Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
In the presence of all three proteins, plasmid inserts of up to 10 kb can be amplified from bacterial colonies, bypassing a DNA purification step.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
146
2,600
0
false
In the presence of all three proteins, plasmid inserts of up to 10 kb can be amplified from bacterial colonies, bypassing a DNA purification step.
[]
In the presence of all three proteins, plasmid inserts of up to 10 kb can be amplified from bacterial colonies, bypassing a DNA purification step.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
Substitution of T7 gp2.5 with the T4 gp32 SSB protein (Figure 5A) or E.coli SSB protein (data not shown) does not support cHDA amplification.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
141
2,601
0
false
Substitution of T7 gp2.5 with the T4 gp32 SSB protein (Figure 5A) or E.coli SSB protein (data not shown) does not support cHDA amplification.
[]
Substitution of T7 gp2.5 with the T4 gp32 SSB protein (Figure 5A) or E.coli SSB protein (data not shown) does not support cHDA amplification.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
The T7 SSB protein displays a high annealing activity that promotes base pairing between complementary sequences (23).
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
118
2,602
1
false
The T7 SSB protein displays a high annealing activity that promotes base pairing between complementary sequences.
[ "23" ]
The T7 SSB protein displays a high annealing activity that promotes base pairing between complementary sequences.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
In a cHDA reaction, primers are highly abundant and predicted to be coated with the SSB protein.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
96
2,603
0
false
In a cHDA reaction, primers are highly abundant and predicted to be coated with the SSB protein.
[]
In a cHDA reaction, primers are highly abundant and predicted to be coated with the SSB protein.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
It is conceivable that the presence of the SSB protein mediates homologous base pairing to stimulate primer annealing and opening at the end of dsDNA to provide an entry point for the T7 helicase, which prefers forked duplex DNA with single-stranded tails (12,24).
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
264
2,604
0
false
It is conceivable that the presence of the SSB protein mediates homologous base pairing to stimulate primer annealing and opening at the end of dsDNA to provide an entry point for the T7 helicase, which prefers forked duplex DNA with single-stranded tails.
[ "12,24" ]
It is conceivable that the presence of the SSB protein mediates homologous base pairing to stimulate primer annealing and opening at the end of dsDNA to provide an entry point for the T7 helicase, which prefers forked duplex DNA with single-stranded tails.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
Binding of the SSB protein to the unwound ssDNA produced by the helicase is expected to stabilize each strand and to inhibit reannealing.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
137
2,605
0
false
Binding of the SSB protein to the unwound ssDNA produced by the helicase is expected to stabilize each strand and to inhibit reannealing.
[]
Binding of the SSB protein to the unwound ssDNA produced by the helicase is expected to stabilize each strand and to inhibit reannealing.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
In addition, the T7 Gp2.5 SSB interacts with T7 DNA polymerase and stimulates DNA synthesis by T7 DNA polymerase (19,20,25).
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
124
2,606
0
false
In addition, the T7 Gp2.5 SSB interacts with T7 DNA polymerase and stimulates DNA synthesis by T7 DNA polymerase.
[ "19,20,25" ]
In addition, the T7 Gp2.5 SSB interacts with T7 DNA polymerase and stimulates DNA synthesis by T7 DNA polymerase.
true
true
true
true
true
442
2
DISCUSSION
1
24
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
It also stimulates the synthesis of RNA primers by T7 helicase and was suggested to interact with T7 helicase (24).
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
115
2,607
1
false
It also stimulates the synthesis of RNA primers by T7 helicase and was suggested to interact with T7 helicase.
[ "24" ]
It also stimulates the synthesis of RNA primers by T7 helicase and was suggested to interact with T7 helicase.
true
true
true
true
true
442
2
DISCUSSION
1
23
[ "b23", "b12", "b24", "b19", "b20", "b25", "b24", "b26", "b29" ]
16,893,951
pmid-15247927|pmid-15247927|pmid-15247927|pmid-8617248|pmid-6315716|pmid-2838482|pmid-4581369|pmid-1634539|pmid-8106511|pmid-2838482|pmid-6411726|pmid-9218486
Furthermore, T7 helicase and T7 DNA polymerase form a complex and both proteins are required for DNA synthesis through a duplex region (26–29).
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
143
2,608
0
false
Furthermore, T7 helicase and T7 DNA polymerase form a complex and both proteins are required for DNA synthesis through a duplex region.
[ "26–29" ]
Furthermore, T7 helicase and T7 DNA polymerase form a complex and both proteins are required for DNA synthesis through a duplex region.
true
true
true
true
true
442
3
DISCUSSION
1
30
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
The strand displacement activity of T7 Sequenase is central to the cHDA platform, supporting displacement of the newly synthesized strand.
[ "30", "31", "32", "32" ]
138
2,609
0
false
The strand displacement activity of T7 Sequenase is central to the cHDA platform, supporting displacement of the newly synthesized strand.
[]
The strand displacement activity of T7 Sequenase is central to the cHDA platform, supporting displacement of the newly synthesized strand.
true
true
true
true
true
443
3
DISCUSSION
1
30
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
The wild-type T7 polymerase lacks strand displacement activity and is unable to support cHDA (data not shown).
[ "30", "31", "32", "32" ]
110
2,610
0
false
The wild-type T7 polymerase lacks strand displacement activity and is unable to support cHDA (data not shown).
[]
The wild-type T7 polymerase lacks strand displacement activity and is unable to support cHDA (data not shown).
true
true
true
true
true
443
3
DISCUSSION
1
30
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
Due to the absence of the 3′–5β€² exonuclease activity, the T7 Sequenase used in cHDA has a lower fidelity (error rate of 3.6 Γ— 10βˆ’5) than the wild-type T7 polymerase, which has a error rate of 1.5 Γ— 10βˆ’6 (30,31).
[ "30", "31", "32", "32" ]
211
2,611
0
false
Due to the absence of the 3′–5β€² exonuclease activity, the T7 Sequenase used in cHDA has a lower fidelity (error rate of 3.6 Γ— 10βˆ’5) than the wild-type T7 polymerase, which has a error rate of 1.5 Γ— 10βˆ’6.
[ "30,31" ]
Due to the absence of the 3′–5β€² exonuclease activity, the T7 Sequenase used in cHDA has a lower fidelity than the wild-type T7 polymerase, which has a error rate of 1.5 Γ— 10βˆ’6.
true
true
true
true
true
443
3
DISCUSSION
1
30
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
One approach to further increase the fidelity is to combine T7 Sequenase with a DNA polymerase possessing proofreading activity in cHDA reactions.
[ "30", "31", "32", "32" ]
146
2,612
0
false
One approach to further increase the fidelity is to combine T7 Sequenase with a DNA polymerase possessing proofreading activity in cHDA reactions.
[]
One approach to further increase the fidelity is to combine T7 Sequenase with a DNA polymerase possessing proofreading activity in cHDA reactions.
true
true
true
true
true
443
3
DISCUSSION
1
32
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
Another approach is to explore the use of the T7 SSB protein mutant allele, F232L, which has been shown to promote strand displacement activity in the native T7 polymerase (32).
