at least in the paradigmatic example of the Lac operon.
null
216
3,711
0
false
null
null
Therefore, the mechanical and biochemical factors that in vivo modulate these energetics can play a crucial role in the modulation of gene expression regulation at least in the paradigmatic example of the Lac operon.
true
true
true
true
true
619
12
DISCUSSION
0
null
null
16,835,309
null
With regard to the protein flexibility, on the other hand, our results show that the hinge flexibility and geometry have a determinant effect especially on the lifetime of the looped state, demonstrating the interplay of the mechanical properties of partners in this classic example of protein–DNA interacting system.
null
317
3,712
0
false
null
null
With regard to the protein flexibility, on the other hand, our results show that the hinge flexibility and geometry have a determinant effect especially on the lifetime of the looped state, demonstrating the interplay of the mechanical properties of partners in this classic example of protein–DNA interacting system.
true
true
true
true
true
619
13
DISCUSSION
0
null
null
16,835,309
null
Future steps aimed at a further characterization of the TPM system will investigate the effect of microspheres of different sizes on TPM measurements.
null
150
3,713
0
false
null
null
Future steps aimed at a further characterization of the TPM system will investigate the effect of microspheres of different sizes on TPM measurements.
true
true
true
true
true
620
13
DISCUSSION
0
null
null
16,835,309
null
Also, the measurement of looping and unlooping kinetics of different constructs in which the distances and phasing between operators is varied will provide important additional information.
null
189
3,714
0
false
null
null
Also, the measurement of looping and unlooping kinetics of different constructs in which the distances and phasing between operators is varied will provide important additional information.
true
true
true
true
true
620
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Biological robustness, a fundamental and ubiquitous phenomenon observed in biological systems, is broadly understood as the ability to maintain stable functioning in the face of various perturbations.
[ "1", "2–4", "5", "6", "7", "8", "9" ]
200
3,715
0
false
Biological robustness, a fundamental and ubiquitous phenomenon observed in biological systems, is broadly understood as the ability to maintain stable functioning in the face of various perturbations.
[]
Biological robustness, a fundamental and ubiquitous phenomenon observed in biological systems, is broadly understood as the ability to maintain stable functioning in the face of various perturbations.
true
true
true
true
true
621
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Depending on whether the perturbations are inheritable or not, robustness is characterized as genetic (mutational) or environmental robustness (1).
[ "1", "2–4", "5", "6", "7", "8", "9" ]
147
3,716
1
false
Depending on whether the perturbations are inheritable or not, robustness is characterized as genetic (mutational) or environmental robustness.
[ "1" ]
Depending on whether the perturbations are inheritable or not, robustness is characterized as genetic (mutational) or environmental robustness.
true
true
true
true
true
621
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Genetic robustness describes insensitivity of a phenotype facing genetic mutations, and the insensitivity to environmental factors is called environmental robustness.
[ "1", "2–4", "5", "6", "7", "8", "9" ]
166
3,717
0
false
Genetic robustness describes insensitivity of a phenotype facing genetic mutations, and the insensitivity to environmental factors is called environmental robustness.
[]
Genetic robustness describes insensitivity of a phenotype facing genetic mutations, and the insensitivity to environmental factors is called environmental robustness.
true
true
true
true
true
621
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Biologists have a long-standing interest in biological robustness, going back to Fisher's work on dominance (2–4) and Waddington's developmental canalization research (5,6).
[ "1", "2–4", "5", "6", "7", "8", "9" ]
173
3,718
1
false
Biologists have a long-standing interest in biological robustness, going back to Fisher's work on dominance and Waddington's developmental canalization research.
[ "2–4", "5,6" ]
Biologists have a long-standing interest in biological robustness, going back to Fisher's work on dominance and Waddington's developmental canalization research.
true
true
true
true
true
621
0
INTRODUCTION
1
7
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Robustness has become a focus of numerous studies in recent years, and has been found at various levels of biological systems, including gene expression, protein folding, metabolic flux, physiological homeostasis, development and even organism fitness (7).
[ "1", "2–4", "5", "6", "7", "8", "9" ]
256
3,719
1
false
Robustness has become a focus of numerous studies in recent years, and has been found at various levels of biological systems, including gene expression, protein folding, metabolic flux, physiological homeostasis, development and even organism fitness.
[ "7" ]
Robustness has become a focus of numerous studies in recent years, and has been found at various levels of biological systems, including gene expression, protein folding, metabolic flux, physiological homeostasis, development and even organism fitness.
true
true
true
true
true
621
0
INTRODUCTION
1
8
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
Hiroaki Kitano argued that the requirements for robustness and evolvability are similar, since robustness facilitates evolution and evolution favors robust traits (8).
[ "1", "2–4", "5", "6", "7", "8", "9" ]
167
3,720
1
false
Hiroaki Kitano argued that the requirements for robustness and evolvability are similar, since robustness facilitates evolution and evolution favors robust traits.
[ "8" ]
Hiroaki Kitano argued that the requirements for robustness and evolvability are similar, since robustness facilitates evolution and evolution favors robust traits.
true
true
true
true
true
621
0
INTRODUCTION
1
9
[ "B1", "B2 B3 B4", "B5", "B6", "B7", "B8", "B9" ]
17,567,615
NA|NA|NA|NA|NA|NA|pmid-14575319|pmid-15520792|NA
A proper understanding of the origins of robustness in biological systems will catalyze our understanding of evolution (9).
[ "1", "2–4", "5", "6", "7", "8", "9" ]
123
3,721
1
false
A proper understanding of the origins of robustness in biological systems will catalyze our understanding of evolution.
[ "9" ]
A proper understanding of the origins of robustness in biological systems will catalyze our understanding of evolution.
true
true
true
true
true
621
1
INTRODUCTION
1
10
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
The secondary structure of RNA is a suitable test bed for studying biological robustness.
