Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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1
INTRODUCTION
1
5
[ "b5", "b7" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
The TRN comprises a significant proportion of the genome in each organism and it constitutes a major component of the genetic basis for the evolution of diverse aspects of bacterial phenotypes.
[ "5", "7" ]
193
6,000
0
false
The TRN comprises a significant proportion of the genome in each organism and it constitutes a major component of the genetic basis for the evolution of diverse aspects of bacterial phenotypes.
[]
The TRN comprises a significant proportion of the genome in each organism and it constitutes a major component of the genetic basis for the evolution of diverse aspects of bacterial phenotypes.
true
true
true
true
true
994
1
INTRODUCTION
1
5
[ "b5", "b7" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
It is important to learn how the TRN evolves as it would enable us to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and pattern of regulatory gene diversity, the phenotypic effects of molecular variation and their ecological consequences.
[ "5", "7" ]
292
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false
It is important to learn how the TRN evolves as it would enable us to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and pattern of regulatory gene diversity, the phenotypic effects of molecular variation and their ecological consequences.
[]
It is important to learn how the TRN evolves as it would enable us to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and pattern of regulatory gene diversity, the phenotypic effects of molecular variation and their ecological consequences.
true
true
true
true
true
994
2
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b9", "b10", "b8", "b11" ]
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
It is also important to recognize that, although abundant sequence data and complete genomes are available, the experimental determination of TRNs has been limited to a few organisms even in prokaryotes.
[ "6", "8", "9", "9", "10", "8", "11" ]
203
6,002
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false
It is also important to recognize that, although abundant sequence data and complete genomes are available, the experimental determination of TRNs has been limited to a few organisms even in prokaryotes.
[]
It is also important to recognize that, although abundant sequence data and complete genomes are available, the experimental determination of TRNs has been limited to a few organisms even in prokaryotes.
true
true
true
true
true
995
2
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b9", "b10", "b8", "b11" ]
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
Besides, there is no clear relationship between the presence of a TF, its TG and DNA-binding site(s), and their structural and biochemical characteristics that could have been transferred between genomes.
[ "6", "8", "9", "9", "10", "8", "11" ]
204
6,003
0
false
Besides, there is no clear relationship between the presence of a TF, its TG and DNA-binding site(s), and their structural and biochemical characteristics that could have been transferred between genomes.
[]
Besides, there is no clear relationship between the presence of a TF, its TG and DNA-binding site(s), and their structural and biochemical characteristics that could have been transferred between genomes.
true
true
true
true
true
995
2
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b9", "b10", "b8", "b11" ]
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
It is also difficult to evaluate a specific measure between sequence homology, function and interaction transfer for any two proteins involved in a regulatory interaction (6,8,9).
[ "6", "8", "9", "9", "10", "8", "11" ]
179
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false
It is also difficult to evaluate a specific measure between sequence homology, function and interaction transfer for any two proteins involved in a regulatory interaction.
[ "6,8,9" ]
It is also difficult to evaluate a specific measure between sequence homology, function and interaction transfer for any two proteins involved in a regulatory interaction.
true
true
true
true
true
995
2
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b9", "b10", "b8", "b11" ]
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
However, several groups have recently examined the transfer of regulatory interaction annotations from one organism to another using comparative genomic approaches (9,10).
[ "6", "8", "9", "9", "10", "8", "11" ]
171
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false
However, several groups have recently examined the transfer of regulatory interaction annotations from one organism to another using comparative genomic approaches.
[ "9,10" ]
However, several groups have recently examined the transfer of regulatory interaction annotations from one organism to another using comparative genomic approaches.
true
true
true
true
true
995
2
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b9", "b10", "b8", "b11" ]
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
The transfer of such interactions involves assigning functional roles to TFs and TGs, based on protein sequence similarity and on the conservation of topological patterns of the TRN, such as motifs and modules (8,11).
[ "6", "8", "9", "9", "10", "8", "11" ]
217
6,006
0
false
The transfer of such interactions involves assigning functional roles to TFs and TGs, based on protein sequence similarity and on the conservation of topological patterns of the TRN, such as motifs and modules.
[ "8,11" ]
The transfer of such interactions involves assigning functional roles to TFs and TGs, based on protein sequence similarity and on the conservation of topological patterns of the TRN, such as motifs and modules.
true
true
true
true
true
995
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
The Regulog approach uses cross-species data to predict DNA–protein interactions across genomes.
[ "9", "12", "12", "9", "13", "7", "9" ]
96
6,007
0
false
The Regulog approach uses cross-species data to predict DNA–protein interactions across genomes.
[]
The Regulog approach uses cross-species data to predict DNA–protein interactions across genomes.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
A TF and TG interaction in one species is predicted to occur in another species if their best sequence matches have been determined in the target group of genomes.
[ "9", "12", "12", "9", "13", "7", "9" ]
163
6,008
0
false
A TF and TG interaction in one species is predicted to occur in another species if their best sequence matches have been determined in the target group of genomes.
[]
A TF and TG interaction in one species is predicted to occur in another species if their best sequence matches have been determined in the target group of genomes.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
The presence of just one of the components of the regulatory interaction is not enough to transfer the interaction annotation, it is necessary that both TF and its TG(s) are detected in another organism.
[ "9", "12", "12", "9", "13", "7", "9" ]
203
6,009
0
false
The presence of just one of the components of the regulatory interaction is not enough to transfer the interaction annotation, it is necessary that both TF and its TG(s) are detected in another organism.
[]
The presence of just one of the components of the regulatory interaction is not enough to transfer the interaction annotation, it is necessary that both TF and its TG(s) are detected in another organism.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
Using this approach, Yu et al.
[ "9", "12", "12", "9", "13", "7", "9" ]
30
6,010
0
false
Using this approach, Yu et al.
[]
Using this approach, Yu et al.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
(9) have shown that orthologous TFs and TGs of Saccharomyces cerevisiae and Drosophila melanogaster tend to share the same regulatory interaction if the eukaryotic TFs have minimal sequence identities of 30–60% depending on the protein family.
[ "9", "12", "12", "9", "13", "7", "9" ]
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6,011
1
false
have shown that orthologous TFs and TGs of Saccharomyces cerevisiae and Drosophila melanogaster tend to share the same regulatory interaction if the eukaryotic TFs have minimal sequence identities of 30–60% depending on the protein family.
[ "9" ]
have shown that orthologous TFs and TGs of Saccharomyces cerevisiae and Drosophila melanogaster tend to share the same regulatory interaction if the eukaryotic TFs have minimal sequence identities of 30–60% depending on the protein family.
false
true
true
true
false
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
More recently, Sharan et al.
[ "9", "12", "12", "9", "13", "7", "9" ]
28
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0
false
More recently, Sharan et al.
[]
More recently, Sharan et al.
