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
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cited_id
string
sentences
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all_sent_cites
list
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sentence_batch_index
int64
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qc_fail
bool
cited_sentence
string
cites_in_sentence
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cln_sentence
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cit_qc
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lgtm
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__index_level_0__
int64
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
[The same is probably true for some other unicellular organisms, judging by the correlation between intron length and frequency of optimal codons (51)].
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
152
2,500
0
false
.
[ "The same is probably true for some other unicellular organisms, judging by the correlation between intron length and frequency of optimal codons (51)" ]
.
false
false
true
true
false
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
This fact indicates that in introns of unicellular organisms, the amount of activating elements outweigh the amount of suppressing ones.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
136
2,501
0
false
This fact indicates that in introns of unicellular organisms, the amount of activating elements outweigh the amount of suppressing ones.
[]
This fact indicates that in introns of unicellular organisms, the amount of activating elements outweigh the amount of suppressing ones.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
The fraction of non-housekeeping (i.e.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
38
2,502
0
false
The fraction of non-housekeeping (i.e.
[]
The fraction of non-housekeeping (i.e.
true
true
true
true
true
427
1
DISCUSSION
1
39
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
generally suppressed) genes is much lower in unicellular organisms, therefore there should be a lower amount of suppressing elements in their introns.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
150
2,503
0
false
generally suppressed) genes is much lower in unicellular organisms, therefore there should be a lower amount of suppressing elements in their introns.
[]
generally suppressed) genes is much lower in unicellular organisms, therefore there should be a lower amount of suppressing elements in their introns.
false
true
true
true
false
427
1
DISCUSSION
1
52
[ "b39", "b41", "b11", "b42", "b47", "b48", "b49", "b10", "b50", "b51", "b51", "b52" ]
17,062,620
pmid-15093836|pmid-16837531|pmid-16461636|pmid-12713906|pmid-16290135|pmid-12466286|pmid-14597721|pmid-15673716|pmid-16647254|pmid-11139289|pmid-11139289|pmid-3518949
The maximum chromatin condensation is 5-fold lower in yeast when compared with mammals (52), which suggests that yeast introns should be less loaded with chromatin-condensation function.
[ "39", "41", "11", "42", "47", "48", "49", "10", "50", "51", "51", "52" ]
186
2,504
1
false
The maximum chromatin condensation is 5-fold lower in yeast when compared with mammals, which suggests that yeast introns should be less loaded with chromatin-condensation function.
[ "52" ]
The maximum chromatin condensation is 5-fold lower in yeast when compared with mammals, which suggests that yeast introns should be less loaded with chromatin-condensation function.
true
true
true
true
true
427
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
It should be noted that the ‘selection for economy’ model comes in two flavors: ‘energy economy’ and ‘time economy’, which were contrasted in the case of human bi-directional genes (6,7).
[ "6", "7", "6", "7", "11", "53", "54" ]
187
2,505
0
false
It should be noted that the ‘selection for economy’ model comes in two flavors: ‘energy economy’ and ‘time economy’, which were contrasted in the case of human bi-directional genes.
[ "6,7" ]
It should be noted that the ‘selection for economy’ model comes in two flavors: ‘energy economy’ and ‘time economy’, which were contrasted in the case of human bi-directional genes.
true
true
true
true
true
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
The former was rejected in favor of the latter because antisense genes expressed are both shorter and narrower than corresponding sense genes (6,7).
[ "6", "7", "6", "7", "11", "53", "54" ]
148
2,506
0
false
The former was rejected in favor of the latter because antisense genes expressed are both shorter and narrower than corresponding sense genes.
[ "6,7" ]
The former was rejected in favor of the latter because antisense genes expressed are both shorter and narrower than corresponding sense genes.
true
true
true
true
true
428
2
DISCUSSION
1
11
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
However, the antisense genes can be miniaturized because they should be accommodated within the loci of the sense genes, which is consistent with the ‘genome design’ model (11).