[ "10", "11", "12", "13", "13" ]
89
3,722
0
false
The secondary structure of RNA is a suitable test bed for studying biological robustness.
[]
The secondary structure of RNA is a suitable test bed for studying biological robustness.
true
true
true
true
true
622
1
INTRODUCTION
1
10
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
Wagner and Stadler provided evidence that robustness of RNA viruses to mutational changes in secondary structure has evolved (10).
[ "10", "11", "12", "13", "13" ]
130
3,723
1
false
Wagner and Stadler provided evidence that robustness of RNA viruses to mutational changes in secondary structure has evolved.
[ "10" ]
Wagner and Stadler provided evidence that robustness of RNA viruses to mutational changes in secondary structure has evolved.
true
true
true
true
true
622
1
INTRODUCTION
1
10
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
Mutational robustness has also been found in viroids (11,12).
[ "10", "11", "12", "13", "13" ]
61
3,724
0
false
Mutational robustness has also been found in viroids.
[ "11,12" ]
Mutational robustness has also been found in viroids.
true
true
true
true
true
622
1
INTRODUCTION
1
13
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
By examining microRNA genes of serveral species, Borenstein and Ruppin (13) recently showed that the structure of miRNA precursor stem-loops exhibits a significantly high level of genetic robustness, compared with random sequences with similar stem-loop structures as native miRNAs which were generated by inverse foldin...
[ "10", "11", "12", "13", "13" ]
453
3,725
1
false
By examining microRNA genes of serveral species, Borenstein and Ruppin recently showed that the structure of miRNA precursor stem-loops exhibits a significantly high level of genetic robustness, compared with random sequences with similar stem-loop structures as native miRNAs which were generated by inverse folding alg...
[ "13" ]
By examining microRNA genes of serveral species, Borenstein and Ruppin recently showed that the structure of miRNA precursor stem-loops exhibits a significantly high level of genetic robustness, compared with random sequences with similar stem-loop structures as native miRNAs which were generated by inverse folding alg...
true
true
true
true
true
622
1
INTRODUCTION
1
10
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
Furthermore, they demonstrated it was not the by-product of a base composition bias.
[ "10", "11", "12", "13", "13" ]
84
3,726
0
false
Furthermore, they demonstrated it was not the by-product of a base composition bias.
[]
Furthermore, they demonstrated it was not the by-product of a base composition bias.
true
true
true
true
true
622
1
INTRODUCTION
1
13
[ "B10", "B11", "B12", "B13", "B13" ]
17,567,615
pmid-10440723|pmid-16679345|pmid-16901984|pmid-16608911|pmid-16608911
Their findings suggest that the excess robustness of miRNA stem-loops is the result of direct evolutionary pressure toward increased robustness (13).
[ "10", "11", "12", "13", "13" ]
149
3,727
1
false
Their findings suggest that the excess robustness of miRNA stem-loops is the result of direct evolutionary pressure toward increased robustness.
[ "13" ]
Their findings suggest that the excess robustness of miRNA stem-loops is the result of direct evolutionary pressure toward increased robustness.
true
true
true
true
true
622
2
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16" ]
17,567,615
pmid-16608911|pmid-16452927|pmid-16248678|pmid-10723034
Although the mechanisms of robustness have been widely explored (13–15), to date, the evolutionary origins of robustness are still controversial, which is partly due to the difficulty in providing evidence for robustness in natural biological systems (16).
[ "13–15", "16" ]
256
3,728
1
false
Although the mechanisms of robustness have been widely explored, to date, the evolutionary origins of robustness are still controversial, which is partly due to the difficulty in providing evidence for robustness in natural biological systems.
[ "13–15", "16" ]
Although the mechanisms of robustness have been widely explored, to date, the evolutionary origins of robustness are still controversial, which is partly due to the difficulty in providing evidence for robustness in natural biological systems.
true
true
true
true
true
623
2
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16" ]
17,567,615
pmid-16608911|pmid-16452927|pmid-16248678|pmid-10723034
Addressing this challenge, a convenient computational tool for the structural robustness evaluation is strongly needed.
[ "13–15", "16" ]
119
3,729
0
false
Addressing this challenge, a convenient computational tool for the structural robustness evaluation is strongly needed.
[]
Addressing this challenge, a convenient computational tool for the structural robustness evaluation is strongly needed.
true
true
true
true
true
623
3
INTRODUCTION
0
null
null
17,567,615
null
The RNA structural robustness evaluator (RSRE) presented here is a web tool developed for RNA structural robustness evaluation, both for genetic robustness and environmental robustness.
null
185
3,730
0
false
null
null
The RNA structural robustness evaluator (RSRE) presented here is a web tool developed for RNA structural robustness evaluation, both for genetic robustness and environmental robustness.
true
true
true
true
true
624
3
INTRODUCTION
0
null
null
17,567,615
null
By using classical RNA structural distance measurement methods, the robustness of a given RNA and its control sequences can be evaluated quantitatively based on a generalized definition of neutrality.
null
200
3,731
0
false
null
null
By using classical RNA structural distance measurement methods, the robustness of a given RNA and its control sequences can be evaluated quantitatively based on a generalized definition of neutrality.
true
true
true
true
true
624
3
INTRODUCTION
0
null
null
17,567,615
null
The RSRE web server will finally give statistical significances of the robustness differences between the given RNA and its control sequences.
null
142
3,732
0
false
null
null
The RSRE web server will finally give statistical significances of the robustness differences between the given RNA and its control sequences.
true
true
true
true
true
624
3
INTRODUCTION
0
null
null
17,567,615
null
The RSRE will facilitate wide exploration on the origins of robustness and catalyze our understanding of RNA evolution.
null
119
3,733
0
false
null
null
The RSRE will facilitate wide exploration on the origins of robustness and catalyze our understanding of RNA evolution.
true
true
true
true
true
624
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,537,815
NA|pmid-12195017|pmid-14729921
DNA and RNA oligomers that contain consecutive guanine (G) nucleotides are capable of folding into stable secondary structures such as G-quadruplexes, wherein four Gs are hydrogen bonded together into a roughly square planar array (1).