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996
3
INTRODUCTION
1
12
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
(12) associated functions to proteins using network-level conservation of protein–protein interactions in eukaryotic genomes.
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1
false
associated functions to proteins using network-level conservation of protein–protein interactions in eukaryotic genomes.
[ "12" ]
associated functions to proteins using network-level conservation of protein–protein interactions in eukaryotic genomes.
false
true
true
true
false
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
This implies that high sequence similarity does not necessarily mean that the function is conserved; but conservation at the level of network modules allows more confident function determination from the context.
[ "9", "12", "12", "9", "13", "7", "9" ]
212
6,014
0
false
This implies that high sequence similarity does not necessarily mean that the function is conserved; but conservation at the level of network modules allows more confident function determination from the context.
[]
This implies that high sequence similarity does not necessarily mean that the function is conserved; but conservation at the level of network modules allows more confident function determination from the context.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
Therefore, the best matches are not always present within conserved protein clusters enforcing the notion that it is advantageous to increase the detection of conserved functions by including paralogous family expansion and contraction, and even gene loss.
[ "9", "12", "12", "9", "13", "7", "9" ]
256
6,015
0
false
Therefore, the best matches are not always present within conserved protein clusters enforcing the notion that it is advantageous to increase the detection of conserved functions by including paralogous family expansion and contraction, and even gene loss.
[]
Therefore, the best matches are not always present within conserved protein clusters enforcing the notion that it is advantageous to increase the detection of conserved functions by including paralogous family expansion and contraction, and even gene loss.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
The high specificity of the predictions attained by Sharan et al.
[ "9", "12", "12", "9", "13", "7", "9" ]
65
6,016
0
false
The high specificity of the predictions attained by Sharan et al.
[]
The high specificity of the predictions attained by Sharan et al.
true
true
true
true
true
996
3
INTRODUCTION
1
12
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
(12) can be maintained because conservation is evaluated in the context of a protein interaction subnetwork and not independently for each interaction.
[ "9", "12", "12", "9", "13", "7", "9" ]
151
6,017
1
false
can be maintained because conservation is evaluated in the context of a protein interaction subnetwork and not independently for each interaction.
[ "12" ]
can be maintained because conservation is evaluated in the context of a protein interaction subnetwork and not independently for each interaction.
false
true
true
true
false
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
However, it has been shown that the patterns of conservation between protein–protein interactions versus protein–DNA interactions is different (9), and that the transcriptional regulatory logic differs radically between Eukaryotes and Prokaryotes (13).
[ "9", "12", "12", "9", "13", "7", "9" ]
252
6,018
1
false
However, it has been shown that the patterns of conservation between protein–protein interactions versus protein–DNA interactions is different, and that the transcriptional regulatory logic differs radically between Eukaryotes and Prokaryotes.
[ "9", "13" ]
However, it has been shown that the patterns of conservation between protein–protein interactions versus protein–DNA interactions is different, and that the transcriptional regulatory logic differs radically between Eukaryotes and Prokaryotes.
true
true
true
true
true
996
3
INTRODUCTION
1
9
[ "b9", "b12", "b12", "b9", "b13", "b7", "b9" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
As a consequence, the performance of transcriptional interaction mapping methods cannot be currently assessed at a large scale (7,9).
[ "9", "12", "12", "9", "13", "7", "9" ]
133
6,019
0
false
As a consequence, the performance of transcriptional interaction mapping methods cannot be currently assessed at a large scale.
[ "7,9" ]
As a consequence, the performance of transcriptional interaction mapping methods cannot be currently assessed at a large scale.
true
true
true
true
true
996
4
INTRODUCTION
0
null
null
16,840,530
null
Given the increasing number of sequenced genomes, it is possible and quite important to have a broader perspective of the evolution of TRNs by mapping the changes in the components of the regulatory interactions, which might differ from the common reconstruction of the metabolic, structural and some transcriptional his...
null
344
6,020
0
false
null
null
Given the increasing number of sequenced genomes, it is possible and quite important to have a broader perspective of the evolution of TRNs by mapping the changes in the components of the regulatory interactions, which might differ from the common reconstruction of the metabolic, structural and some transcriptional his...
true
true
true
true
true
997
4
INTRODUCTION
0
null
null
16,840,530
null
Understanding the evolution of TRNs will not only improve our insight over the biological constraints different organisms have acquired over time but also enable us to decipher the basic design principles underlying them.
null
221
6,021
0
false
null
null
Understanding the evolution of TRNs will not only improve our insight over the biological constraints different organisms have acquired over time but also enable us to decipher the basic design principles underlying them.
true
true
true
true
true
997
4
INTRODUCTION
0
null
null
16,840,530
null
Besides, one can reconstruct a regulatory history from the core of the transcriptional regulatory interactions that have been shared in the cellular processes of bacteria.
null
171
6,022
0
false
null
null
Besides, one can reconstruct a regulatory history from the core of the transcriptional regulatory interactions that have been shared in the cellular processes of bacteria.
true
true
true
true
true
997
5
INTRODUCTION
1
14
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
We used the TRNs of two different model Bacteria.
[ "14", "5", "15" ]
49
6,023
0
false
We used the TRNs of two different model Bacteria.
[]
We used the TRNs of two different model Bacteria.
true
true
true
true
true
998
5
INTRODUCTION
1
14
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
One of these is the TRN of the Gram-negative bacterium Escherichia coli K12 contained in RegulonDB, which is probably the best known in bacteria (14).
[ "14", "5", "15" ]
150
6,024
1
false
One of these is the TRN of the Gram-negative bacterium Escherichia coli K12 contained in RegulonDB, which is probably the best known in bacteria.
[ "14" ]
One of these is the TRN of the Gram-negative bacterium Escherichia coli K12 contained in RegulonDB, which is probably the best known in bacteria.
true
true
true
true
true
998
5
INTRODUCTION
1
5
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
This database contains experimental information corresponding to nearly 20% of the TRN of E.coli (5).
[ "14", "5", "15" ]
101
6,025
1
false
This database contains experimental information corresponding to nearly 20% of the TRN of E.coli.
[ "5" ]
This database contains experimental information corresponding to nearly 20% of the TRN of E.coli.
true
true
true
true
true
998
5
INTRODUCTION
1
14
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
The second best studied Prokaryote in terms of transcriptional regulation is the Gram-positive Bacillus subtilis.
[ "14", "5", "15" ]
113
6,026
0
false
The second best studied Prokaryote in terms of transcriptional regulation is the Gram-positive Bacillus subtilis.
[]
The second best studied Prokaryote in terms of transcriptional regulation is the Gram-positive Bacillus subtilis.
true
true
true
true
true
998
5
INTRODUCTION
1
15
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
We obtained the complete set of regulatory interactions in this bacterium documented in DataBase of Transcriptional regulation in Bacillus subtilis (DBTBS) (15).