[ "30", "31", "32", "32" ]
177
2,613
1
false
Another approach is to explore the use of the T7 SSB protein mutant allele, F232L, which has been shown to promote strand displacement activity in the native T7 polymerase.
[ "32" ]
Another approach is to explore the use of the T7 SSB protein mutant allele, F232L, which has been shown to promote strand displacement activity in the native T7 polymerase.
true
true
true
true
true
443
3
DISCUSSION
1
32
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
The F232L SSB protein has also been demonstrated to possess a higher binding affinity for ssDNA and to stimulate T7 DNA polymerase activity (32).
[ "30", "31", "32", "32" ]
145
2,614
1
false
The F232L SSB protein has also been demonstrated to possess a higher binding affinity for ssDNA and to stimulate T7 DNA polymerase activity.
[ "32" ]
The F232L SSB protein has also been demonstrated to possess a higher binding affinity for ssDNA and to stimulate T7 DNA polymerase activity.
true
true
true
true
true
443
3
DISCUSSION
1
30
[ "b30", "b31", "b32", "b32" ]
16,893,951
pmid-8156591|pmid-9651583|pmid-3316214|pmid-2703498|pmid-6864790|pmid-6344999|pmid-6454135|pmid-2829184|pmid-12206763|pmid-1634538|pmid-11481454|pmid-4581369|pmid-2838481|pmid-2594764|pmid-1923765|pmid-12766155|pmid-12766155
Developing a cHDA system that utilizes the F232L SSB protein may allow the use of the wild-type T7 DNA polymerase and will improve the potential error rate associated with the T7 Sequenase enzyme.
[ "30", "31", "32", "32" ]
196
2,615
0
false
Developing a cHDA system that utilizes the F232L SSB protein may allow the use of the wild-type T7 DNA polymerase and will improve the potential error rate associated with the T7 Sequenase enzyme.
[]
Developing a cHDA system that utilizes the F232L SSB protein may allow the use of the wild-type T7 DNA polymerase and will improve the potential error rate associated with the T7 Sequenase enzyme.
true
true
true
true
true
443
4
DISCUSSION
0
null
null
16,893,951
null
Currently, an isothermal plasmid amplification system utilizing the Ξ¦29 polymerase is available for research use (GE Healthcare).
null
129
2,616
0
false
null
null
Currently, an isothermal plasmid amplification system utilizing the Ξ¦29 polymerase is available for research use (GE Healthcare).
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
Development of the T7 bacteriophage based cHDA system overcomes many of the drawbacks associated with the Ξ¦29 system, allowing a more efficient isothermal plasmid amplification.
null
177
2,617
0
false
null
null
Development of the T7 bacteriophage based cHDA system overcomes many of the drawbacks associated with the Ξ¦29 system, allowing a more efficient isothermal plasmid amplification.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
Amplification with the Ξ¦29 system requires heat denaturation of the template DNA at 95Β°C, followed by incubation at 30Β°C for the reaction to proceed; therefore, the system is not a true isothermal reaction.
null
206
2,618
0
false
null
null
Amplification with the Ξ¦29 system requires heat denaturation of the template DNA at 95Β°C, followed by incubation at 30Β°C for the reaction to proceed; therefore, the system is not a true isothermal reaction.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
The use of helicase in cHDA reactions eliminates the need for temperature cycling to facilitate access to the template sequence by enzymatically melting duplex DNA.
null
164
2,619
0
false
null
null
The use of helicase in cHDA reactions eliminates the need for temperature cycling to facilitate access to the template sequence by enzymatically melting duplex DNA.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
Furthermore, primers in the Ξ¦29 system are random hexamers and, in contrast, only sequence specific primers are utilized in cHDA.
null
129
2,620
0
false
null
null
Furthermore, primers in the Ξ¦29 system are random hexamers and, in contrast, only sequence specific primers are utilized in cHDA.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
Multiply primed random hexamers mediate efficient amplification, but also render the system sensitive to the presence of contaminating DNAs.
null
140
2,621
0
false
null
null
Multiply primed random hexamers mediate efficient amplification, but also render the system sensitive to the presence of contaminating DNAs.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
Additionally, the product from the Ξ¦29 platform is a hyperbranched and viscous.
null
79
2,622
0
false
null
null
Additionally, the product from the Ξ¦29 platform is a hyperbranched and viscous.
true
true
true
true
true
444
4
DISCUSSION
0
null
null
16,893,951
null
In the event that the Ξ¦29 system is being used for plasmid analysis, an additional screening step is necessary to determine the identity of the amplified plasmids.
null
163
2,623
0
false
null
null
In the event that the Ξ¦29 system is being used for plasmid analysis, an additional screening step is necessary to determine the identity of the amplified plasmids.
true
true
true
true
true
444
5
DISCUSSION
0
null
null
16,893,951
null
Researchers typically rely on E.coli cells to amplify plasmid DNA, by growing cultures of transformed cells harboring the plasmid and purifying the DNA.
null
152
2,624
0
false
null
null
Researchers typically rely on E.coli cells to amplify plasmid DNA, by growing cultures of transformed cells harboring the plasmid and purifying the DNA.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
This technique can be time consuming and labor intensive when analyzing numerous isolates.
null
90
2,625
0
false
null
null
This technique can be time consuming and labor intensive when analyzing numerous isolates.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
A faster, isothermal method that selectively amplifies the target of interest for analyzing plasmids at room temperature has the potential to reduce the time necessary for analyzing DNA constructs and facilitate high throughput genetic screens.
null
244
2,626
0
false
null
null
A faster, isothermal method that selectively amplifies the target of interest for analyzing plasmids at room temperature has the potential to reduce the time necessary for analyzing DNA constructs and facilitate high throughput genetic screens.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
The unmatched ability of the cHDA system to simultaneously amplify plasmids and screen for specific inserts reduces plasmid analysis procedures to one time saving reaction.
null
172
2,627
0
false
null
null
The unmatched ability of the cHDA system to simultaneously amplify plasmids and screen for specific inserts reduces plasmid analysis procedures to one time saving reaction.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
The true isothermal nature of cHDA will also allow performing specific DNA amplification where a thermocycler is not readily available.
null
135
2,628
0
false
null
null
The true isothermal nature of cHDA will also allow performing specific DNA amplification where a thermocycler is not readily available.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
In addition, since cHDA specifically amplifies circular DNA, this technology will be useful when circular DNA needs to be amplified in the presence of contaminating linear DNA.
null
176
2,629
0
false
null
null
In addition, since cHDA specifically amplifies circular DNA, this technology will be useful when circular DNA needs to be amplified in the presence of contaminating linear DNA.
true
true
true
true
true
445
5
DISCUSSION
0
null
null
16,893,951
null
For example, the cHDA technology can be further developed to preferentially amplify mitochondrial DNA from human cells for further genetic analysis, or to detect the presence of circular DNA virus in a clinical specimen or a specific plasmid in the pathogenic bacteria.
null
269
2,630
0
false
null
null
For example, the cHDA technology can be further developed to preferentially amplify mitochondrial DNA from human cells for further genetic analysis, or to detect the presence of circular DNA virus in a clinical specimen or a specific plasmid in the pathogenic bacteria.
true
true
true
true
true
445
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
Eukaryotic genomes contain characteristically G-rich regions, including single-copy genes; the rDNA; and repetitive sequences, such as the telomeres and the immunoglobulin heavy chain switch (S) regions of higher vertebrates.