[ "6", "7", "6", "7", "11", "53", "54" ]
177
2,507
1
false
However, the antisense genes can be miniaturized because they should be accommodated within the loci of the sense genes, which is consistent with the ‘genome design’ model.
[ "11" ]
However, the antisense genes can be miniaturized because they should be accommodated within the loci of the sense genes, which is consistent with the ‘genome design’ model.
true
true
true
true
true
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
(Also, their shorter length may be adequate for their function.)
[ "6", "7", "6", "7", "11", "53", "54" ]
64
2,508
0
false
(Also, their shorter length may be adequate for their function.)
[]
(Also, their shorter length may be adequate for their function.)
false
false
false
true
false
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
Moreover, in contrast to the energy economy, time economy is not additive in a piecemeal way
[ "6", "7", "6", "7", "11", "53", "54" ]
92
2,509
0
false
Moreover, in contrast to the energy economy, time economy is not additive in a piecemeal way
[]
Moreover, in contrast to the energy economy, time economy is not additive in a piecemeal way
true
true
false
true
false
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
[as in ‘beanbag genetics’ (53)].
[ "6", "7", "6", "7", "11", "53", "54" ]
32
2,510
0
false
.
[ "as in ‘beanbag genetics’ (53)" ]
.
false
false
true
true
false
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
In other words, the speed of an intracellular event probably cannot be changed without corresponding changes in other parts of the system.
[ "6", "7", "6", "7", "11", "53", "54" ]
138
2,511
0
false
In other words, the speed of an intracellular event probably cannot be changed without corresponding changes in other parts of the system.
[]
In other words, the speed of an intracellular event probably cannot be changed without corresponding changes in other parts of the system.
true
true
true
true
true
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
(Imagine an electronic circuit where some events are accelerated without adjustment of the others.)
[ "6", "7", "6", "7", "11", "53", "54" ]
99
2,512
0
false
(Imagine an electronic circuit where some events are accelerated without adjustment of the others.)
[]
(Imagine an electronic circuit where some events are accelerated without adjustment of the others.)
false
false
false
true
false
428
2
DISCUSSION
1
6
[ "b6", "b7", "b6", "b7", "b11", "b53", "b54" ]
17,062,620
pmid-15797613|pmid-16143605|pmid-15797613|pmid-16143605|pmid-16461636|pmid-11236977|pmid-15107854
Therefore, time economy is closer in sense to ‘genome design’ because in this case genomic structure should be selected as a system [for timing design (54)].
[ "6", "7", "6", "7", "11", "53", "54" ]
157
2,513
0
false
Therefore, time economy is closer in sense to ‘genome design’ because in this case genomic structure should be selected as a system.
[ "for timing design (54)" ]
Therefore, time economy is closer in sense to ‘genome design’ because in this case genomic structure should be selected as a system.
true
true
true
true
true
428
3
DISCUSSION
1
50
[ "b50", "b55", "b56", "b54", "b57", "b61" ]
17,062,620
pmid-16647254|pmid-12581658|pmid-15332082|pmid-15107854|pmid-14512615|pmid-16859507
The combinatorial control of gene expression involving cooperation of multiple transcription factors is now an emerging theme (50,55,56).
[ "50", "55", "56", "54", "57", "61" ]
137
2,514
0
false
The combinatorial control of gene expression involving cooperation of multiple transcription factors is now an emerging theme.
[ "50,55,56" ]
The combinatorial control of gene expression involving cooperation of multiple transcription factors is now an emerging theme.
true
true
true
true
true
429
3
DISCUSSION
1
50
[ "b50", "b55", "b56", "b54", "b57", "b61" ]
17,062,620
pmid-16647254|pmid-12581658|pmid-15332082|pmid-15107854|pmid-14512615|pmid-16859507
Due to the most complex choice of switch-on/off transition in the case of intermediately expressed genes (according to the information theory), regulation of these genes should be more complex.