[ "14", "5", "15" ]
161
6,027
1
false
We obtained the complete set of regulatory interactions in this bacterium documented in DataBase of Transcriptional regulation in Bacillus subtilis (DBTBS).
[ "15" ]
We obtained the complete set of regulatory interactions in this bacterium documented in DataBase of Transcriptional regulation in Bacillus subtilis (DBTBS).
true
true
true
true
true
998
5
INTRODUCTION
1
14
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
It is interesting to note that even though both are free-living bacteria and require similar concentrations of oxygen and temperature levels, E.coli has adapted to thrive inside its host while B.subtilis has adapted to soil environments.
[ "14", "5", "15" ]
237
6,028
0
false
It is interesting to note that even though both are free-living bacteria and require similar concentrations of oxygen and temperature levels, E.coli has adapted to thrive inside its host while B.subtilis has adapted to soil environments.
[]
It is interesting to note that even though both are free-living bacteria and require similar concentrations of oxygen and temperature levels, E.coli has adapted to thrive inside its host while B.subtilis has adapted to soil environments.
true
true
true
true
true
998
5
INTRODUCTION
1
14
[ "b14", "b5", "b15" ]
16,840,530
pmid-14681419|pmid-14572541|pmid-14681362
In this work we used a modified version of the Regulog approach described above to identify the interaction pairs and regulons of these networks through a comparison against complete genomes of Bacteria, Archaea and Eukarya.
[ "14", "5", "15" ]
224
6,029
0
false
In this work we used a modified version of the Regulog approach described above to identify the interaction pairs and regulons of these networks through a comparison against complete genomes of Bacteria, Archaea and Eukarya.
[]
In this work we used a modified version of the Regulog approach described above to identify the interaction pairs and regulons of these networks through a comparison against complete genomes of Bacteria, Archaea and Eukarya.
true
true
true
true
true
998
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
The complexity of the TRNs in bacterial organisms is largely affected by their adaptation to the dynamically changing environmental stresses that are characteristic of an organism's niche.
[ "46", "47", "49", "46", "50", "5" ]
188
6,030
0
false
The complexity of the TRNs in bacterial organisms is largely affected by their adaptation to the dynamically changing environmental stresses that are characteristic of an organism's niche.
[]
The complexity of the TRNs in bacterial organisms is largely affected by their adaptation to the dynamically changing environmental stresses that are characteristic of an organism's niche.
true
true
true
true
true
999
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
For example, enteric bacteria, soil bacteria and other free-living bacteria live in complex environments and have correspondingly complex sensor-response-control subsystems (46).
[ "46", "47", "49", "46", "50", "5" ]
178
6,031
1
false
For example, enteric bacteria, soil bacteria and other free-living bacteria live in complex environments and have correspondingly complex sensor-response-control subsystems.
[ "46" ]
For example, enteric bacteria, soil bacteria and other free-living bacteria live in complex environments and have correspondingly complex sensor-response-control subsystems.
true
true
true
true
true
999
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
In contrast, the narrow ecological ranges and frequent population bottlenecks of obligate pathogens and symbionts have resulted in increased rates of genetic drift and reduced selective constraint on gene function and number (47–49).
[ "46", "47", "49", "46", "50", "5" ]
233
6,032
0
false
In contrast, the narrow ecological ranges and frequent population bottlenecks of obligate pathogens and symbionts have resulted in increased rates of genetic drift and reduced selective constraint on gene function and number.
[ "47–49" ]
In contrast, the narrow ecological ranges and frequent population bottlenecks of obligate pathogens and symbionts have resulted in increased rates of genetic drift and reduced selective constraint on gene function and number.
true
true
true
true
true
999
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
Our results indicate that obligate symbiotic as well as parasitic life styles share only ∼10% of the orthologous components of the TRNs of E.coli and B.subtilis.
[ "46", "47", "49", "46", "50", "5" ]
161
6,033
0
false
Our results indicate that obligate symbiotic as well as parasitic life styles share only ∼10% of the orthologous components of the TRNs of E.coli and B.subtilis.
[]
Our results indicate that obligate symbiotic as well as parasitic life styles share only ∼10% of the orthologous components of the TRNs of E.coli and B.subtilis.
true
true
true
true
true
999
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
The loss of regulatory elements may reflect a relative constancy in the host environment, allowing these organisms to have a simplified regulatory structure (46,50).
[ "46", "47", "49", "46", "50", "5" ]
165
6,034
0
false
The loss of regulatory elements may reflect a relative constancy in the host environment, allowing these organisms to have a simplified regulatory structure.
[ "46,50" ]
The loss of regulatory elements may reflect a relative constancy in the host environment, allowing these organisms to have a simplified regulatory structure.
true
true
true
true
true
999
0
DISCUSSION
1
46
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
According to our results, the loss of TFs more than TGs could be the main cause of these dramatic changes in the TRN.
[ "46", "47", "49", "46", "50", "5" ]
117
6,035
0
false
According to our results, the loss of TFs more than TGs could be the main cause of these dramatic changes in the TRN.
[]
According to our results, the loss of TFs more than TGs could be the main cause of these dramatic changes in the TRN.
true
true
true
true
true
999
0
DISCUSSION
1
5
[ "b46", "b47", "b49", "b46", "b50", "b5" ]
16,840,530
pmid-11062388|pmid-11967538|pmid-12823939|pmid-8610134|pmid-9717214|pmid-12823939|pmid-12791133|pmid-14572541
This can also be seen from the specific scenario of the conservation of GRs of E.coli which have a limited biological distribution although they directly modulate the expression of ∼51% of its genes (5).
[ "46", "47", "49", "46", "50", "5" ]
203
6,036
1
false
This can also be seen from the specific scenario of the conservation of GRs of E.coli which have a limited biological distribution although they directly modulate the expression of ∼51% of its genes.
[ "5" ]
This can also be seen from the specific scenario of the conservation of GRs of E.coli which have a limited biological distribution although they directly modulate the expression of ∼51% of its genes.
true
true
true
true
true
999
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
As reported previously, the conservation of genes and regulatory interactions is related to the phylogenetic distance and to the life style of the organisms (10,38).
[ "10", "38", "51" ]
165
6,037
0
false
As reported previously, the conservation of genes and regulatory interactions is related to the phylogenetic distance and to the life style of the organisms.
[ "10,38" ]
As reported previously, the conservation of genes and regulatory interactions is related to the phylogenetic distance and to the life style of the organisms.
true
true
true
true
true
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
Based on our results, we can see that quantitatively the TFs are less conserved than the TGs as phylogenetic distance increases, which could suggest that transcriptional regulation of genes changes faster through evolution than the genes themselves.
[ "10", "38", "51" ]
249
6,038
0
false
Based on our results, we can see that quantitatively the TFs are less conserved than the TGs as phylogenetic distance increases, which could suggest that transcriptional regulation of genes changes faster through evolution than the genes themselves.