[ "1", "2", "3", "4", "5", "6" ]
225
2,631
0
false
Eukaryotic genomes contain characteristically G-rich regions, including single-copy genes; the rDNA; and repetitive sequences, such as the telomeres and the immunoglobulin heavy chain switch (S) regions of higher vertebrates.
[]
Eukaryotic genomes contain characteristically G-rich regions, including single-copy genes; the rDNA; and repetitive sequences, such as the telomeres and the immunoglobulin heavy chain switch (S) regions of higher vertebrates.
true
true
true
true
true
446
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
G-rich nucleic acids have the potential to form G-quadruplex or β€˜G4 DNA’, a structure in which intra- or inter-strand interactions are stabilized by G-quartets, planar arrays of four guanines, paired by Hoogsteen bonding (1,2).
[ "1", "2", "3", "4", "5", "6" ]
227
2,632
0
false
G-rich nucleic acids have the potential to form G-quadruplex or β€˜G4 DNA’, a structure in which intra- or inter-strand interactions are stabilized by G-quartets, planar arrays of four guanines, paired by Hoogsteen bonding.
[ "1,2" ]
G-rich nucleic acids have the potential to form G-quadruplex or β€˜G4 DNA’, a structure in which intra- or inter-strand interactions are stabilized by G-quartets, planar arrays of four guanines, paired by Hoogsteen bonding.
true
true
true
true
true
446
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
G-quartets can stabilize a remarkable diversity of structures, in which the lengths and positions of the G-runs and the β€˜loops’ separating them both contribute to overall topology (3,4).
[ "1", "2", "3", "4", "5", "6" ]
186
2,633
0
false
G-quartets can stabilize a remarkable diversity of structures, in which the lengths and positions of the G-runs and the β€˜loops’ separating them both contribute to overall topology.
[ "3,4" ]
G-quartets can stabilize a remarkable diversity of structures, in which the lengths and positions of the G-runs and the β€˜loops’ separating them both contribute to overall topology.
true
true
true
true
true
446
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6" ]
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
In the human genome, the number of distinct sites with potential to form G4 DNA is estimated at more than 300 000, and specific loop sequences are prominent at some of these sites (5,6).
[ "1", "2", "3", "4", "5", "6" ]
186
2,634
0
false
In the human genome, the number of distinct sites with potential to form G4 DNA is estimated at more than 300 000, and specific loop sequences are prominent at some of these sites.
[ "5,6" ]
In the human genome, the number of distinct sites with potential to form G4 DNA is estimated at more than 300 000, and specific loop sequences are prominent at some of these sites.
true
true
true
true
true
446
1
INTRODUCTION
1
7
[ "b7", "b15", "b16", "b17" ]
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
Key cellular processes are identified with repetitive G-rich chromosomal regions, where regulated formation of G4 DNA may contribute to biological function.
[ "7", "15", "16", "17" ]
156
2,635
0
false
Key cellular processes are identified with repetitive G-rich chromosomal regions, where regulated formation of G4 DNA may contribute to biological function.
[]
Key cellular processes are identified with repetitive G-rich chromosomal regions, where regulated formation of G4 DNA may contribute to biological function.
true
true
true
true
true
447
1
INTRODUCTION
1
7
[ "b7", "b15", "b16", "b17" ]
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
At the G-rich telomere tails, the presence of G4 DNA inhibits extension by telomerase, and proteins that bind specifically to telomeric sequences regulate the formation and resolution of G4 DNA (7–15).
[ "7", "15", "16", "17" ]
201
2,636
0
false
At the G-rich telomere tails, the presence of G4 DNA inhibits extension by telomerase, and proteins that bind specifically to telomeric sequences regulate the formation and resolution of G4 DNA.
[ "7–15" ]
At the G-rich telomere tails, the presence of G4 DNA inhibits extension by telomerase, and proteins that bind specifically to telomeric sequences regulate the formation and resolution of G4 DNA.
true
true
true
true
true
447
1
INTRODUCTION
1
7
[ "b7", "b15", "b16", "b17" ]
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
The G-rich immunoglobulin switch regions are sites of recombination that is critical to B-cell development and the immune response, and regulated transcription of the switch regions induces the formation of DNA structures targeted by factors essential to class switch recombination (16,17).
[ "7", "15", "16", "17" ]
290
2,637
0
false
The G-rich immunoglobulin switch regions are sites of recombination that is critical to B-cell development and the immune response, and regulated transcription of the switch regions induces the formation of DNA structures targeted by factors essential to class switch recombination.
[ "16,17" ]
The G-rich immunoglobulin switch regions are sites of recombination that is critical to B-cell development and the immune response, and regulated transcription of the switch regions induces the formation of DNA structures targeted by factors essential to class switch recombination.
true
true
true
true
true
447
2
INTRODUCTION
1
18
[ "b18", "b19", "b20", "b21", "b22", "b23" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
G-rich regions can also be sites of unprogrammed genomic instability.
[ "18", "19", "20", "21", "22", "23" ]
69
2,638
0
false
G-rich regions can also be sites of unprogrammed genomic instability.
[]
G-rich regions can also be sites of unprogrammed genomic instability.
true
true
true
true
true
448
2
INTRODUCTION
1
18
[ "b18", "b19", "b20", "b21", "b22", "b23" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Many B-cell lymphomas carry a translocation of the MYC proto-oncogene to the immunoglobulin heavy chain switch region (18), and the common translocation breakpoints map to G-rich regions of MYC that form structures similar to those formed by transcribed G-rich switch regions (19,20).
[ "18", "19", "20", "21", "22", "23" ]
284
2,639
1
false
Many B-cell lymphomas carry a translocation of the MYC proto-oncogene to the immunoglobulin heavy chain switch region, and the common translocation breakpoints map to G-rich regions of MYC that form structures similar to those formed by transcribed G-rich switch regions.
[ "18", "19,20" ]
Many B-cell lymphomas carry a translocation of the MYC proto-oncogene to the immunoglobulin heavy chain switch region, and the common translocation breakpoints map to G-rich regions of MYC that form structures similar to those formed by transcribed G-rich switch regions.
true
true
true
true
true
448
2
INTRODUCTION
1
21
[ "b18", "b19", "b20", "b21", "b22", "b23" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Some of the most unstable human minisatellites are G-rich sequences predicted to form G4 DNA (21); and G4 DNA formation in vitro has been directly confirmed for two G-rich VNTRs, D4S43, and the insulin-linked hypervariable repeat (22).
[ "18", "19", "20", "21", "22", "23" ]
235
2,640
1
false
Some of the most unstable human minisatellites are G-rich sequences predicted to form G4 DNA ; and G4 DNA formation in vitro has been directly confirmed for two G-rich VNTRs, D4S43, and the insulin-linked hypervariable repeat.