[ "50", "55", "56", "54", "57", "61" ]
193
2,515
0
false
Due to the most complex choice of switch-on/off transition in the case of intermediately expressed genes (according to the information theory), regulation of these genes should be more complex.
[]
Due to the most complex choice of switch-on/off transition in the case of intermediately expressed genes (according to the information theory), regulation of these genes should be more complex.
true
true
true
true
true
429
3
DISCUSSION
1
50
[ "b50", "b55", "b56", "b54", "b57", "b61" ]
17,062,620
pmid-16647254|pmid-12581658|pmid-15332082|pmid-15107854|pmid-14512615|pmid-16859507
Therefore, it may involve a greater amount of multiple regulatory factors (and their binding sites).
[ "50", "55", "56", "54", "57", "61" ]
100
2,516
0
false
Therefore, it may involve a greater amount of multiple regulatory factors (and their binding sites).
[]
Therefore, it may involve a greater amount of multiple regulatory factors (and their binding sites).
true
true
true
true
true
429
3
DISCUSSION
1
50
[ "b50", "b55", "b56", "b54", "b57", "b61" ]
17,062,620
pmid-16647254|pmid-12581658|pmid-15332082|pmid-15107854|pmid-14512615|pmid-16859507
Finally, evolutionary design becomes a recurrent theme in systems biology of gene and protein networks (54,57–61).
[ "50", "55", "56", "54", "57", "61" ]
114
2,517
0
false
Finally, evolutionary design becomes a recurrent theme in systems biology of gene and protein networks.
[ "54,57–61" ]
Finally, evolutionary design becomes a recurrent theme in systems biology of gene and protein networks.
true
true
true
true
true
429
3
DISCUSSION
1
50
[ "b50", "b55", "b56", "b54", "b57", "b61" ]
17,062,620
pmid-16647254|pmid-12581658|pmid-15332082|pmid-15107854|pmid-14512615|pmid-16859507
It may have a counterpart in the blueprint of these networks (genomic structure).
[ "50", "55", "56", "54", "57", "61" ]
81
2,518
0
false
It may have a counterpart in the blueprint of these networks (genomic structure).
[]
It may have a counterpart in the blueprint of these networks (genomic structure).
true
true
true
true
true
429
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
Mutations in the DNA molecule are the basis of evolution.
[ "1", "2", "3", "4", "5" ]
57
2,519
0
false
Mutations in the DNA molecule are the basis of evolution.
[]
Mutations in the DNA molecule are the basis of evolution.
true
true
true
true
true
430
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
It is widely accepted that tautomerism of the canonical nucleobases and the formation of wobble base pairs play an important role in this phenomenon (1,2).
[ "1", "2", "3", "4", "5" ]
155
2,520
0
false
It is widely accepted that tautomerism of the canonical nucleobases and the formation of wobble base pairs play an important role in this phenomenon.
[ "1,2" ]
It is widely accepted that tautomerism of the canonical nucleobases and the formation of wobble base pairs play an important role in this phenomenon.
true
true
true
true
true
430
0
INTRODUCTION
1
3
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
To keep the number of errors low, enzymatic proof reading during nucleoside triphosphates incorporation takes place with the help of polymerases (3).
[ "1", "2", "3", "4", "5" ]
149
2,521
1
false
To keep the number of errors low, enzymatic proof reading during nucleoside triphosphates incorporation takes place with the help of polymerases.
[ "3" ]
To keep the number of errors low, enzymatic proof reading during nucleoside triphosphates incorporation takes place with the help of polymerases.
true
true
true
true
true
430
0
INTRODUCTION
1
4
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
DNA mutation is caused by mismatches of the normal bases because of a failure of proofreading during DNA replication (4).
[ "1", "2", "3", "4", "5" ]
121
2,522
1
false
DNA mutation is caused by mismatches of the normal bases because of a failure of proofreading during DNA replication.
[ "4" ]
DNA mutation is caused by mismatches of the normal bases because of a failure of proofreading during DNA replication.
true
true
true
true
true
430
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
DNA is also damaged continuously by oxidation, by depurination, by light or other processes occurring within the cellular environment.