[]
Based on our results, we can see that quantitatively the TFs are less conserved than the TGs as phylogenetic distance increases, which could suggest that transcriptional regulation of genes changes faster through evolution than the genes themselves.
true
true
true
true
true
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
Related to this, Maslov et al.
[ "10", "38", "51" ]
30
6,039
0
false
Related to this, Maslov et al.
[]
Related to this, Maslov et al.
true
true
true
true
true
1,000
1
DISCUSSION
1
51
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
(51) found that the rate of evolutionary differentiation of transcriptional regulatory interactions proceeds faster than that of TGs and their protein interactions.
[ "10", "38", "51" ]
164
6,040
1
false
found that the rate of evolutionary differentiation of transcriptional regulatory interactions proceeds faster than that of TGs and their protein interactions.
[ "51" ]
found that the rate of evolutionary differentiation of transcriptional regulatory interactions proceeds faster than that of TGs and their protein interactions.
false
true
true
true
false
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
However, an analysis of the conservation of pairs of regulatory interactions across genomes indicated different tendencies in the conservation of TF–TG pairs, suggesting that TF–TG pairs often do not co-evolve in the evolution of TRNs.
[ "10", "38", "51" ]
235
6,041
0
false
However, an analysis of the conservation of pairs of regulatory interactions across genomes indicated different tendencies in the conservation of TF–TG pairs, suggesting that TF–TG pairs often do not co-evolve in the evolution of TRNs.
[]
However, an analysis of the conservation of pairs of regulatory interactions across genomes indicated different tendencies in the conservation of TF–TG pairs, suggesting that TF–TG pairs often do not co-evolve in the evolution of TRNs.
true
true
true
true
true
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
Nevertheless it should be clear that in the first case, when a TF is conserved in different species without its corresponding TG, it would imply that the TF is indeed involved in the regulation of a different set of TGs than those in the genome under consideration and in the second case, when a TG is conserved and its ...
[ "10", "38", "51" ]
409
6,042
0
false
Nevertheless it should be clear that in the first case, when a TF is conserved in different species without its corresponding TG, it would imply that the TF is indeed involved in the regulation of a different set of TGs than those in the genome under consideration and in the second case, when a TG is conserved and its ...
[]
Nevertheless it should be clear that in the first case, when a TF is conserved in different species without its corresponding TG, it would imply that the TF is indeed involved in the regulation of a different set of TGs than those in the genome under consideration and in the second case, when a TG is conserved and its ...
true
true
true
true
true
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
Both cases suggest a level of plasticity that TRNs can impose on the evolution of genomes to different environments.
[ "10", "38", "51" ]
116
6,043
0
false
Both cases suggest a level of plasticity that TRNs can impose on the evolution of genomes to different environments.
[]
Both cases suggest a level of plasticity that TRNs can impose on the evolution of genomes to different environments.
true
true
true
true
true
1,000
1
DISCUSSION
1
10
[ "b10", "b38", "b51" ]
16,840,530
pmid-14572541|pmid-15102470|pmid-15193307|pmid-16530225|pmid-15070432
The evolutionary reasons for the observed tendencies in the conservation of TF–TG pairs need to be analyzed more specifically.
[ "10", "38", "51" ]
126
6,044
0
false
The evolutionary reasons for the observed tendencies in the conservation of TF–TG pairs need to be analyzed more specifically.
[]
The evolutionary reasons for the observed tendencies in the conservation of TF–TG pairs need to be analyzed more specifically.
true
true
true
true
true
1,000
2
DISCUSSION
0
null
null
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
Despite poor conservation of the regulatory interactions across genomes, certain individual interactions have been well conserved across different eubacterial phyla, which could regulate essential transcriptional processes in Bacteria.
null
235
6,045
0
false
null
null
Despite poor conservation of the regulatory interactions across genomes, certain individual interactions have been well conserved across different eubacterial phyla, which could regulate essential transcriptional processes in Bacteria.
true
true
true
true
true
1,001
2
DISCUSSION
0
null
null
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
Most of these processes are well characterized and are related directly or indirectly to the translational, structural and transcriptional machinery of the cell, suggesting a cause for their conserved nature across wide phylogenetic distances.
null
243
6,046
0
false
null
null
Most of these processes are well characterized and are related directly or indirectly to the translational, structural and transcriptional machinery of the cell, suggesting a cause for their conserved nature across wide phylogenetic distances.
true
true
true
true
true
1,001
2
DISCUSSION
0
null
null
16,840,530
pmid-15604457|pmid-15833122|pmid-15173116|pmid-15173116|pmid-15193307|pmid-15833122|pmid-15079056
Despite the type of regulation (repressor or activator) and that DNA-binding site(s) can change across genomes, it is reasonable to think that it is important to maintain the regulation of these core processes through the same elements, as in the case of BirA and DnaA regulators which seem to be a result of common ance...
null
341
6,047
0
false
null
null
Despite the type of regulation (repressor or activator) and that DNA-binding site(s) can change across genomes, it is reasonable to think that it is important to maintain the regulation of these core processes through the same elements, as in the case of BirA and DnaA regulators which seem to be a result of common ance...
true
true
true
true
true
1,001
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
The TRN appears to evolve in a step-wise manner, with loss and gain of individual interactions probably playing a greater role than loss and gain of whole motifs or modules of interactions.
[ "52" ]
189
6,048
0
false
The TRN appears to evolve in a step-wise manner, with loss and gain of individual interactions probably playing a greater role than loss and gain of whole motifs or modules of interactions.
[]
The TRN appears to evolve in a step-wise manner, with loss and gain of individual interactions probably playing a greater role than loss and gain of whole motifs or modules of interactions.
true
true
true
true
true
1,002
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
As Teichmann and Babu (52) reported previously, most network motifs have risen by convergent evolution and not by genetic duplication of ancestral circuits.
[ "52" ]
156
6,049
1
false
As Teichmann and Babu reported previously, most network motifs have risen by convergent evolution and not by genetic duplication of ancestral circuits.
[ "52" ]
As Teichmann and Babu reported previously, most network motifs have risen by convergent evolution and not by genetic duplication of ancestral circuits.
true
true
true
true
true
1,002
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
Thus, with the exception of a small fraction of the TRN, it could be possible that large portions of the TRNs might have evolved through extensive changes and re-connections among the components of the network in the evolution of the species.
[ "52" ]
242
6,050
0
false
Thus, with the exception of a small fraction of the TRN, it could be possible that large portions of the TRNs might have evolved through extensive changes and re-connections among the components of the network in the evolution of the species.
[]
Thus, with the exception of a small fraction of the TRN, it could be possible that large portions of the TRNs might have evolved through extensive changes and re-connections among the components of the network in the evolution of the species.
true
true
true
true
true
1,002
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
Here we demonstrate that individual elements, interacting pairs and groups of interactions are not conserved, in fact even in closely related species.