[ "1", "2", "3" ]
235
3,734
1
false
DNA and RNA oligomers that contain consecutive guanine (G) nucleotides are capable of folding into stable secondary structures such as G-quadruplexes, wherein four Gs are hydrogen bonded together into a roughly square planar array.
[ "1" ]
DNA and RNA oligomers that contain consecutive guanine (G) nucleotides are capable of folding into stable secondary structures such as G-quadruplexes, wherein four Gs are hydrogen bonded together into a roughly square planar array.
true
true
true
true
true
625
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,537,815
NA|pmid-12195017|pmid-14729921
G-quadruplexes are of remarkable stability and have been proposed to be involved in regulation of gene expression.
[ "1", "2", "3" ]
114
3,735
0
false
G-quadruplexes are of remarkable stability and have been proposed to be involved in regulation of gene expression.
[]
G-quadruplexes are of remarkable stability and have been proposed to be involved in regulation of gene expression.
true
true
true
true
true
625
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,537,815
NA|pmid-12195017|pmid-14729921
For example, a DNA G-quadruplex structure formed in the c-myc promoter region functions as a transcriptional repressor element and an RNA G-quadruplex is believed to regulate alternative splicing of the pre-mRNA coding for hTERT, the reverse transcriptase component of the enzyme telomerase (2,3).
[ "1", "2", "3" ]
297
3,736
0
false
For example, a DNA G-quadruplex structure formed in the c-myc promoter region functions as a transcriptional repressor element and an RNA G-quadruplex is believed to regulate alternative splicing of the pre-mRNA coding for hTERT, the reverse transcriptase component of the enzyme telomerase.
[ "2,3" ]
For example, a DNA G-quadruplex structure formed in the c-myc promoter region functions as a transcriptional repressor element and an RNA G-quadruplex is believed to regulate alternative splicing of the pre-mRNA coding for hTERT, the reverse transcriptase component of the enzyme telomerase.
true
true
true
true
true
625
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B8" ]
17,537,815
pmid-8475087|pmid-12466553|pmid-14500839|pmid-7906414|pmid-15642696
Human immunodeficiency virus type-1 (HIV-1) contains the 5′A4GA4G6A polypurine tract sequence (PPT) that is conserved in all HIV-1 strains and is present in the coding region of integrase (IN) and nef messenger RNAs.
[ "4", "5", "6", "7", "8" ]
216
3,737
0
false
Human immunodeficiency virus type-1 (HIV-1) contains the 5′A4GA4G6A polypurine tract sequence (PPT) that is conserved in all HIV-1 strains and is present in the coding region of integrase (IN) and nef messenger RNAs.
[]
Human immunodeficiency virus type-1 (HIV-1) contains the 5′A4GA4G6A polypurine tract sequence (PPT) that is conserved in all HIV-1 strains and is present in the coding region of integrase (IN) and nef messenger RNAs.
true
true
true
true
true
626
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B8" ]
17,537,815
pmid-8475087|pmid-12466553|pmid-14500839|pmid-7906414|pmid-15642696
G-quadruplexes have been implicated in HIV-1 RNA dimerization (4) and recently were shown to occur in a reverse transcription intermediate, namely between the overlapping strands of the HIV-1 central DNA flap (5).
[ "4", "5", "6", "7", "8" ]
213
3,738
1
false
G-quadruplexes have been implicated in HIV-1 RNA dimerization and recently were shown to occur in a reverse transcription intermediate, namely between the overlapping strands of the HIV-1 central DNA flap.
[ "4", "5" ]
G-quadruplexes have been implicated in HIV-1 RNA dimerization and recently were shown to occur in a reverse transcription intermediate, namely between the overlapping strands of the HIV-1 central DNA flap.
true
true
true
true
true
626
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B8" ]
17,537,815
pmid-8475087|pmid-12466553|pmid-14500839|pmid-7906414|pmid-15642696
It has been shown that HIV-1 nucleocapsid (NCp) and gp 120 envelope protein exhibit a high affinity for several tetramolecular quadruplexes (6,7).
[ "4", "5", "6", "7", "8" ]
146
3,739
0
false
It has been shown that HIV-1 nucleocapsid (NCp) and gp 120 envelope protein exhibit a high affinity for several tetramolecular quadruplexes.
[ "6,7" ]
It has been shown that HIV-1 nucleocapsid (NCp) and gp 120 envelope protein exhibit a high affinity for several tetramolecular quadruplexes.
true
true
true
true
true
626
1
INTRODUCTION
1
4
[ "B4", "B5", "B6", "B7", "B8" ]
17,537,815
pmid-8475087|pmid-12466553|pmid-14500839|pmid-7906414|pmid-15642696
RNA quadruplexes are more stable than their DNA counterparts and in most cases no dissociation is experimentally observed for G tracts involving five guanine quartets (
[ "4", "5", "6", "7", "8" ]
168
3,740
0
false
RNA quadruplexes are more stable than their DNA counterparts and in most cases no dissociation is experimentally observed for G tracts involving five guanine quartets (
[]
RNA quadruplexes are more stable than their DNA counterparts and in most cases no dissociation is experimentally observed for G tracts involving five guanine quartets (
true
true
false
true
false
626
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
In the present study, we have used peptide nucleic acid (PNA) targeted to the folded PPT sequence of HIV-1 messenger RNA.
[ "9–11", "9–11", "11–14", "15" ]
121
3,741
0
false
In the present study, we have used peptide nucleic acid (PNA) targeted to the folded PPT sequence of HIV-1 messenger RNA.
[]
In the present study, we have used peptide nucleic acid (PNA) targeted to the folded PPT sequence of HIV-1 messenger RNA.
true
true
true
true
true
627
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
PNAs are DNA analogues in which the N-(2-aminoethyl) glycine units replace the deoxyribose phosphate backbone (9–11).