[ "1", "2", "3", "4", "5" ]
134
2,523
0
false
DNA is also damaged continuously by oxidation, by depurination, by light or other processes occurring within the cellular environment.
[]
DNA is also damaged continuously by oxidation, by depurination, by light or other processes occurring within the cellular environment.
true
true
true
true
true
430
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
The daily number of errors in a human is estimated to be several thousands.
[ "1", "2", "3", "4", "5" ]
75
2,524
0
false
The daily number of errors in a human is estimated to be several thousands.
[]
The daily number of errors in a human is estimated to be several thousands.
true
true
true
true
true
430
0
INTRODUCTION
1
5
[ "b1", "b2", "b3", "b4", "b5" ]
17,071,713
pmid-958482|pmid-8328014|pmid-15035983|NA|pmid-16623698
This damage is removed by repair enzymes (5).
[ "1", "2", "3", "4", "5" ]
45
2,525
1
false
This damage is removed by repair enzymes.
[ "5" ]
This damage is removed by repair enzymes.
true
true
true
true
true
430
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
Several diagnostic tools have been developed to detect such single nucleotide polymorphisms (SNPs) by hybridization in solution or on polymer surfaces (biochips).
[ "6", "7", "6", "8" ]
162
2,526
0
false
Several diagnostic tools have been developed to detect such single nucleotide polymorphisms (SNPs) by hybridization in solution or on polymer surfaces (biochips).
[]
Several diagnostic tools have been developed to detect such single nucleotide polymorphisms (SNPs) by hybridization in solution or on polymer surfaces (biochips).
true
true
true
true
true
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
Modified nucleosides are used in these protocols as fluorescent dyes to be anchored to them without disturbing the DNA structure (6,7).
[ "6", "7", "6", "8" ]
135
2,527
0
false
Modified nucleosides are used in these protocols as fluorescent dyes to be anchored to them without disturbing the DNA structure.
[ "6,7" ]
Modified nucleosides are used in these protocols as fluorescent dyes to be anchored to them without disturbing the DNA structure.
true
true
true
true
true
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
7-Deazapurine nucleoside triphosphates are commonly used for these purposes (6–8).
[ "6", "7", "6", "8" ]
82
2,528
0
false
7-Deazapurine nucleoside triphosphates are commonly used for these purposes.
[ "6–8" ]
7-Deazapurine nucleoside triphosphates are commonly used for these purposes.
false
false
true
true
false
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
Thus, the knowledge about their recognition properties and base discrimination is of mutual interest.
[ "6", "7", "6", "8" ]
101
2,529
0
false
Thus, the knowledge about their recognition properties and base discrimination is of mutual interest.
[]
Thus, the knowledge about their recognition properties and base discrimination is of mutual interest.
true
true
true
true
true
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
Mismatch discrimination is evaluated from the difference in melting temperatures (Tm) between matched and mismatched base pairs within an oligonucleotide duplex.
[ "6", "7", "6", "8" ]
161
2,530
0
false
Mismatch discrimination is evaluated from the difference in melting temperatures (Tm) between matched and mismatched base pairs within an oligonucleotide duplex.
[]
Mismatch discrimination is evaluated from the difference in melting temperatures (Tm) between matched and mismatched base pairs within an oligonucleotide duplex.
true
true
true
true
true
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
For a given mismatch, the properties of the modified nucleosides incorporated in the DNA chain and the environmental conditions are of utmost importance for the stability of base pairs.
[ "6", "7", "6", "8" ]
185
2,531
0
false
For a given mismatch, the properties of the modified nucleosides incorporated in the DNA chain and the environmental conditions are of utmost importance for the stability of base pairs.
[]
For a given mismatch, the properties of the modified nucleosides incorporated in the DNA chain and the environmental conditions are of utmost importance for the stability of base pairs.
true
true
true
true
true
431
1
INTRODUCTION
1
6
[ "b6", "b7", "b6", "b8" ]
17,071,713
NA|pmid-2443975|NA|NA
Although studies on the mispairing of modified nucleosides have been performed, little attention has been paid to the influence of the pH values of the reaction medium on the recognition of canonical and modified nucleosides.