[ "52" ]
150
6,051
0
false
Here we demonstrate that individual elements, interacting pairs and groups of interactions are not conserved, in fact even in closely related species.
[]
Here we demonstrate that individual elements, interacting pairs and groups of interactions are not conserved, in fact even in closely related species.
true
true
true
true
true
1,002
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
This reflects that in each speciation event to adapt to environmental changes, transcriptional regulation is more flexible than the genetic component of the organisms for phenotypic adaptation.
[ "52" ]
193
6,052
0
false
This reflects that in each speciation event to adapt to environmental changes, transcriptional regulation is more flexible than the genetic component of the organisms for phenotypic adaptation.
[]
This reflects that in each speciation event to adapt to environmental changes, transcriptional regulation is more flexible than the genetic component of the organisms for phenotypic adaptation.
true
true
true
true
true
1,002
3
DISCUSSION
1
52
[ "b52" ]
16,840,530
pmid-15173116|pmid-15687504|pmid-15687504|pmid-15173116|pmid-10412974|pmid-15102470|pmid-15173116|pmid-15107850
This work should provide a perspective of the plasticity of the TRN in bacteria, which could contribute to understand the transcriptional basis of natural variation.
[ "52" ]
165
6,053
0
false
This work should provide a perspective of the plasticity of the TRN in bacteria, which could contribute to understand the transcriptional basis of natural variation.
[]
This work should provide a perspective of the plasticity of the TRN in bacteria, which could contribute to understand the transcriptional basis of natural variation.
true
true
true
true
true
1,002
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
All nonobligate organisms possess repair systems responsible for the maintenance of genomic DNA in the presence of cellular reactive oxygen species (ROS).
[ "1", "2", "3", "4", "5" ]
154
6,054
0
false
All nonobligate organisms possess repair systems responsible for the maintenance of genomic DNA in the presence of cellular reactive oxygen species (ROS).
[]
All nonobligate organisms possess repair systems responsible for the maintenance of genomic DNA in the presence of cellular reactive oxygen species (ROS).
true
true
true
true
true
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
The majority of single base lesions generated by ROS are abstracted by DNA glycosylases as the initial step in the base excision repair pathway [for reviews, see (1,2)].
[ "1", "2", "3", "4", "5" ]
169
6,055
0
false
The majority of single base lesions generated by ROS are abstracted by DNA glycosylases as the initial step in the base excision repair pathway.
[ "for reviews, see (1,2)" ]
The majority of single base lesions generated by ROS are abstracted by DNA glycosylases as the initial step in the base excision repair pathway.
true
true
true
true
true
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Mechanistically, these enzymes are classified by either the presence of an associated AP lyase activity (bifunctional), or the lack of this activity (monofunctional).
[ "1", "2", "3", "4", "5" ]
166
6,056
0
false
Mechanistically, these enzymes are classified by either the presence of an associated AP lyase activity (bifunctional), or the lack of this activity (monofunctional).
[]
Mechanistically, these enzymes are classified by either the presence of an associated AP lyase activity (bifunctional), or the lack of this activity (monofunctional).
true
true
true
true
true
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Monofunctional glycosylases cleave the glycosyl bond via either an associative SN2 reaction utilizing an activated water molecule or a dissociative SN1-like mechanism.
[ "1", "2", "3", "4", "5" ]
167
6,057
0
false
Monofunctional glycosylases cleave the glycosyl bond via either an associative SN2 reaction utilizing an activated water molecule or a dissociative SN1-like mechanism.
[]
Monofunctional glycosylases cleave the glycosyl bond via either an associative SN2 reaction utilizing an activated water molecule or a dissociative SN1-like mechanism.
true
true
true
true
true
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Bifunctional glycosylases employ an amine for nucleophilic (SN2) attack of the sugar backbone, proceeding through a Schiff base intermediate which can undergo a β-elimination that leads to cleavage of the lesion-containing strand [for reviews, see (3,4)].
[ "1", "2", "3", "4", "5" ]
255
6,058
0
false
Bifunctional glycosylases employ an amine for nucleophilic attack of the sugar backbone, proceeding through a Schiff base intermediate which can undergo a β-elimination that leads to cleavage of the lesion-containing strand.
[ "SN2", "for reviews, see (3,4)" ]
Bifunctional glycosylases employ an amine for nucleophilic attack of the sugar backbone, proceeding through a Schiff base intermediate which can undergo a β-elimination that leads to cleavage of the lesion-containing strand.
true
true
true
true
true
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Enzymes whose mechanism proceed through a transient Schiff base intermediate can be trapped by the addition of a reducing agent such as NaBH4 or NaCNBH3
[ "1", "2", "3", "4", "5" ]
152
6,059
0
false
Enzymes whose mechanism proceed through a transient Schiff base intermediate can be trapped by the addition of a reducing agent such as NaBH4 or NaCNBH3
[]
Enzymes whose mechanism proceed through a transient Schiff base intermediate can be trapped by the addition of a reducing agent such as NaBH4 or NaCNBH3
true
true
false
true
false
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
[for reviews, see (5)].
[ "1", "2", "3", "4", "5" ]
23
6,060
0
false
.
[ "for reviews, see (5)" ]
.
false
false
true
true
false
1,003
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Once covalently bound, trapped molecules no longer participate in the overall reaction resulting in stable protein–DNA complexes.
[ "1", "2", "3", "4", "5" ]
129
6,061
0
false
Once covalently bound, trapped molecules no longer participate in the overall reaction resulting in stable protein–DNA complexes.
[]
Once covalently bound, trapped molecules no longer participate in the overall reaction resulting in stable protein–DNA complexes.
true
true
true
true
true
1,003
1
INTRODUCTION
1
6–8
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
The ability to efficiently generate stable, covalently bound glycosylase–DNA complexes has broad-reaching applications and has been used extensively in the literature.
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
167
6,062
0
false
The ability to efficiently generate stable, covalently bound glycosylase–DNA complexes has broad-reaching applications and has been used extensively in the literature.
[]
The ability to efficiently generate stable, covalently bound glycosylase–DNA complexes has broad-reaching applications and has been used extensively in the literature.
true
true
true
true
true
1,004
1
INTRODUCTION
1
6–8
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
Studies utilizing this procedure include, but are not limited to, bifunctional versus monofunctional classification (6–8), determination of the fraction of active molecules in enzyme preparations (9,10), reaction rate analyses (11,12), glycosylase activity comparisons (13–15), iron–sulfur cluster domain analysis (16), ...
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
387
6,063
1
false
Studies utilizing this procedure include, but are not limited to, bifunctional versus monofunctional classification, determination of the fraction of active molecules in enzyme preparations, reaction rate analyses, glycosylase activity comparisons, iron–sulfur cluster domain analysis, and the characterization of enzyme...