[ "9–11", "9–11", "11–14", "15" ]
117
3,742
1
false
PNAs are DNA analogues in which the N-(2-aminoethyl) glycine units replace the deoxyribose phosphate backbone.
[ "9–11" ]
PNAs are DNA analogues in which the N-(2-aminoethyl) glycine units replace the deoxyribose phosphate backbone.
true
true
true
true
true
627
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
PNAs are capable of sequence specific recognition of DNA and RNA, obeying the Watson–Crick hydrogen-bonding or/and Hoogsteen schemes (9–11).
[ "9–11", "9–11", "11–14", "15" ]
140
3,743
1
false
PNAs are capable of sequence specific recognition of DNA and RNA, obeying the Watson–Crick hydrogen-bonding or/and Hoogsteen schemes.
[ "9–11" ]
PNAs are capable of sequence specific recognition of DNA and RNA, obeying the Watson–Crick hydrogen-bonding or/and Hoogsteen schemes.
true
true
true
true
true
627
2
INTRODUCTION
1
11–14
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
The neutral amide backbone of PNAs increases their binding affinity to DNA and RNA and the hybrid complexes exhibit high thermal stability (11–14).
[ "9–11", "9–11", "11–14", "15" ]
147
3,744
1
false
The neutral amide backbone of PNAs increases their binding affinity to DNA and RNA and the hybrid complexes exhibit high thermal stability.
[ "11–14" ]
The neutral amide backbone of PNAs increases their binding affinity to DNA and RNA and the hybrid complexes exhibit high thermal stability.
true
true
true
true
true
627
2
INTRODUCTION
1
15
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
Short PNA probes were shown to be able to disturb and finally to bind folded RNA structures used as target sequences (15).
[ "9–11", "9–11", "11–14", "15" ]
122
3,745
1
false
Short PNA probes were shown to be able to disturb and finally to bind folded RNA structures used as target sequences.
[ "15" ]
Short PNA probes were shown to be able to disturb and finally to bind folded RNA structures used as target sequences.
true
true
true
true
true
627
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
Here, we show that pyrimidine PNAs overcome kinetic and thermodynamic obstacles and succeed to hybridize to folded PPT sequence and finally to unfold it.
[ "9–11", "9–11", "11–14", "15" ]
153
3,746
0
false
Here, we show that pyrimidine PNAs overcome kinetic and thermodynamic obstacles and succeed to hybridize to folded PPT sequence and finally to unfold it.
[]
Here, we show that pyrimidine PNAs overcome kinetic and thermodynamic obstacles and succeed to hybridize to folded PPT sequence and finally to unfold it.
true
true
true
true
true
627
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
We have examined whether complexes formed with PNAs on the PPT sequence, likely triplex and duplex structures, affect RNA translation elongation in vitro.
[ "9–11", "9–11", "11–14", "15" ]
154
3,747
0
false
We have examined whether complexes formed with PNAs on the PPT sequence, likely triplex and duplex structures, affect RNA translation elongation in vitro.
[]
We have examined whether complexes formed with PNAs on the PPT sequence, likely triplex and duplex structures, affect RNA translation elongation in vitro.
true
true
true
true
true
627
2
INTRODUCTION
1
9–11
[ "B9 B10 B11", "B9 B10 B11", "B11 B12 B13 B14", "B15" ]
17,537,815
pmid-1962210|pmid-10807005|pmid-7692304|pmid-1962210|pmid-10807005|pmid-7692304|pmid-7692304|pmid-11926811|pmid-11425312|pmid-12426578|pmid-15926825
The cellular antisense activity of the best inhibitors in vitro was tested in streptolysin-O (SLO) permeabilized cells stably transformed with two reporter genes, the firefly luciferase (luc) and GFP that contain upstream of the reporter genes either the wild-type HIV-1 PPT target sequence, or a mutated HIV-2 PPT seque...
[ "9–11", "9–11", "11–14", "15" ]
338
3,748
0
false
The cellular antisense activity of the best inhibitors in vitro was tested in streptolysin-O (SLO) permeabilized cells stably transformed with two reporter genes, the firefly luciferase (luc) and GFP that contain upstream of the reporter genes either the wild-type HIV-1 PPT target sequence, or a mutated HIV-2 PPT seque...
[]
The cellular antisense activity of the best inhibitors in vitro was tested in streptolysin-O (SLO) permeabilized cells stably transformed with two reporter genes, the firefly luciferase (luc) and GFP that contain upstream of the reporter genes either the wild-type HIV-1 PPT target sequence, or a mutated HIV-2 PPT seque...
true
true
true
true
true
627
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,517,783
pmid-15601259|NA
Bilipid membranes divide eukaryotic cells into various types of organelles containing characteristic proteins and performing specialized functions.
[ "1", "2" ]
147
3,749
0
false
Bilipid membranes divide eukaryotic cells into various types of organelles containing characteristic proteins and performing specialized functions.
[]
Bilipid membranes divide eukaryotic cells into various types of organelles containing characteristic proteins and performing specialized functions.
true
true
true
true
true
628
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,517,783
pmid-15601259|NA
Thus, subcellular localization information gives an important clue to a protein's function.
[ "1", "2" ]
91
3,750
0
false
Thus, subcellular localization information gives an important clue to a protein's function.
[]
Thus, subcellular localization information gives an important clue to a protein's function.
true
true
true
true
true
628
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,517,783
pmid-15601259|NA
Although localization signals in mRNA appear to play some role (1), the main determinant of a protein's localization residues in the protein's amino acid sequence.
[ "1", "2" ]
163
3,751
1
false
Although localization signals in mRNA appear to play some role, the main determinant of a protein's localization residues in the protein's amino acid sequence.