[ "6", "7", "6", "8" ]
225
2,532
0
false
Although studies on the mispairing of modified nucleosides have been performed, little attention has been paid to the influence of the pH values of the reaction medium on the recognition of canonical and modified nucleosides.
[]
Although studies on the mispairing of modified nucleosides have been performed, little attention has been paid to the influence of the pH values of the reaction medium on the recognition of canonical and modified nucleosides.
true
true
true
true
true
431
2
INTRODUCTION
1
6
[ "b6", "b9", "b10", "b14" ]
17,071,713
NA|pmid-3951988|pmid-8760882|pmid-15913364
Among the modified nucleosides, 7-deazapurine (pyrrolo[2,3-d]pyrimidine) nucleosides and 7-substituted derivatives (purine numbering is used throughout the discussion)
[ "6", "9", "10", "14" ]
167
2,533
0
false
Among the modified nucleosides, 7-deazapurine (pyrrolo[2,3-d]pyrimidine) nucleosides and 7-substituted derivatives (purine numbering is used throughout the discussion)
[]
Among the modified nucleosides, 7-deazapurine (pyrrolo[2,3-d]pyrimidine) nucleosides and 7-substituted derivatives (purine numbering is used throughout the discussion)
true
true
false
true
false
432
2
INTRODUCTION
1
6
[ "b6", "b9", "b10", "b14" ]
17,071,713
NA|pmid-3951988|pmid-8760882|pmid-15913364
have attracted attention because they closely resemble the structure of purine nucleosides and are therefore ideal shape mimics of the canonical DNA constituents.
[ "6", "9", "10", "14" ]
162
2,534
0
false
have attracted attention because they closely resemble the structure of purine nucleosides and are therefore ideal shape mimics of the canonical DNA constituents.
[]
have attracted attention because they closely resemble the structure of purine nucleosides and are therefore ideal shape mimics of the canonical DNA constituents.
false
true
true
true
false
432
2
INTRODUCTION
1
6
[ "b6", "b9", "b10", "b14" ]
17,071,713
NA|pmid-3951988|pmid-8760882|pmid-15913364
They are well accepted by DNA polymerases and made a significant contribution to DNA and RNA sequencing and diagnostics (6–9).
[ "6", "9", "10", "14" ]
126
2,535
0
false
They are well accepted by DNA polymerases and made a significant contribution to DNA and RNA sequencing and diagnostics.
[ "6–9" ]
They are well accepted by DNA polymerases and made a significant contribution to DNA and RNA sequencing and diagnostics.
true
true
true
true
true
432
2
INTRODUCTION
1
6
[ "b6", "b9", "b10", "b14" ]
17,071,713
NA|pmid-3951988|pmid-8760882|pmid-15913364
Reporter groups that are necessary to generate high-sensitivity probes are usually introduced at the 7-position of a 7-deazapurine giving them steric freedom in duplex DNA.
[ "6", "9", "10", "14" ]
172
2,536
0
false
Reporter groups that are necessary to generate high-sensitivity probes are usually introduced at the 7-position of a 7-deazapurine giving them steric freedom in duplex DNA.
[]
Reporter groups that are necessary to generate high-sensitivity probes are usually introduced at the 7-position of a 7-deazapurine giving them steric freedom in duplex DNA.
true
true
true
true
true
432
2
INTRODUCTION
1
6
[ "b6", "b9", "b10", "b14" ]
17,071,713
NA|pmid-3951988|pmid-8760882|pmid-15913364
Substituents of moderate size incorporated into the DNA chain have shown to increase duplex stability with the potential of a better mismatch discrimination (10–14).
[ "6", "9", "10", "14" ]
165
2,537
0
false
Substituents of moderate size incorporated into the DNA chain have shown to increase duplex stability with the potential of a better mismatch discrimination.