[ "21", "22" ]
Some of the most unstable human minisatellites are G-rich sequences predicted to form G4 DNA ; and G4 DNA formation in vitro has been directly confirmed for two G-rich VNTRs, D4S43, and the insulin-linked hypervariable repeat.
true
true
true
true
true
448
2
INTRODUCTION
1
23
[ "b18", "b19", "b20", "b21", "b22", "b23" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Reporter constructs carrying interstitial telomeric repeats display high levels of instability (23), which may be analogous to the instability of G-rich VNTRs.
[ "18", "19", "20", "21", "22", "23" ]
159
2,641
1
false
Reporter constructs carrying interstitial telomeric repeats display high levels of instability, which may be analogous to the instability of G-rich VNTRs.
[ "23" ]
Reporter constructs carrying interstitial telomeric repeats display high levels of instability, which may be analogous to the instability of G-rich VNTRs.
true
true
true
true
true
448
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Specialized mechanisms may regulate the expression of G-rich genes at the levels of transcription, RNA processing and translation.
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
130
2,642
0
false
Specialized mechanisms may regulate the expression of G-rich genes at the levels of transcription, RNA processing and translation.
[]
Specialized mechanisms may regulate the expression of G-rich genes at the levels of transcription, RNA processing and translation.
true
true
true
true
true
449
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Cotranscriptional RNA:DNA hybrid formation occurs readily within G-rich regions (19,24,25).
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
91
2,643
0
false
Cotranscriptional RNA:DNA hybrid formation occurs readily within G-rich regions.
[ "19,24,25" ]
Cotranscriptional RNA:DNA hybrid formation occurs readily within G-rich regions.
true
true
true
true
true
449
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Factors associated with RNA processing pathways, including THO/TREX and ASF/SF2, normally prevent cotranscriptional RNA:DNA hybrid formation, and promote gene expression; and genomic instability ensues in their absence (26,27).
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
227
2,644
0
false
Factors associated with RNA processing pathways, including THO/TREX and ASF/SF2, normally prevent cotranscriptional RNA:DNA hybrid formation, and promote gene expression; and genomic instability ensues in their absence.
[ "26,27" ]
Factors associated with RNA processing pathways, including THO/TREX and ASF/SF2, normally prevent cotranscriptional RNA:DNA hybrid formation, and promote gene expression; and genomic instability ensues in their absence.
true
true
true
true
true
449
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Factors involved in translational regulation may target RNA transcripts that contain G-quartets (28,29).
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
104
2,645
0
false
Factors involved in translational regulation may target RNA transcripts that contain G-quartets.
[ "28,29" ]
Factors involved in translational regulation may target RNA transcripts that contain G-quartets.
true
true
true
true
true
449
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Regions with the potential to form G4 DNA have been identified in the promoters of several proto-oncogenes, including c-MYC, VEGF, c-KIT and BCL2 (30–33).
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
154
2,646
0
false
Regions with the potential to form G4 DNA have been identified in the promoters of several proto-oncogenes, including c-MYC, VEGF, c-KIT and BCL2.
[ "30–33" ]
Regions with the potential to form G4 DNA have been identified in the promoters of several proto-oncogenes, including c-MYC, VEGF, c-KIT and BCL2.
true
true
true
true
true
449
3
INTRODUCTION
1
19
[ "b19", "b24", "b25", "b26", "b27", "b28", "b29", "b30", "b33", "b34", "b39" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
This has led to suggestions that formation or resolution of specific quadruplex structures may contribute to the regulation of gene expression, and prompted the design of therapeutics targeted to these structures, but the biological specificity of such compounds is yet to be established rigorously (34–39).
[ "19", "24", "25", "26", "27", "28", "29", "30", "33", "34", "39" ]
307
2,647
0
false
This has led to suggestions that formation or resolution of specific quadruplex structures may contribute to the regulation of gene expression, and prompted the design of therapeutics targeted to these structures, but the biological specificity of such compounds is yet to be established rigorously.
[ "34–39" ]
This has led to suggestions that formation or resolution of specific quadruplex structures may contribute to the regulation of gene expression, and prompted the design of therapeutics targeted to these structures, but the biological specificity of such compounds is yet to be established rigorously.
true
true
true
true
true
449
4
INTRODUCTION
1
42
[ "b40", "b41", "b42", "b16", "b43", "b44", "b45", "b46", "b16" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
Conserved and ubiquitous repair factors recognize G4 DNA, including the human RecQ family helicases BLM and WRN (40,41); the Saccharomyces cerevisiae RecQ family helicase Sgs1 (42); and the mismatch repair factor MutSΞ±, a heterodimer of MSH2/MSH6 (16).
[ "40", "41", "42", "16", "43", "44", "45", "46", "16" ]
252
2,648
1
false
Conserved and ubiquitous repair factors recognize G4 DNA, including the human RecQ family helicases BLM and WRN ; the Saccharomyces cerevisiae RecQ family helicase Sgs1 ; and the mismatch repair factor MutSΞ±, a heterodimer of MSH2/MSH6.
[ "40,41", "42", "16" ]
Conserved and ubiquitous repair factors recognize G4 DNA, including the human RecQ family helicases BLM and WRN ; the Saccharomyces cerevisiae RecQ family helicase Sgs1 ; and the mismatch repair factor MutSΞ±, a heterodimer of MSH2/MSH6.
true
true
true
true
true
450
4
INTRODUCTION
1
40
[ "b40", "b41", "b42", "b16", "b43", "b44", "b45", "b46", "b16" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
RecQ family helicases maintain G-rich regions during replication.
[ "40", "41", "42", "16", "43", "44", "45", "46", "16" ]
65
2,649
0
false
RecQ family helicases maintain G-rich regions during replication.
[]
RecQ family helicases maintain G-rich regions during replication.
true
true
true
true
true
450
4
INTRODUCTION
1
45
[ "b40", "b41", "b42", "b16", "b43", "b44", "b45", "b46", "b16" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
Sgs1 is required for nucleolar stability and replication of the G-rich rDNA (43,44); and in the absence of WRN helicase, telomeric sequence is lost due to impaired replication of the G-rich strand (45).
[ "40", "41", "42", "16", "43", "44", "45", "46", "16" ]
202
2,650
1
false
Sgs1 is required for nucleolar stability and replication of the G-rich rDNA ; and in the absence of WRN helicase, telomeric sequence is lost due to impaired replication of the G-rich strand.
[ "43,44", "45" ]
Sgs1 is required for nucleolar stability and replication of the G-rich rDNA ; and in the absence of WRN helicase, telomeric sequence is lost due to impaired replication of the G-rich strand.
true
true
true
true
true
450
4
INTRODUCTION
1
46
[ "b40", "b41", "b42", "b16", "b43", "b44", "b45", "b46", "b16" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
The mismatch repair factor, MutSΞ±, may cooperate with BLM helicase to promote the resolution of G4 DNA during replication (46).
[ "40", "41", "42", "16", "43", "44", "45", "46", "16" ]
127
2,651
1
false
The mismatch repair factor, MutSΞ±, may cooperate with BLM helicase to promote the resolution of G4 DNA during replication.