[ "1" ]
Although localization signals in mRNA appear to play some role, the main determinant of a protein's localization residues in the protein's amino acid sequence.
true
true
true
true
true
628
0
INTRODUCTION
1
1
[ "B1", "B2" ]
17,517,783
pmid-15601259|NA
(We recommend wikipedia.org/wiki/Protein_targeting for a brief overview and Alberts et al.
[ "1", "2" ]
90
3,752
0
false
(We recommend wikipedia.org/wiki/Protein_targeting for a brief overview and Alberts et al.
[]
(We recommend wikipedia.org/wiki/Protein_targeting for a brief overview and Alberts et al.
false
false
true
true
false
628
0
INTRODUCTION
1
2
[ "B1", "B2" ]
17,517,783
pmid-15601259|NA
(2) for a textbook description.)
[ "1", "2" ]
32
3,753
1
false
for a textbook description.)
[ "2" ]
for a textbook description.)
false
true
false
true
false
628
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,517,783
pmid-15608167|pmid-10802651|pmid-11914276|pmid-14562095|pmid-15208715|pmid-16615899
Numerous experiments to determine protein localization have been performed to date.
[ "3", "4", "5", "6", "7", "8" ]
83
3,754
0
false
Numerous experiments to determine protein localization have been performed to date.
[]
Numerous experiments to determine protein localization have been performed to date.
true
true
true
true
true
629
1
INTRODUCTION
1
3
[ "B3", "B4", "B5", "B6", "B7", "B8" ]
17,517,783
pmid-15608167|pmid-10802651|pmid-11914276|pmid-14562095|pmid-15208715|pmid-16615899
These can broadly be classified as: small-scale experiments—the results of which continue to accumulate in public databases, such as UniProt (3) and Gene Ontology (4); and large-scale experiments using epitope (5) or green fluorescent protein (GFP) (6) tagging, or by separation of organelles by centrifugation combined ...
[ "3", "4", "5", "6", "7", "8" ]
375
3,755
1
false
These can broadly be classified as: small-scale experiments—the results of which continue to accumulate in public databases, such as UniProt and Gene Ontology ; and large-scale experiments using epitope or green fluorescent protein (GFP) tagging, or by separation of organelles by centrifugation combined with protein id...
[ "3", "4", "5", "6", "7,8" ]
These can broadly be classified as: small-scale experiments—the results of which continue to accumulate in public databases, such as UniProt and Gene Ontology ; and large-scale experiments using epitope or green fluorescent protein (GFP) tagging, or by separation of organelles by centrifugation combined with protein id...
true
true
true
true
true
629
2
INTRODUCTION
1
6–9
[ "B6 B7 B8 B9" ]
17,517,783
pmid-14562095|pmid-15208715|pmid-16615899|NA
Although they provide invaluable information, the coverage of experimental data is only high for model organisms, particularly yeast.
[ "6–9" ]
133
3,756
0
false
Although they provide invaluable information, the coverage of experimental data is only high for model organisms, particularly yeast.
[]
Although they provide invaluable information, the coverage of experimental data is only high for model organisms, particularly yeast.
true
true
true
true
true
630
2
INTRODUCTION
1
6–9
[ "B6 B7 B8 B9" ]
17,517,783
pmid-14562095|pmid-15208715|pmid-16615899|NA
Moreover, the agreement amongst large-scale experimental data is only 75–80% (6–9).
[ "6–9" ]
83
3,757
1
false
Moreover, the agreement amongst large-scale experimental data is only 75–80%.
[ "6–9" ]
Moreover, the agreement amongst large-scale experimental data is only 75–80%.
true
true
true
true
true
630
2
INTRODUCTION
1
6–9
[ "B6 B7 B8 B9" ]
17,517,783
pmid-14562095|pmid-15208715|pmid-16615899|NA
Thus, computational prediction of localization from amino acid remains an important topic.
[ "6–9" ]
90
3,758
0
false
Thus, computational prediction of localization from amino acid remains an important topic.
[]
Thus, computational prediction of localization from amino acid remains an important topic.
true
true
true
true
true
630
3
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
Numerous computational methods are available
[ "10", "11", "12" ]
44
3,759
0
false
Numerous computational methods are available
[]
Numerous computational methods are available
true
true
false
true
false
631
3
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
[reviewed in (10,11)].
[ "10", "11", "12" ]
22
3,760
0
false
.
[ "reviewed in (10,11)" ]
.
false
false
true
true
false
631
3
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
Some (including WoLF PSORT) have recently been benchmarked by Sprenger et al.
[ "10", "11", "12" ]
77
3,761
0
false
Some (including WoLF PSORT) have recently been benchmarked by Sprenger et al.
[]
Some (including WoLF PSORT) have recently been benchmarked by Sprenger et al.
true
true
true
true
true
631
3
INTRODUCTION
1
12
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
(12), who found the computational methods to be useful for sites, such as the nucleus, for which many training examples can be easily obtained from UniProt (which is the source of most or all of the training data for most prediction methods—including WoLF PSORT).
[ "10", "11", "12" ]
263
3,762
1
false
, who found the computational methods to be useful for sites, such as the nucleus, for which many training examples can be easily obtained from UniProt (which is the source of most or all of the training data for most prediction methods—including WoLF PSORT).
[ "12" ]
, who found the computational methods to be useful for sites, such as the nucleus, for which many training examples can be easily obtained from UniProt (which is the source of most or all of the training data for most prediction methods—including WoLF PSORT).
false
false
true
true
false
631
3
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
The different methods they benchmarked were found to have different strengths.
[ "10", "11", "12" ]
78
3,763
0
false
The different methods they benchmarked were found to have different strengths.
[]
The different methods they benchmarked were found to have different strengths.
true
true
true
true
true
631
3
INTRODUCTION
1
10
[ "B10", "B11", "B12" ]
17,517,783
pmid-12511065|NA|pmid-17254308
Here, we describe the public server for our WoLF PSORT method.