[ "6–8", "9,10", "11,12", "13–15", "16", "10,17–21" ]
Studies utilizing this procedure include, but are not limited to, bifunctional versus monofunctional classification, determination of the fraction of active molecules in enzyme preparations, reaction rate analyses, glycosylase activity comparisons, iron–sulfur cluster domain analysis, and the characterization of enzyme...
true
true
true
true
true
1,004
1
INTRODUCTION
1
6–8
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
A commonality among these techniques is the almost universal requirement for separation of the trapped complex from unbound DNA via polyacrylamide gel electrophoresis (PAGE) prior to phosphorimager analysis.
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
207
6,064
0
false
A commonality among these techniques is the almost universal requirement for separation of the trapped complex from unbound DNA via polyacrylamide gel electrophoresis (PAGE) prior to phosphorimager analysis.
[]
A commonality among these techniques is the almost universal requirement for separation of the trapped complex from unbound DNA via polyacrylamide gel electrophoresis (PAGE) prior to phosphorimager analysis.
true
true
true
true
true
1,004
1
INTRODUCTION
1
6–8
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
It should be noted that while the characterization of active-site residues may alternatively employ tryptic digestion of the trapped complex in order to identify the bound peptide (20,21), targeted mutagenesis experiments require a gel-based approach (10,17–19).
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
262
6,065
0
false
It should be noted that while the characterization of active-site residues may alternatively employ tryptic digestion of the trapped complex in order to identify the bound peptide, targeted mutagenesis experiments require a gel-based approach.
[ "20,21", "10,17–19" ]
It should be noted that while the characterization of active-site residues may alternatively employ tryptic digestion of the trapped complex in order to identify the bound peptide, targeted mutagenesis experiments require a gel-based approach.
true
true
true
true
true
1,004
1
INTRODUCTION
1
22
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
A gel-based approach may be necessary in some circumstances; for example, the determination of specific reaction intermediates (22).
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
132
6,066
1
false
A gel-based approach may be necessary in some circumstances; for example, the determination of specific reaction intermediates.
[ "22" ]
A gel-based approach may be necessary in some circumstances; for example, the determination of specific reaction intermediates.
true
true
true
true
true
1,004
1
INTRODUCTION
1
6–8
[ "B6 B7 B8", "B9", "B10", "B11", "B12", "B13 B14 B15", "B16", "B10", "B17 B18 B19 B20 B21", "B20", "B21", "B10", "B17 B18 B19", "B22" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
However, a faster, less cumbersome technique would be useful for the majority of situations.
[ "6–8", "9", "10", "11", "12", "13–15", "16", "10", "17–21", "20", "21", "10", "17–19", "22" ]
92
6,067
0
false
However, a faster, less cumbersome technique would be useful for the majority of situations.
[]
However, a faster, less cumbersome technique would be useful for the majority of situations.
true
true
true
true
true
1,004
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
The properties of 4′,6-diamidino-2-phenylindole (DAPI) have been well studied for more than 30 years, from pH and ionic strength influences (23,24) to the solved crystal structure of DAPI-DNA complexes (25,26).
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
210
6,068
0
false
The properties of 4′,6-diamidino-2-phenylindole (DAPI) have been well studied for more than 30 years, from pH and ionic strength influences to the solved crystal structure of DAPI-DNA complexes.
[ "23,24", "25,26" ]
The properties of 4′,6-diamidino-2-phenylindole (DAPI) have been well studied for more than 30 years, from pH and ionic strength influences to the solved crystal structure of DAPI-DNA complexes.
true
true
true
true
true
1,005
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Similar to distamycin and its analogs, DAPI preferentially binds to the minor groove of AT-rich regions of double-stranded DNA (24,27–31).
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
138
6,069
0
false
Similar to distamycin and its analogs, DAPI preferentially binds to the minor groove of AT-rich regions of double-stranded DNA.
[ "24,27–31" ]
Similar to distamycin and its analogs, DAPI preferentially binds to the minor groove of AT-rich regions of double-stranded DNA.
true
true
true
true
true
1,005
2
INTRODUCTION
1
31
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Due to its unique fluorescent characteristics (31) it has been employed successfully in various dye displacement assays (32,33).
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
128
6,070
1
false
Due to its unique fluorescent characteristics it has been employed successfully in various dye displacement assays.
[ "31", "32,33" ]
Due to its unique fluorescent characteristics it has been employed successfully in various dye displacement assays.
true
true
true
true
true
1,005
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
In this article, we describe a novel approach for using DAPI as a fluorescent reporter molecule to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following protein–DNA cross-linking.
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
228
6,071
0
false
In this article, we describe a novel approach for using DAPI as a fluorescent reporter molecule to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following protein–DNA cross-linking.
[]
In this article, we describe a novel approach for using DAPI as a fluorescent reporter molecule to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following protein–DNA cross-linking.
true
true
true
true
true
1,005
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Although the focus of this work is on determining the fraction of active molecules in enzyme preparations, the technique is equally applicable to the studies listed above.
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
171
6,072
0
false
Although the focus of this work is on determining the fraction of active molecules in enzyme preparations, the technique is equally applicable to the studies listed above.
[]
Although the focus of this work is on determining the fraction of active molecules in enzyme preparations, the technique is equally applicable to the studies listed above.
true
true
true
true
true
1,005
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Any study which necessitates analyzing the total number of trapped enzyme–DNA moieties, and does not require discrimination of the trapped intermediates themselves, may benefit from this approach.
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
196
6,073
0
false
Any study which necessitates analyzing the total number of trapped enzyme–DNA moieties, and does not require discrimination of the trapped intermediates themselves, may benefit from this approach.
[]
Any study which necessitates analyzing the total number of trapped enzyme–DNA moieties, and does not require discrimination of the trapped intermediates themselves, may benefit from this approach.
true
true
true
true
true
1,005
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B24", "B27 B28 B29 B30 B31", "B31", "B32", "B33" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
We foresee this molecular accessibility assay being useful in the study of numerous DNA-binding proteins.
[ "23", "24", "25", "26", "24", "27–31", "31", "32", "33" ]
105
6,074
0
false
We foresee this molecular accessibility assay being useful in the study of numerous DNA-binding proteins.
[]
We foresee this molecular accessibility assay being useful in the study of numerous DNA-binding proteins.
true
true
true
true
true
1,005
0
DISCUSSION
1
39
[ "B39" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
In this article, we have described a novel approach to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following Schiff base trapping.
[ "39" ]
179
6,075
0
false
In this article, we have described a novel approach to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following Schiff base trapping.
[]
In this article, we have described a novel approach to rapidly differentiate the number of bound versus unbound enzymes to damaged oligonucleotides following Schiff base trapping.
true
true
true
true
true
1,006
0
DISCUSSION
1
39
[ "B39" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Though the assay described focused on determining the fraction of active molecules in enzyme preparations, the technique itself should be applicable to any study which necessitates quantifying the total number of bound enzyme–DNA moieties.