[ "46" ]
The mismatch repair factor, MutSΞ±, may cooperate with BLM helicase to promote the resolution of G4 DNA during replication.
true
true
true
true
true
450
4
INTRODUCTION
1
16
[ "b40", "b41", "b42", "b16", "b43", "b44", "b45", "b46", "b16" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
In immunoglobulin switch recombination, MutSΞ± recognizes G4 DNA formed during transcription of the G-rich switch regions to promote their synapsis and recombination (16).
[ "40", "41", "42", "16", "43", "44", "45", "46", "16" ]
170
2,652
1
false
In immunoglobulin switch recombination, MutSΞ± recognizes G4 DNA formed during transcription of the G-rich switch regions to promote their synapsis and recombination.
[ "16" ]
In immunoglobulin switch recombination, MutSΞ± recognizes G4 DNA formed during transcription of the G-rich switch regions to promote their synapsis and recombination.
true
true
true
true
true
450
5
INTRODUCTION
1
4
[ "b4", "b5" ]
16,914,419
pmid-16641317|pmid-15914667
Genomic regions with potential to form G4 DNA have been enumerated (4,5), but they have not been correlated with specific gene functions.
[ "4", "5" ]
137
2,653
0
false
Genomic regions with potential to form G4 DNA have been enumerated, but they have not been correlated with specific gene functions.
[ "4,5" ]
Genomic regions with potential to form G4 DNA have been enumerated, but they have not been correlated with specific gene functions.
true
true
true
true
true
451
5
INTRODUCTION
1
4
[ "b4", "b5" ]
16,914,419
pmid-16641317|pmid-15914667
The link between potential for G4 DNA formation and genomic instability suggests that the identification of human genes with relatively high or low potential to form G4 DNA might provide insights into the evolution of genomic structure, or identify mechanisms that could account for genomic instability in human malignan...
[ "4", "5" ]
325
2,654
0
false
The link between potential for G4 DNA formation and genomic instability suggests that the identification of human genes with relatively high or low potential to form G4 DNA might provide insights into the evolution of genomic structure, or identify mechanisms that could account for genomic instability in human malignan...
[]
The link between potential for G4 DNA formation and genomic instability suggests that the identification of human genes with relatively high or low potential to form G4 DNA might provide insights into the evolution of genomic structure, or identify mechanisms that could account for genomic instability in human malignan...
true
true
true
true
true
451
5
INTRODUCTION
1
4
[ "b4", "b5" ]
16,914,419
pmid-16641317|pmid-15914667
The possibility that G-richness can contribute to shared regulation suggests that genes with similar or related functions may share features of genomic structure.
[ "4", "5" ]
162
2,655
0
false
The possibility that G-richness can contribute to shared regulation suggests that genes with similar or related functions may share features of genomic structure.
[]
The possibility that G-richness can contribute to shared regulation suggests that genes with similar or related functions may share features of genomic structure.
true
true
true
true
true
451
5
INTRODUCTION
1
4
[ "b4", "b5" ]
16,914,419
pmid-16641317|pmid-15914667
We therefore set out to determine the prevalence of G-rich sequences capable of forming G4 DNA among human genes, and to determine if particular functional classes of genes might be characterized by the presence or absence of G-rich regions.
[ "4", "5" ]
241
2,656
0
false
We therefore set out to determine the prevalence of G-rich sequences capable of forming G4 DNA among human genes, and to determine if particular functional classes of genes might be characterized by the presence or absence of G-rich regions.
[]
We therefore set out to determine the prevalence of G-rich sequences capable of forming G4 DNA among human genes, and to determine if particular functional classes of genes might be characterized by the presence or absence of G-rich regions.
true
true
true
true
true
451
0
DISCUSSION
0
null
null
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
We have investigated the relationship between potential to form G4 DNA and gene function for the 16 654 human RefSeq genes.
null
123
2,657
0
false
null
null
We have investigated the relationship between potential to form G4 DNA and gene function for the 16 654 human RefSeq genes.
true
true
true
true
true
452
0
DISCUSSION
0
null
null
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
We find that there is a highly skewed distribution of G4P among human genes, and that there are robust correlations between G4P and gene function.
null
146
2,658
0
false
null
null
We find that there is a highly skewed distribution of G4P among human genes, and that there are robust correlations between G4P and gene function.
true
true
true
true
true
452
0
DISCUSSION
0
null
null
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
Interrogation of the subset of 218 GO terms assigned to 50 or more genes showed that low G4P corresponds with functions including G-protein-coupled receptors, olfaction, nucleosome assembly, nucleic acid binding, ubiquitin cycle, cell adhesion and cell division; and high G4P with functions including transcription facto...
null
390
2,659
0
false
null
null
Interrogation of the subset of 218 GO terms assigned to 50 or more genes showed that low G4P corresponds with functions including G-protein-coupled receptors, olfaction, nucleosome assembly, nucleic acid binding, ubiquitin cycle, cell adhesion and cell division; and high G4P with functions including transcription facto...
true
true
true
true
true
452
0
DISCUSSION
0
null
null
16,914,419
pmid-3393228|pmid-13947099|pmid-16714104|pmid-16641317|pmid-15914667|pmid-15914666
These findings motivated interrogation of two contrasting gene categories defined by the OMIM database, tumor suppressor genes and proto-oncogenes, which showed that genes in these categories are distinguished by low and high G4P, respectively (Figure 3).
null
255
2,660
0
false
null
null
These findings motivated interrogation of two contrasting gene categories defined by the OMIM database, tumor suppressor genes and proto-oncogenes, which showed that genes in these categories are distinguished by low and high G4P, respectively (Figure 3).
true
true
true
true
true
452
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
In contrast to the robust relationship between G4P and gene function, G4P did not correspond to any of several well-established parameters used to characterize genomic structure.
null
178
2,661
0
false
null
null
In contrast to the robust relationship between G4P and gene function, G4P did not correspond to any of several well-established parameters used to characterize genomic structure.
true
true
true
true
true
453
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
G4P does correlate with GC-content, but not with the number of CpG islands (Figure 4).
null
86
2,662
0
false
null
null
G4P does correlate with GC-content, but not with the number of CpG islands (Figure 4).
true
true
true
true
true
453
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
Both exons and introns contribute to the difference in G4P between tumor suppressor genes and proto-oncogenes (Figure 5).
null
121
2,663
0
false
null
null
Both exons and introns contribute to the difference in G4P between tumor suppressor genes and proto-oncogenes (Figure 5).
true
true
true
true
true
453
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
Furthermore, G4P does not reflect the local genomic environment (Figure 6).
null
75
2,664
0
false
null
null
Furthermore, G4P does not reflect the local genomic environment (Figure 6).
true
true
true
true
true
453
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
In fact, tumor suppressor genes have much lower G4P than would be predicted by their genomic environment as compared to the RefSeq genes, whereas proto-oncogenes have higher G4P than would be predicted.
null
202
2,665
0
false
null
null
In fact, tumor suppressor genes have much lower G4P than would be predicted by their genomic environment as compared to the RefSeq genes, whereas proto-oncogenes have higher G4P than would be predicted.
true
true
true
true
true
453
1
DISCUSSION
0
null
null
16,914,419
pmid-2023635|pmid-16603717|pmid-16285851|pmid-15753043
The most straightforward interpretation of these results is that genes with specific functions have undergone selection based on G4P.
null
133
2,666
0
false
null
null
The most straightforward interpretation of these results is that genes with specific functions have undergone selection based on G4P.
true
true
true
true
true
453
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
One source of selective pressure that could contribute to determining G4P is suggested by the association between G-rich regions and genomic instability.