[ "10", "11", "12" ]
62
3,764
0
false
Here, we describe the public server for our WoLF PSORT method.
[]
Here, we describe the public server for our WoLF PSORT method.
true
true
true
true
true
631
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-4927945|pmid-2843517|pmid-186775|pmid-2170028|pmid-15535862|pmid-17009874
In prokaryotes, DNA is maintained in negatively supercoiled state, which is essential for various cellular processes.
[ "1", "2", "3", "4", "5", "6" ]
117
3,765
0
false
In prokaryotes, DNA is maintained in negatively supercoiled state, which is essential for various cellular processes.
[]
In prokaryotes, DNA is maintained in negatively supercoiled state, which is essential for various cellular processes.
true
true
true
true
true
632
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-4927945|pmid-2843517|pmid-186775|pmid-2170028|pmid-15535862|pmid-17009874
DNA topoisomerases are responsible for controlling the superhelicity of DNA (1,2).
[ "1", "2", "3", "4", "5", "6" ]
82
3,766
0
false
DNA topoisomerases are responsible for controlling the superhelicity of DNA.
[ "1,2" ]
DNA topoisomerases are responsible for controlling the superhelicity of DNA.
true
true
true
true
true
632
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-4927945|pmid-2843517|pmid-186775|pmid-2170028|pmid-15535862|pmid-17009874
Thus, topoisomerases play critical roles in many aspects of DNA transaction, as well as in the maintenance of chromosome structure.
[ "1", "2", "3", "4", "5", "6" ]
131
3,767
0
false
Thus, topoisomerases play critical roles in many aspects of DNA transaction, as well as in the maintenance of chromosome structure.
[]
Thus, topoisomerases play critical roles in many aspects of DNA transaction, as well as in the maintenance of chromosome structure.
true
true
true
true
true
632
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-4927945|pmid-2843517|pmid-186775|pmid-2170028|pmid-15535862|pmid-17009874
There are four topoisomerases in Escherichia coli.
[ "1", "2", "3", "4", "5", "6" ]
50
3,768
0
false
There are four topoisomerases in Escherichia coli.
[]
There are four topoisomerases in Escherichia coli.
true
true
true
true
true
632
0
INTRODUCTION
1
3
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-4927945|pmid-2843517|pmid-186775|pmid-2170028|pmid-15535862|pmid-17009874
Topoisomerase I (Topo I) (3) and topoisomerase III (Topo III) (4) are type IA enzymes; DNA gyrase (5) and topoisomerase IV (Topo IV) (6) are type IIA enzymes.
[ "1", "2", "3", "4", "5", "6" ]
158
3,769
1
false
Topoisomerase I (Topo I) and topoisomerase III (Topo III) are type IA enzymes; DNA gyrase and topoisomerase IV (Topo IV) are type IIA enzymes.
[ "3", "4", "5", "6" ]
Topoisomerase I (Topo I) and topoisomerase III (Topo III) are type IA enzymes; DNA gyrase and topoisomerase IV (Topo IV) are type IIA enzymes.
true
true
true
true
true
632
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
Type IA enzymes are monomeric proteins that can relax negative supercoils, and catenate and decatenate nicked or gapped, double-stranded circular DNA molecules (1,2).
[ "1", "2", "1", "2", "7", "8" ]
166
3,770
0
false
Type IA enzymes are monomeric proteins that can relax negative supercoils, and catenate and decatenate nicked or gapped, double-stranded circular DNA molecules.
[ "1,2" ]
Type IA enzymes are monomeric proteins that can relax negative supercoils, and catenate and decatenate nicked or gapped, double-stranded circular DNA molecules.
true
true
true
true
true
633
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
These enzymes require a single-stranded region to bind to DNA.
[ "1", "2", "1", "2", "7", "8" ]
62
3,771
0
false
These enzymes require a single-stranded region to bind to DNA.
[]
These enzymes require a single-stranded region to bind to DNA.
true
true
true
true
true
633
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
Topo I is the prototype of type IA protein family (1,2).
[ "1", "2", "1", "2", "7", "8" ]
56
3,772
0
false
Topo I is the prototype of type IA protein family.
[ "1,2" ]
Topo I is the prototype of type IA protein family.
true
true
true
true
true
633
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
The N-terminal 582 amino acid residues correspond to the catalytic domain containing the active site Tyr at position 319.
[ "1", "2", "1", "2", "7", "8" ]
121
3,773
0
false
The N-terminal 582 amino acid residues correspond to the catalytic domain containing the active site Tyr at position 319.
[]
The N-terminal 582 amino acid residues correspond to the catalytic domain containing the active site Tyr at position 319.
true
true
true
true
true
633
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
The catalytic domain is followed by a non-homologous carboxyl-terminal domain.
[ "1", "2", "1", "2", "7", "8" ]
78
3,774
0
false
The catalytic domain is followed by a non-homologous carboxyl-terminal domain.
[]
The catalytic domain is followed by a non-homologous carboxyl-terminal domain.
true
true
true
true
true
633
1
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b7", "b8" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-7510701|pmid-8621552|pmid-15535862|pmid-8980760|pmid-15535862|pmid-7968526
The non-homologous carboxyl-terminal domains are involved in determining the distinct substrate specificities and catalytic properties of these enzymes (7,8).
[ "1", "2", "1", "2", "7", "8" ]
158
3,775
0
false
The non-homologous carboxyl-terminal domains are involved in determining the distinct substrate specificities and catalytic properties of these enzymes.
[ "7,8" ]
The non-homologous carboxyl-terminal domains are involved in determining the distinct substrate specificities and catalytic properties of these enzymes.
true
true
true
true
true
633
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
Type IIA topoisomerases alter the linking number in steps of two by breaking both strands, passing another segment of the helix through the break and then resealing the broken strands (1,2).