[ "39" ]
239
6,076
0
false
Though the assay described focused on determining the fraction of active molecules in enzyme preparations, the technique itself should be applicable to any study which necessitates quantifying the total number of bound enzyme–DNA moieties.
[]
Though the assay described focused on determining the fraction of active molecules in enzyme preparations, the technique itself should be applicable to any study which necessitates quantifying the total number of bound enzyme–DNA moieties.
true
true
true
true
true
1,006
0
DISCUSSION
1
39
[ "B39" ]
17,289,752
pmid-15941573|pmid-12086677|pmid-16464017|pmid-12848584|pmid-14527324|pmid-9778350
Previous approaches have been limited to either a traditional PAGE analysis or to the analysis of specific enzymes; for example, activity determination via the burst phase for glycosylases with slow product release (39).
[ "39" ]
220
6,077
1
false
Previous approaches have been limited to either a traditional PAGE analysis or to the analysis of specific enzymes; for example, activity determination via the burst phase for glycosylases with slow product release.
[ "39" ]
Previous approaches have been limited to either a traditional PAGE analysis or to the analysis of specific enzymes; for example, activity determination via the burst phase for glycosylases with slow product release.
true
true
true
true
true
1,006
1
DISCUSSION
1
40
[ "B40", "B41", "B42 B43 B44 B45" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
For either the gel-based or DAPI-based approach, the crucial step is the ability to form trapped enzyme–DNA complexes.
[ "40", "41", "42–45" ]
118
6,078
0
false
For either the gel-based or DAPI-based approach, the crucial step is the ability to form trapped enzyme–DNA complexes.
[]
For either the gel-based or DAPI-based approach, the crucial step is the ability to form trapped enzyme–DNA complexes.
true
true
true
true
true
1,007
1
DISCUSSION
1
40
[ "B40", "B41", "B42 B43 B44 B45" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
Though Schiff base formation is typically limited to bifunctional glycosylases, some monofunctional glycosylases may also be trapped by borohydride reduction (40,41).
[ "40", "41", "42–45" ]
166
6,079
0
false
Though Schiff base formation is typically limited to bifunctional glycosylases, some monofunctional glycosylases may also be trapped by borohydride reduction.
[ "40,41" ]
Though Schiff base formation is typically limited to bifunctional glycosylases, some monofunctional glycosylases may also be trapped by borohydride reduction.
true
true
true
true
true
1,007
1
DISCUSSION
1
40
[ "B40", "B41", "B42 B43 B44 B45" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
For monofunctional glycosylases which cannot be trapped via borohydride reduction, alternative trapping agents might prove useful.
[ "40", "41", "42–45" ]
130
6,080
0
false
For monofunctional glycosylases which cannot be trapped via borohydride reduction, alternative trapping agents might prove useful.
[]
For monofunctional glycosylases which cannot be trapped via borohydride reduction, alternative trapping agents might prove useful.
true
true
true
true
true
1,007
1
DISCUSSION
1
42–45
[ "B40", "B41", "B42 B43 B44 B45" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
The use of 2-deoxyribonolactone and oxanine are both promising covalent trapping agents for various bifunctional and monofunctional glycosylases (42–45).
[ "40", "41", "42–45" ]
153
6,081
1
false
The use of 2-deoxyribonolactone and oxanine are both promising covalent trapping agents for various bifunctional and monofunctional glycosylases.
[ "42–45" ]
The use of 2-deoxyribonolactone and oxanine are both promising covalent trapping agents for various bifunctional and monofunctional glycosylases.
true
true
true
true
true
1,007
1
DISCUSSION
1
40
[ "B40", "B41", "B42 B43 B44 B45" ]
17,289,752
pmid-16336782|pmid-12509226|pmid-11361340|pmid-9705289|pmid-11711552|pmid-10884383|pmid-11287425|pmid-12718542|pmid-16547199|pmid-16781198|pmid-12667065|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|pmid-10833024|pmid-9030608|pmid-10833024|pmid-9030608|pmid-11711552|pmid-10744666|pmid-11813291|pmid-11101292|p...
The use of these compounds for active fraction analysis is currently being investigated.
[ "40", "41", "42–45" ]
88
6,082
0
false
The use of these compounds for active fraction analysis is currently being investigated.
[]
The use of these compounds for active fraction analysis is currently being investigated.
true
true
true
true
true
1,007
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Throughout this study a single damaged nucleotide, DHU, was used for all substrates.
[ "13", "22" ]
84
6,083
0
false
Throughout this study a single damaged nucleotide, DHU, was used for all substrates.
[]
Throughout this study a single damaged nucleotide, DHU, was used for all substrates.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
While this is adequate for comparisons made as a proof of concept, accurate determination of the active fraction of numerous enzymes requires additional substrates.
[ "13", "22" ]
164
6,084
0
false
While this is adequate for comparisons made as a proof of concept, accurate determination of the active fraction of numerous enzymes requires additional substrates.
[]
While this is adequate for comparisons made as a proof of concept, accurate determination of the active fraction of numerous enzymes requires additional substrates.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
For example, for accurate determination of the active fraction of EcoFpg, 7,8-dihydro-8-oxoguanine (8-oxoG) should be used based on the greater affinity for that damage.
[ "13", "22" ]
169
6,085
0
false
For example, for accurate determination of the active fraction of EcoFpg, 7,8-dihydro-8-oxoguanine (8-oxoG) should be used based on the greater affinity for that damage.
[]
For example, for accurate determination of the active fraction of EcoFpg, 7,8-dihydro-8-oxoguanine (8-oxoG) should be used based on the greater affinity for that damage.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Some damaged nucleotides, such as 5-formyluracil, would be inappropriate for the activity determination of certain enzymes, due to their low affinity for the damage (13).
[ "13", "22" ]
170
6,086
1
false
Some damaged nucleotides, such as 5-formyluracil, would be inappropriate for the activity determination of certain enzymes, due to their low affinity for the damage.
[ "13" ]
Some damaged nucleotides, such as 5-formyluracil, would be inappropriate for the activity determination of certain enzymes, due to their low affinity for the damage.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
The ‘best’ substrate for a given enzyme, based on prior knowledge, should always be used for accurate activity calculations.
[ "13", "22" ]
124
6,087
0
false
The ‘best’ substrate for a given enzyme, based on prior knowledge, should always be used for accurate activity calculations.
[]
The ‘best’ substrate for a given enzyme, based on prior knowledge, should always be used for accurate activity calculations.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
For previously uncharacterized enzymes, analysis of numerous substrates is required.
[ "13", "22" ]
84
6,088
0
false
For previously uncharacterized enzymes, analysis of numerous substrates is required.
[]
For previously uncharacterized enzymes, analysis of numerous substrates is required.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Strong reducing agents, such as NaBH4, should not be used in combination with damages which are extremely prone to reduction such as AP sites.