[ "56", "25", "26" ]
153
2,667
0
false
One source of selective pressure that could contribute to determining G4P is suggested by the association between G-rich regions and genomic instability.
[]
One source of selective pressure that could contribute to determining G4P is suggested by the association between G-rich regions and genomic instability.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Transcription-induced or replication-induced DNA structures can form within regions of high G4P, and if these structures are not faithfully resolved, the result may be genomic instability and impaired gene function.
[ "56", "25", "26" ]
215
2,668
0
false
Transcription-induced or replication-induced DNA structures can form within regions of high G4P, and if these structures are not faithfully resolved, the result may be genomic instability and impaired gene function.
[]
Transcription-induced or replication-induced DNA structures can form within regions of high G4P, and if these structures are not faithfully resolved, the result may be genomic instability and impaired gene function.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
In this view, the low G4P of tumor suppressor genes could reflect evolution that minimized potential instability of genes which function to maintain genomic stability.
[ "56", "25", "26" ]
167
2,669
0
false
In this view, the low G4P of tumor suppressor genes could reflect evolution that minimized potential instability of genes which function to maintain genomic stability.
[]
In this view, the low G4P of tumor suppressor genes could reflect evolution that minimized potential instability of genes which function to maintain genomic stability.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
There is considerable evidence for haploinsufficiency of tumor suppressor genes [reviewed in (56)], and this would contribute to pressure to minimize genomic instability.
[ "56", "25", "26" ]
170
2,670
0
false
There is considerable evidence for haploinsufficiency of tumor suppressor genes, and this would contribute to pressure to minimize genomic instability.
[ "reviewed in (56)" ]
There is considerable evidence for haploinsufficiency of tumor suppressor genes, and this would contribute to pressure to minimize genomic instability.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Conversely, the high G4P that characterizes the proto-oncogenes would be predicted to contribute to their destabilization.
[ "56", "25", "26" ]
122
2,671
0
false
Conversely, the high G4P that characterizes the proto-oncogenes would be predicted to contribute to their destabilization.
[]
Conversely, the high G4P that characterizes the proto-oncogenes would be predicted to contribute to their destabilization.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Could instability provide a selective advantage?
[ "56", "25", "26" ]
48
2,672
0
false
Could instability provide a selective advantage?
[]
Could instability provide a selective advantage?
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Under some circumstances, it may.
[ "56", "25", "26" ]
33
2,673
0
false
Under some circumstances, it may.
[]
Under some circumstances, it may.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Proto-oncogenes are transcribed in rapidly dividing cells and tissues.
[ "56", "25", "26" ]
70
2,674
0
false
Proto-oncogenes are transcribed in rapidly dividing cells and tissues.
[]
Proto-oncogenes are transcribed in rapidly dividing cells and tissues.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Transcription-induced structures have considerable potential to contribute to genomic instability (25,26), but they can form only within genes, which represent a relatively small fraction of genomic DNA.
[ "56", "25", "26" ]
203
2,675
0
false
Transcription-induced structures have considerable potential to contribute to genomic instability, but they can form only within genes, which represent a relatively small fraction of genomic DNA.
[ "25,26" ]
Transcription-induced structures have considerable potential to contribute to genomic instability, but they can form only within genes, which represent a relatively small fraction of genomic DNA.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
The high G4P of the proto-oncogenes would make them targets for transcription-induced destabilization.
[ "56", "25", "26" ]
102
2,676
0
false
The high G4P of the proto-oncogenes would make them targets for transcription-induced destabilization.
[]
The high G4P of the proto-oncogenes would make them targets for transcription-induced destabilization.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Proto-oncogenes encode key factors that promote cell proliferation and development, and impaired expression of a proto-oncogene could in turn diminish or prevent cell proliferation, either by decreasing expression of an essential factor, or signaling cell death via apoptosis.
[ "56", "25", "26" ]
276
2,677
0
false
Proto-oncogenes encode key factors that promote cell proliferation and development, and impaired expression of a proto-oncogene could in turn diminish or prevent cell proliferation, either by decreasing expression of an essential factor, or signaling cell death via apoptosis.
[]
Proto-oncogenes encode key factors that promote cell proliferation and development, and impaired expression of a proto-oncogene could in turn diminish or prevent cell proliferation, either by decreasing expression of an essential factor, or signaling cell death via apoptosis.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
Proto-oncogenes may therefore carry out a passive surveillance function, monitoring instability that specifically affected the transcribed fraction of the genome.
[ "56", "25", "26" ]
162
2,678
0
false
Proto-oncogenes may therefore carry out a passive surveillance function, monitoring instability that specifically affected the transcribed fraction of the genome.
[]
Proto-oncogenes may therefore carry out a passive surveillance function, monitoring instability that specifically affected the transcribed fraction of the genome.
true
true
true
true
true
454
2
DISCUSSION
1
56
[ "b56", "b25", "b26" ]
16,914,419
pmid-11460166|pmid-15231739|pmid-15940261|pmid-3482146|pmid-9083093|pmid-11113187|pmid-16150895|pmid-12475983|pmid-14527416
This surveillance function would necessarily be vested in genes, rather than in the vast landscape of nontranscribed sequences, consistent with the clear differences between G4P of genes and their flanking sequences.
[ "56", "25", "26" ]
216
2,679
0
false
This surveillance function would necessarily be vested in genes, rather than in the vast landscape of nontranscribed sequences, consistent with the clear differences between G4P of genes and their flanking sequences.
[]
This surveillance function would necessarily be vested in genes, rather than in the vast landscape of nontranscribed sequences, consistent with the clear differences between G4P of genes and their flanking sequences.
true
true
true
true
true
454
3
DISCUSSION
1
29
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Another mechanism that may contribute to selection based on G4P is shared regulation.
[ "29", "32", "28", "57", "4" ]
85
2,680
0
false
Another mechanism that may contribute to selection based on G4P is shared regulation.
[]
Another mechanism that may contribute to selection based on G4P is shared regulation.
true
true
true
true
true
455
3
DISCUSSION
1
29
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Sequences within promoter regions of several proto-oncogenes have been shown to form G4 DNA in vitro (29–32), and factors that bind G4 DNA have been implicated in both transcriptional and translational regulation (28,57).
[ "29", "32", "28", "57", "4" ]
221
2,681
0
false
Sequences within promoter regions of several proto-oncogenes have been shown to form G4 DNA in vitro, and factors that bind G4 DNA have been implicated in both transcriptional and translational regulation.