[ "10–14" ]
Substituents of moderate size incorporated into the DNA chain have shown to increase duplex stability with the potential of a better mismatch discrimination.
true
true
true
true
true
432
3
INTRODUCTION
1
15
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
2′-Deoxytubercidin (1a) and its 2-amino derivative 2a can substitute 2′-deoxyadenosine (dA) without significantly changing the base pair stability with dT (15,16) (see also Table 2).
[ "15", "16", "17", "18", "17" ]
182
2,538
0
false
2′-Deoxytubercidin (1a) and its 2-amino derivative 2a can substitute 2′-deoxyadenosine (dA) without significantly changing the base pair stability with dT (see also Table 2).
[ "15,16" ]
2′-Deoxytubercidin and its 2-amino derivative 2a can substitute 2′-deoxyadenosine (dA) without significantly changing the base pair stability with dT (see also Table 2).
false
false
true
true
false
433
3
INTRODUCTION
1
17
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
Studies on the pKa values of 7-deazapurine nucleosides show that compared to the parent dA (pKa = 3.50) (17) compounds 1a (pKa = 5.30) (18) and 2a (pKa = 5.71; Supplementary Data) are much more easily protonated.
[ "15", "16", "17", "18", "17" ]
212
2,539
1
false
Studies on the pKa values of 7-deazapurine nucleosides show that compared to the parent dA (pKa = 3.50) compounds 1a (pKa = 5.30) and 2a (pKa = 5.71; Supplementary Data) are much more easily protonated.
[ "17", "18" ]
Studies on the pKa values of 7-deazapurine nucleosides show that compared to the parent dA (pKa = 3.50) compounds 1a (pKa = 5.30) and 2a are much more easily protonated.
true
true
true
true
true
433
3
INTRODUCTION
1
17
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
Moreover, it is shown that the pKa values of nucleobases present in stacked oligonucleotides can be significantly higher due to the attractive force of the phosphodiester backbone for the protons (17).
[ "15", "16", "17", "18", "17" ]
201
2,540
1
false
Moreover, it is shown that the pKa values of nucleobases present in stacked oligonucleotides can be significantly higher due to the attractive force of the phosphodiester backbone for the protons.
[ "17" ]
Moreover, it is shown that the pKa values of nucleobases present in stacked oligonucleotides can be significantly higher due to the attractive force of the phosphodiester backbone for the protons.
true
true
true
true
true
433
3
INTRODUCTION
1
15
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
Thus, the pKa values of nucleobases are shifted by one or two pKa units towards neutral conditions.
[ "15", "16", "17", "18", "17" ]
99
2,541
0
false
Thus, the pKa values of nucleobases are shifted by one or two pKa units towards neutral conditions.
[]
Thus, the pKa values of nucleobases are shifted by one or two pKa units towards neutral conditions.
true
true
true
true
true
433
3
INTRODUCTION
1
15
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
This indicates that 7-deazaadenine nucleosides such as 1a or 2a as constituents of oligonucleosides might be protonated already under neutral conditions.
[ "15", "16", "17", "18", "17" ]
153
2,542
0
false
This indicates that 7-deazaadenine nucleosides such as 1a or 2a as constituents of oligonucleosides might be protonated already under neutral conditions.
[]
This indicates that 7-deazaadenine nucleosides such as 1a or 2a as constituents of oligonucleosides might be protonated already under neutral conditions.
true
true
true
true
true
433
3
INTRODUCTION
1
15
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
In order to investigate this matter in more detail, 2′-deoxytubercidin (1a) as well as 2-, or 7-substituted derivatives (1d, 2a–d, 3) or 4 were incorporated into oligonucleotides and their hybridization properties were studied (Scheme 1).
[ "15", "16", "17", "18", "17" ]
238
2,543
0
false
In order to investigate this matter in more detail, 2′-deoxytubercidin (1a) as well as 2-, or 7-substituted derivatives (1d, 2a–d, 3) or 4 were incorporated into oligonucleotides and their hybridization properties were studied (Scheme 1).