[ "13", "22" ]
142
6,089
0
false
Strong reducing agents, such as NaBH4, should not be used in combination with damages which are extremely prone to reduction such as AP sites.
[]
Strong reducing agents, such as NaBH4, should not be used in combination with damages which are extremely prone to reduction such as AP sites.
true
true
true
true
true
1,008
2
DISCUSSION
1
22
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
In these cases, the use of NaCNBH3, where the half-life of an AP site has been reported to be about 6 h, is required (22).
[ "13", "22" ]
122
6,090
1
false
In these cases, the use of NaCNBH3, where the half-life of an AP site has been reported to be about 6 h, is required.
[ "22" ]
In these cases, the use of NaCNBH3, where the half-life of an AP site has been reported to be about 6 h, is required.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Regardless, it should also be noted that partial destruction of the substrate via reduction will not affect calculation of the α value, only the β value will be affected.
[ "13", "22" ]
170
6,091
0
false
Regardless, it should also be noted that partial destruction of the substrate via reduction will not affect calculation of the α value, only the β value will be affected.
[]
Regardless, it should also be noted that partial destruction of the substrate via reduction will not affect calculation of the α value, only the β value will be affected.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
With either the gel-based or DAPI-based methods, a strong reducing environment may possibly lead to inactivation of some enzyme molecules.
[ "13", "22" ]
138
6,092
0
false
With either the gel-based or DAPI-based methods, a strong reducing environment may possibly lead to inactivation of some enzyme molecules.
[]
With either the gel-based or DAPI-based methods, a strong reducing environment may possibly lead to inactivation of some enzyme molecules.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
Nonetheless, it is unlikely that both NaBH4 and NaCNBH3 will show the same rate of inactivation due to the inherent differences in their rate of reduction.
[ "13", "22" ]
155
6,093
0
false
Nonetheless, it is unlikely that both NaBH4 and NaCNBH3 will show the same rate of inactivation due to the inherent differences in their rate of reduction.
[]
Nonetheless, it is unlikely that both NaBH4 and NaCNBH3 will show the same rate of inactivation due to the inherent differences in their rate of reduction.
true
true
true
true
true
1,008
2
DISCUSSION
1
13
[ "B13", "B22" ]
17,289,752
pmid-31603|pmid-6672773|pmid-2627296|pmid-10600105|pmid-6672773|pmid-8382683|pmid-2252904|pmid-8204219|pmid-10433722|pmid-8457562|pmid-8457562|pmid-9421529|pmid-8614617|pmid-12718542|pmid-15326180
A side-by-side test with both reducing agents (as was done in Figures 3 and 4) is arguably a valid control for demonstrating the lack of enzyme inactivation.
[ "13", "22" ]
157
6,094
0
false
A side-by-side test with both reducing agents (as was done in Figures 3 and 4) is arguably a valid control for demonstrating the lack of enzyme inactivation.
[]
A side-by-side test with both reducing agents is arguably a valid control for demonstrating the lack of enzyme inactivation.
true
true
true
true
true
1,008
3
DISCUSSION
1
46–50
[ "B46 B47 B48 B49 B50", "B32", "B33" ]
17,289,752
pmid-2673015|pmid-1544428|pmid-1988954|pmid-10600373|pmid-16008554|pmid-9421529|pmid-8614617
The accessibility, and inaccessibility, of the reporter dye to its binding site is obviously a hallmark of this assay.
[ "46–50", "32", "33" ]
118
6,095
0
false
The accessibility, and inaccessibility, of the reporter dye to its binding site is obviously a hallmark of this assay.
[]
The accessibility, and inaccessibility, of the reporter dye to its binding site is obviously a hallmark of this assay.
true
true
true
true
true
1,009
3
DISCUSSION
1
46–50
[ "B46 B47 B48 B49 B50", "B32", "B33" ]
17,289,752
pmid-2673015|pmid-1544428|pmid-1988954|pmid-10600373|pmid-16008554|pmid-9421529|pmid-8614617
The preference of DNA minor groove-binding drugs for AT-rich sequences is thought to be primarily due to the narrow minor groove width which influences hydrogen bonding and van der Waals’ interactions, and interrelationships of the positively charged amino ends of the drugs with the more negatively charged minor groove...
[ "46–50", "32", "33" ]
345
6,096
1
false
The preference of DNA minor groove-binding drugs for AT-rich sequences is thought to be primarily due to the narrow minor groove width which influences hydrogen bonding and van der Waals’ interactions, and interrelationships of the positively charged amino ends of the drugs with the more negatively charged minor groove...
[ "46–50" ]
The preference of DNA minor groove-binding drugs for AT-rich sequences is thought to be primarily due to the narrow minor groove width which influences hydrogen bonding and van der Waals’ interactions, and interrelationships of the positively charged amino ends of the drugs with the more negatively charged minor groove...
true
true
true
true
true
1,009
3
DISCUSSION
1
46–50
[ "B46 B47 B48 B49 B50", "B32", "B33" ]
17,289,752
pmid-2673015|pmid-1544428|pmid-1988954|pmid-10600373|pmid-16008554|pmid-9421529|pmid-8614617
The choice to use DAPI was primarily based on its well-known binding properties, ease of use with our current fluorimeter and the success of its use in other fluorescence assays (32,33).
[ "46–50", "32", "33" ]
186
6,097
0
false
The choice to use DAPI was primarily based on its well-known binding properties, ease of use with our current fluorimeter and the success of its use in other fluorescence assays.
[ "32,33" ]
The choice to use DAPI was primarily based on its well-known binding properties, ease of use with our current fluorimeter and the success of its use in other fluorescence assays.
true
true
true
true
true
1,009
3
DISCUSSION
1
46–50
[ "B46 B47 B48 B49 B50", "B32", "B33" ]
17,289,752
pmid-2673015|pmid-1544428|pmid-1988954|pmid-10600373|pmid-16008554|pmid-9421529|pmid-8614617
That said, other minor groove-binding dyes may prove useful in accessibility assays, notably ones with a larger minor groove footprint.
[ "46–50", "32", "33" ]
135
6,098
0
false
That said, other minor groove-binding dyes may prove useful in accessibility assays, notably ones with a larger minor groove footprint.
[]
That said, other minor groove-binding dyes may prove useful in accessibility assays, notably ones with a larger minor groove footprint.
true
true
true
true
true
1,009
4
DISCUSSION
1
26
[ "B26" ]
17,289,752
pmid-10600105
Comparing results of the molecular accessibility assay with the modeling results presented in Table 1, a number of insights can be drawn.
[ "26" ]
137
6,099
0
false
Comparing results of the molecular accessibility assay with the modeling results presented in Table 1, a number of insights can be drawn.
[]
Comparing results of the molecular accessibility assay with the modeling results presented in Table 1, a number of insights can be drawn.
true
true
true
true
true
1,010