[ "29–32", "28,57" ]
Sequences within promoter regions of several proto-oncogenes have been shown to form G4 DNA in vitro, and factors that bind G4 DNA have been implicated in both transcriptional and translational regulation.
true
true
true
true
true
455
3
DISCUSSION
1
29
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
However, regulatory factors typically exert their effects within limited genomic regions, so commonality of short cis-regulatory elements is unlikely to provide a complete explanation for a feature of sequence composition that distinguishes both exons and introns, and extends throughout a gene (Figure 5).
[ "29", "32", "28", "57", "4" ]
306
2,682
0
false
However, regulatory factors typically exert their effects within limited genomic regions, so commonality of short cis-regulatory elements is unlikely to provide a complete explanation for a feature of sequence composition that distinguishes both exons and introns, and extends throughout a gene (Figure 5).
[]
However, regulatory factors typically exert their effects within limited genomic regions, so commonality of short cis-regulatory elements is unlikely to provide a complete explanation for a feature of sequence composition that distinguishes both exons and introns, and extends throughout a gene (Figure 5).
true
true
true
true
true
455
3
DISCUSSION
1
29
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Similarly, G4P is unlikely to reflect selection for coding capacity, as this sort of selection would affect exons alone.
[ "29", "32", "28", "57", "4" ]
120
2,683
0
false
Similarly, G4P is unlikely to reflect selection for coding capacity, as this sort of selection would affect exons alone.
[]
Similarly, G4P is unlikely to reflect selection for coding capacity, as this sort of selection would affect exons alone.
true
true
true
true
true
455
3
DISCUSSION
1
29
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Nonetheless, there does appear to be some selection against regions of high G4P within exons, as in both gene categories, the median G4P of exons was lower than for introns: 1.9% versus 2.4% for tumor suppressor genes; and 7.6% versus 11% for proto-oncogenes (Figures 3B and 5).
[ "29", "32", "28", "57", "4" ]
278
2,684
0
false
Nonetheless, there does appear to be some selection against regions of high G4P within exons, as in both gene categories, the median G4P of exons was lower than for introns: 1.9% versus 2.4% for tumor suppressor genes; and 7.6% versus 11% for proto-oncogenes (Figures 3B and 5).
[]
Nonetheless, there does appear to be some selection against regions of high G4P within exons, as in both gene categories, the median G4P of exons was lower than for introns: 1.9% versus 2.4% for tumor suppressor genes; and 7.6% versus 11% for proto-oncogenes (Figures 3B and 5).
true
true
true
true
true
455
3
DISCUSSION
1
4
[ "b29", "b32", "b28", "b57", "b4" ]
16,914,419
pmid-15231739|pmid-1701219|pmid-12475983|pmid-14527416|pmid-16096057|pmid-15805463|pmid-11719189|pmid-9469822|pmid-16433524|pmid-12540745|pmid-16687659|pmid-11719189|pmid-16045346|pmid-15805463|pmid-11070077|pmid-16641317
Thus high G4P may be disfavored in mature RNAs, as has been proposed previously (4); or incompatible with efficient translation or effective coding.
[ "29", "32", "28", "57", "4" ]
148
2,685
1
false
Thus high G4P may be disfavored in mature RNAs, as has been proposed previously ; or incompatible with efficient translation or effective coding.
[ "4" ]
Thus high G4P may be disfavored in mature RNAs, as has been proposed previously ; or incompatible with efficient translation or effective coding.
true
true
true
true
true
455
4
DISCUSSION
1
61
[ "b58", "b60", "b61" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
Several lines of evidence suggest that GC-content may broadly correlate with gene expression levels (58–60); in particular, GC-richness correlates with open chromatin structure, which may in turn facilitate transcription (61).
[ "58", "60", "61" ]
226
2,686
1
false
Several lines of evidence suggest that GC-content may broadly correlate with gene expression levels ; in particular, GC-richness correlates with open chromatin structure, which may in turn facilitate transcription.
[ "58–60", "61" ]
Several lines of evidence suggest that GC-content may broadly correlate with gene expression levels ; in particular, GC-richness correlates with open chromatin structure, which may in turn facilitate transcription.
true
true
true
true
true
456
4
DISCUSSION
1
58
[ "b58", "b60", "b61" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
Proto-oncogenes are rapidly transcribed during early development and in response to cell activation, and the high G4P of the proto-oncogenes might reflect GC-richness that contributes to high transcription levels of genes in this group.
[ "58", "60", "61" ]
236
2,687
0
false
Proto-oncogenes are rapidly transcribed during early development and in response to cell activation, and the high G4P of the proto-oncogenes might reflect GC-richness that contributes to high transcription levels of genes in this group.
[]
Proto-oncogenes are rapidly transcribed during early development and in response to cell activation, and the high G4P of the proto-oncogenes might reflect GC-richness that contributes to high transcription levels of genes in this group.
true
true
true
true
true
456
4
DISCUSSION
1
58
[ "b58", "b60", "b61" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
The finding that potential for G4 DNA formation correlates robustly with specific gene functions suggests that G4P may be a useful parameter to include in global analyses of gene expression, regulation and interactions.
[ "58", "60", "61" ]
219
2,688
0
false
The finding that potential for G4 DNA formation correlates robustly with specific gene functions suggests that G4P may be a useful parameter to include in global analyses of gene expression, regulation and interactions.
[]
The finding that potential for G4 DNA formation correlates robustly with specific gene functions suggests that G4P may be a useful parameter to include in global analyses of gene expression, regulation and interactions.
true
true
true
true
true
456
4
DISCUSSION
1
58
[ "b58", "b60", "b61" ]
16,914,419
pmid-12235379|pmid-10212265|pmid-10198430|pmid-16285851|pmid-9428525|pmid-12682026|pmid-15591207|pmid-15064730|pmid-16285851|pmid-12915492|pmid-15590696|pmid-15339661
Systems-based analyses of this sort should establish whether regulation could contribute to selection based on G4P.
[ "58", "60", "61" ]
115
2,689
0
false
Systems-based analyses of this sort should establish whether regulation could contribute to selection based on G4P.
[]
Systems-based analyses of this sort should establish whether regulation could contribute to selection based on G4P.
true
true
true
true
true
456
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,935,884
pmid-12621862|pmid-15128295
Helicases and DNA translocases are motors that move along or pump DNA by converting the energy from NTP (or dNTP) hydrolysis into mechanical work (1–4).
[ "1", "4" ]
152
2,690
0
false
Helicases and DNA translocases are motors that move along or pump DNA by converting the energy from NTP (or dNTP) hydrolysis into mechanical work.
[ "1–4" ]
Helicases and DNA translocases are motors that move along or pump DNA by converting the energy from NTP (or dNTP) hydrolysis into mechanical work.
true
true
true
true
true
457
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,935,884
pmid-12621862|pmid-15128295
The amount of energy available from one such reaction, under physiological conditions, is about 20 kBT (kB is Boltzmann's constant and T ∼ 300 K at room temperature; 20 kBT ∼ 8 Γ— 10βˆ’20 J ∼ 80 pN.nm ∼ 12 kcal/mol).
[ "1", "4" ]
213
2,691
0
false
The amount of energy available from one such reaction, under physiological conditions, is about 20 kBT.