[ "1", "2", "1", "2", "9" ]
190
3,776
0
false
Type IIA topoisomerases alter the linking number in steps of two by breaking both strands, passing another segment of the helix through the break and then resealing the broken strands.
[ "1,2" ]
Type IIA topoisomerases alter the linking number in steps of two by breaking both strands, passing another segment of the helix through the break and then resealing the broken strands.
true
true
true
true
true
634
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
DNA gyrase and Topo IV consist of GyrA and GyrB subunits and ParC and ParE subunits, respectively.
[ "1", "2", "1", "2", "9" ]
98
3,777
0
false
DNA gyrase and Topo IV consist of GyrA and GyrB subunits and ParC and ParE subunits, respectively.
[]
DNA gyrase and Topo IV consist of GyrA and GyrB subunits and ParC and ParE subunits, respectively.
true
true
true
true
true
634
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
GyrA and ParC subunits catalyze strand-breakage and reunion reactions, whereas GyrB and ParE subunits hydrolyze ATP.
[ "1", "2", "1", "2", "9" ]
116
3,778
0
false
GyrA and ParC subunits catalyze strand-breakage and reunion reactions, whereas GyrB and ParE subunits hydrolyze ATP.
[]
GyrA and ParC subunits catalyze strand-breakage and reunion reactions, whereas GyrB and ParE subunits hydrolyze ATP.
true
true
true
true
true
634
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
The active forms of gyrase and Topo IV are an α2β2 tetramer; these topoisomerases bind double-stranded DNA.
[ "1", "2", "1", "2", "9" ]
107
3,779
0
false
The active forms of gyrase and Topo IV are an α2β2 tetramer; these topoisomerases bind double-stranded DNA.
[]
The active forms of gyrase and Topo IV are an α2β2 tetramer; these topoisomerases bind double-stranded DNA.
true
true
true
true
true
634
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
Despite the high degree of similarity between gyrase and Topo IV, these two enzymes display distinct cellular functions.
[ "1", "2", "1", "2", "9" ]
120
3,780
0
false
Despite the high degree of similarity between gyrase and Topo IV, these two enzymes display distinct cellular functions.
[]
Despite the high degree of similarity between gyrase and Topo IV, these two enzymes display distinct cellular functions.
true
true
true
true
true
634
2
INTRODUCTION
1
1
[ "b1", "b2", "b1", "b2", "b9" ]
17,151,069
pmid-8811192|pmid-11395412|pmid-8811192|pmid-11395412|pmid-1330320|pmid-17009874
Gyrase is the only topoisomerase that introduces negative supercoils into DNA, whereas Topo IV is responsible for decatenation of replicating DNA molecules (1,2,9).
[ "1", "2", "1", "2", "9" ]
164
3,781
0
false
Gyrase is the only topoisomerase that introduces negative supercoils into DNA, whereas Topo IV is responsible for decatenation of replicating DNA molecules.
[ "1,2,9" ]
Gyrase is the only topoisomerase that introduces negative supercoils into DNA, whereas Topo IV is responsible for decatenation of replicating DNA molecules.
true
true
true
true
true
634
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
E.coli RecA has DNA-dependent ATPase activity and ATP-dependent DNA binding activity (10,11).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
93
3,782
0
false
E.coli RecA has DNA-dependent ATPase activity and ATP-dependent DNA binding activity.
[ "10,11" ]
E.coli RecA has DNA-dependent ATPase activity and ATP-dependent DNA binding activity.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
RecA proteins from various bacteria are highly conserved and homologues have been identified in eukaryotes as well.
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
115
3,783
0
false
RecA proteins from various bacteria are highly conserved and homologues have been identified in eukaryotes as well.
[]
RecA proteins from various bacteria are highly conserved and homologues have been identified in eukaryotes as well.
true
true
true
true
true
635
3
INTRODUCTION
1
11
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
RecA catalyzes strand-exchange reactions and thus plays a central role in the homologous recombination process (11).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
116
3,784
1
false
RecA catalyzes strand-exchange reactions and thus plays a central role in the homologous recombination process.
[ "11" ]
RecA catalyzes strand-exchange reactions and thus plays a central role in the homologous recombination process.
true
true
true
true
true
635
3
INTRODUCTION
1
11
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
In addition, RecA, when activated, causes proteolytic cleavage of the LexA repressor to trigger the induction of the SOS response (11).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
135
3,785
1
false
In addition, RecA, when activated, causes proteolytic cleavage of the LexA repressor to trigger the induction of the SOS response.
[ "11" ]
In addition, RecA, when activated, causes proteolytic cleavage of the LexA repressor to trigger the induction of the SOS response.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
RecA is also required for mutagenic lesion bypass synthesis during the SOS response and is involved in replication restart (11,12).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
131
3,786
0
false
RecA is also required for mutagenic lesion bypass synthesis during the SOS response and is involved in replication restart.
[ "11,12" ]
RecA is also required for mutagenic lesion bypass synthesis during the SOS response and is involved in replication restart.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
RecA monomers polymerize on DNA to form a nucleoprotein filament.
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
65
3,787
0
false
RecA monomers polymerize on DNA to form a nucleoprotein filament.
[]
RecA monomers polymerize on DNA to form a nucleoprotein filament.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
RecA can bind to and form a nucleoprotein filament on either single- or double-stranded DNA, although nucleation on single-stranded DNA is much faster than that on double-stranded DNA (13–17).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
192
3,788
0
false
RecA can bind to and form a nucleoprotein filament on either single- or double-stranded DNA, although nucleation on single-stranded DNA is much faster than that on double-stranded DNA.
[ "13–17" ]
RecA can bind to and form a nucleoprotein filament on either single- or double-stranded DNA, although nucleation on single-stranded DNA is much faster than that on double-stranded DNA.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
Both assembly and disassembly of RecA filaments take place in the 5′ to 3′ direction (14,15,18).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
96
3,789
0
false
Both assembly and disassembly of RecA filaments take place in the 5′ to 3′ direction.