[ "kB is Boltzmann's constant and T ∼ 300 K at room temperature; 20 kBT ∼ 8 Γ— 10βˆ’20 J ∼ 80 pN.nm ∼ 12 kcal/mol" ]
The amount of energy available from one such reaction, under physiological conditions, is about 20 kBT.
true
true
true
true
true
457
0
INTRODUCTION
1
1
[ "b1", "b4" ]
16,935,884
pmid-12621862|pmid-15128295
The distance traveled by these motors during an enzymatic cycle is a few base pairs (∼1 nm); thus, at 100% efficiency, the motors can generate maximum forces of tens of picoNewtons.
[ "1", "4" ]
181
2,692
0
false
The distance traveled by these motors during an enzymatic cycle is a few base pairs ; thus, at 100% efficiency, the motors can generate maximum forces of tens of picoNewtons.
[ "∼1 nm" ]
The distance traveled by these motors during an enzymatic cycle is a few base pairs ; thus, at 100% efficiency, the motors can generate maximum forces of tens of picoNewtons.
true
true
true
true
true
457
1
INTRODUCTION
1
5
[ "b5", "b10", "b11", "b12", "b14", "b15", "b16", "b17", "b18", "b9", "b19", "b20", "b21", "b22" ]
16,935,884
pmid-15749023|pmid-16251956|NA|pmid-11201749|pmid-7696485|pmid-7939660|pmid-7647261|pmid-8628993|pmid-1830130|pmid-11201750|pmid-16878180|pmid-12023254|NA|NA
How these translocases convert the chemical energy derived from ATP hydrolysis into mechanical work is a question that has been addressed through various single molecule techniques.
[ "5", "10", "11", "12", "14", "15", "16", "17", "18", "9", "19", "20", "21", "22" ]
181
2,693
0
false
How these translocases convert the chemical energy derived from ATP hydrolysis into mechanical work is a question that has been addressed through various single molecule techniques.
[]
How these translocases convert the chemical energy derived from ATP hydrolysis into mechanical work is a question that has been addressed through various single molecule techniques.
true
true
true
true
true
458
1
INTRODUCTION
1
5
[ "b5", "b10", "b11", "b12", "b14", "b15", "b16", "b17", "b18", "b9", "b19", "b20", "b21", "b22" ]
16,935,884
pmid-15749023|pmid-16251956|NA|pmid-11201749|pmid-7696485|pmid-7939660|pmid-7647261|pmid-8628993|pmid-1830130|pmid-11201750|pmid-16878180|pmid-12023254|NA|NA
Fluorescence techniques, such as FRET, allow one to detect and measure translocase activity at the single molecule level (5–10), see also the review by Rasnik et al.
[ "5", "10", "11", "12", "14", "15", "16", "17", "18", "9", "19", "20", "21", "22" ]
165
2,694
0
false
Fluorescence techniques, such as FRET, allow one to detect and measure translocase activity at the single molecule level, see also the review by Rasnik et al.
[ "5–10" ]
Fluorescence techniques, such as FRET, allow one to detect and measure translocase activity at the single molecule level, see also the review by Rasnik et al.
true
true
true
true
true
458
1
INTRODUCTION
1
11
[ "b5", "b10", "b11", "b12", "b14", "b15", "b16", "b17", "b18", "b9", "b19", "b20", "b21", "b22" ]
16,935,884
pmid-15749023|pmid-16251956|NA|pmid-11201749|pmid-7696485|pmid-7939660|pmid-7647261|pmid-8628993|pmid-1830130|pmid-11201750|pmid-16878180|pmid-12023254|NA|NA
in this issue (11).
[ "5", "10", "11", "12", "14", "15", "16", "17", "18", "9", "19", "20", "21", "22" ]
19
2,695
1
false
in this issue.
[ "11" ]
in this issue.
false
true
true
true
false
458
1
INTRODUCTION
1
15
[ "b5", "b10", "b11", "b12", "b14", "b15", "b16", "b17", "b18", "b9", "b19", "b20", "b21", "b22" ]
16,935,884
pmid-15749023|pmid-16251956|NA|pmid-11201749|pmid-7696485|pmid-7939660|pmid-7647261|pmid-8628993|pmid-1830130|pmid-11201750|pmid-16878180|pmid-12023254|NA|NA
In addition, numerous single molecule manipulation methods have been developed, such as tethered particle motion (TPM) (12–14), atomic force microscopy (15), biomembrane force probe (16), glass microfiber manipulation (17,18), flow induced force (9), optical (19) and magnetic tweezers (20)
[ "5", "10", "11", "12", "14", "15", "16", "17", "18", "9", "19", "20", "21", "22" ]
290
2,696
1
false
In addition, numerous single molecule manipulation methods have been developed, such as tethered particle motion (TPM), atomic force microscopy, biomembrane force probe, glass microfiber manipulation, flow induced force, optical and magnetic tweezers
[ "12–14", "15", "16", "17,18", "9", "19", "20" ]
In addition, numerous single molecule manipulation methods have been developed, such as tethered particle motion (TPM), atomic force microscopy, biomembrane force probe, glass microfiber manipulation, flow induced force, optical and magnetic tweezers
true
true
false
true
false
458
1
INTRODUCTION
1
5
[ "b5", "b10", "b11", "b12", "b14", "b15", "b16", "b17", "b18", "b9", "b19", "b20", "b21", "b22" ]
16,935,884
pmid-15749023|pmid-16251956|NA|pmid-11201749|pmid-7696485|pmid-7939660|pmid-7647261|pmid-8628993|pmid-1830130|pmid-11201750|pmid-16878180|pmid-12023254|NA|NA
[see (21,22) and references therein].
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37
2,697
0
false
.
[ "see (21,22) and references therein" ]
.
false
false
true
true
false
458
2
INTRODUCTION
1
23
[ "b23", "b31", "b32" ]
16,935,884
pmid-15292508|pmid-15821742|pmid-15189157
Using these methods (except the TPM) one can apply a picoNewton force on the motor or its DNA substrate.
[ "23", "31", "32" ]
104
2,698
0
false
Using these methods (except the TPM) one can apply a picoNewton force on the motor or its DNA substrate.
[]
Using these methods (except the TPM) one can apply a picoNewton force on the motor or its DNA substrate.
true
true
true
true
true
459
2
INTRODUCTION
1
23
[ "b23", "b31", "b32" ]
16,935,884
pmid-15292508|pmid-15821742|pmid-15189157
Single-particle tracking offers nanometer resolution of the changes in DNA length (or enzyme position) resulting from translocase activity, thus allowing real-time detection of enzymatic dynamics (23–31).
[ "23", "31", "32" ]
204
2,699
0
false
Single-particle tracking offers nanometer resolution of the changes in DNA length (or enzyme position) resulting from translocase activity, thus allowing real-time detection of enzymatic dynamics.
[ "23–31" ]
Single-particle tracking offers nanometer resolution of the changes in DNA length (or enzyme position) resulting from translocase activity, thus allowing real-time detection of enzymatic dynamics.
true
true
true
true
true
459