[ "14,15,18" ]
Both assembly and disassembly of RecA filaments take place in the 5′ to 3′ direction.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
In the presence of ATP, dATP or an ATP analogue, such as ATPγS, RecA forms an ‘active’ filament (19–21).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
104
3,790
0
false
In the presence of ATP, dATP or an ATP analogue, such as ATPγS, RecA forms an ‘active’ filament.
[ "19–21" ]
In the presence of ATP, dATP or an ATP analogue, such as ATPγS, RecA forms an ‘active’ filament.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
The active RecA filament is a right-handed helical filament with six RecA monomers per turn and 3 nt per RecA monomer.
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
118
3,791
0
false
The active RecA filament is a right-handed helical filament with six RecA monomers per turn and 3 nt per RecA monomer.
[]
The active RecA filament is a right-handed helical filament with six RecA monomers per turn and 3 nt per RecA monomer.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
When it is formed on double-stranded DNA, the DNA is underwound relative to the B-form helix (22,23).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
101
3,792
0
false
When it is formed on double-stranded DNA, the DNA is underwound relative to the B-form helix.
[ "22,23" ]
When it is formed on double-stranded DNA, the DNA is underwound relative to the B-form helix.
true
true
true
true
true
635
3
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b11", "b11", "b12", "b13", "b17", "b14", "b15", "b18", "b19", "b21", "b22", "b23", "b21", "b24" ]
17,151,069
pmid-9187054|NA|NA|NA|NA|pmid-10716434|pmid-3900072|pmid-3058986|pmid-2188972|pmid-9048946|pmid-11574550|pmid-7050394|pmid-1522597|pmid-7050731|pmid-2538631|pmid-1522597|pmid-2693735|pmid-17009874
In contrast, RecA forms an ‘inactive’ filament in the absence of cofactor or presence of ADP (21,24).
[ "10", "11", "11", "11", "11", "12", "13", "17", "14", "15", "18", "19", "21", "22", "23", "21", "24" ]
101
3,793
0
false
In contrast, RecA forms an ‘inactive’ filament in the absence of cofactor or presence of ADP.
[ "21,24" ]
In contrast, RecA forms an ‘inactive’ filament in the absence of cofactor or presence of ADP.
true
true
true
true
true
635
4
INTRODUCTION
1
25
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
The ability of DNA microarrays to monitor transcriptional activity of entire genomes has allowed an assessment of transcriptional and replication states of the E.coli chromosome following inhibition of DNA gyrase (25–27).
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
221
3,794
0
false
The ability of DNA microarrays to monitor transcriptional activity of entire genomes has allowed an assessment of transcriptional and replication states of the E.coli chromosome following inhibition of DNA gyrase.
[ "25–27" ]
The ability of DNA microarrays to monitor transcriptional activity of entire genomes has allowed an assessment of transcriptional and replication states of the E.coli chromosome following inhibition of DNA gyrase.
true
true
true
true
true
636
4
INTRODUCTION
1
25
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
These studies confirmed that treating cells with norfloxacin, a fluoroquinolone inhibitor of gyrase, affects transcription of a largenumber of genes in the genome.
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
163
3,795
0
false
These studies confirmed that treating cells with norfloxacin, a fluoroquinolone inhibitor of gyrase, affects transcription of a largenumber of genes in the genome.
[]
These studies confirmed that treating cells with norfloxacin, a fluoroquinolone inhibitor of gyrase, affects transcription of a largenumber of genes in the genome.
true
true
true
true
true
636
4
INTRODUCTION
1
25
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
Quinolone treatment also causes the replication fork arrest and generation of double-strand breaks (28–30).
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
107
3,796
0
false
Quinolone treatment also causes the replication fork arrest and generation of double-strand breaks.
[ "28–30" ]
Quinolone treatment also causes the replication fork arrest and generation of double-strand breaks.
true
true
true
true
true
636
4
INTRODUCTION
1
25
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
A systematic analysis of transcriptional effects would not be possible, however, without accounting for a various cellular responses, such as the SOS response, DNA relaxation and replication inhibition (26,31–33).
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
213
3,797
0
false
A systematic analysis of transcriptional effects would not be possible, however, without accounting for a various cellular responses, such as the SOS response, DNA relaxation and replication inhibition.
[ "26,31–33" ]
A systematic analysis of transcriptional effects would not be possible, however, without accounting for a various cellular responses, such as the SOS response, DNA relaxation and replication inhibition.
true
true
true
true
true
636
4
INTRODUCTION
1
34
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
We modeled transcriptional responses to the quinolone-induced inhibition of gyrase in E.coli as a function of the downstream processes, including DNA repair, supercoiling and DNA replication (34).
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
196
3,798
1
false
We modeled transcriptional responses to the quinolone-induced inhibition of gyrase in E.coli as a function of the downstream processes, including DNA repair, supercoiling and DNA replication.
[ "34" ]
We modeled transcriptional responses to the quinolone-induced inhibition of gyrase in E.coli as a function of the downstream processes, including DNA repair, supercoiling and DNA replication.
true
true
true
true
true
636
4
INTRODUCTION
1
25
[ "b25", "b27", "b28", "b30", "b26", "b31", "b33", "b34" ]
17,151,069
pmid-15535863|pmid-12566398|pmid-5327367|pmid-15916595|pmid-10944214|pmid-8824300|pmid-16377712|pmid-17009874|pmid-8811192|pmid-11395412
We found that relaxation by Topo I was the dominant factor behind the transcriptional response followed by the effects of DNA replication and RecA.
[ "25", "27", "28", "30", "26", "31", "33", "34" ]
147
3,799
0
false
We found that relaxation by Topo I was the dominant factor behind the transcriptional response followed by the effects of DNA replication and RecA.
[]
We found that relaxation by Topo I was the dominant factor behind the transcriptional response followed by the effects of DNA replication and RecA.
true
true
true
true
true
636