[]
In order to investigate this matter in more detail, 2′-deoxytubercidin as well as 2-, or 7-substituted derivatives or 4 were incorporated into oligonucleotides and their hybridization properties were studied.
true
true
true
true
true
433
3
INTRODUCTION
1
15
[ "b15", "b16", "b17", "b18", "b17" ]
17,071,713
NA|pmid-11738582|NA|pmid-1630898|NA
For this, the phosphoramidites (5a–d and 6) were synthesized and the base pair stability as well as the pH-dependent mismatch discrimination of oligonucleotides were investigated.
[ "15", "16", "17", "18", "17" ]
179
2,544
0
false
For this, the phosphoramidites (5a–d and 6) were synthesized and the base pair stability as well as the pH-dependent mismatch discrimination of oligonucleotides were investigated.
[]
For this, the phosphoramidites were synthesized and the base pair stability as well as the pH-dependent mismatch discrimination of oligonucleotides were investigated.
true
true
true
true
true
433
4
INTRODUCTION
0
null
null
17,071,713
null
The structures of nucleosides and phosphoramidites.
null
51
2,545
0
false
null
null
The structures of nucleosides and phosphoramidites.
true
true
true
true
true
434
0
INTRODUCTION
1
1
[ "b1" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
DNA amplification is a basic technique and an essential tool in biomedical research and diagnostics.
[ "1" ]
100
2,546
0
false
DNA amplification is a basic technique and an essential tool in biomedical research and diagnostics.
[]
DNA amplification is a basic technique and an essential tool in biomedical research and diagnostics.
true
true
true
true
true
435
0
INTRODUCTION
1
1
[ "b1" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
The most widely used method, the polymerase chain reaction (PCR), amplifies specific DNAs, delimited by two complementary oligonucleotide primers, using a thermostable DNA polymerase (1).
[ "1" ]
187
2,547
1
false
The most widely used method, the polymerase chain reaction (PCR), amplifies specific DNAs, delimited by two complementary oligonucleotide primers, using a thermostable DNA polymerase.
[ "1" ]
The most widely used method, the polymerase chain reaction (PCR), amplifies specific DNAs, delimited by two complementary oligonucleotide primers, using a thermostable DNA polymerase.
true
true
true
true
true
435
0
INTRODUCTION
1
1
[ "b1" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
In PCR, temperature cycling mediates strand separation, primer annealing and primer extension, to produce two replicates of the template that are used in the next round of amplification.
[ "1" ]
186
2,548
0
false
In PCR, temperature cycling mediates strand separation, primer annealing and primer extension, to produce two replicates of the template that are used in the next round of amplification.
[]
In PCR, temperature cycling mediates strand separation, primer annealing and primer extension, to produce two replicates of the template that are used in the next round of amplification.
true
true
true
true
true
435
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Despite its widespread appeal, the need for temperature cycling in PCR limits its portability due to the significant energy used in such sensitive instrumentation.
[ "2", "3" ]
163
2,549
0
false
Despite its widespread appeal, the need for temperature cycling in PCR limits its portability due to the significant energy used in such sensitive instrumentation.
[]
Despite its widespread appeal, the need for temperature cycling in PCR limits its portability due to the significant energy used in such sensitive instrumentation.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
As a result, several isothermal DNA amplification methods have been developed.
[ "2", "3" ]
78
2,550
0
false
As a result, several isothermal DNA amplification methods have been developed.
[]
As a result, several isothermal DNA amplification methods have been developed.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Strand displacement amplification (SDA) utilizes restriction endonucleases to nick double-stranded (ds) DNAs that are extended by nuclease-deficient DNA polymerases.
[ "2", "3" ]
165
2,551
0
false
Strand displacement amplification (SDA) utilizes restriction endonucleases to nick double-stranded (ds) DNAs that are extended by nuclease-deficient DNA polymerases.
[]
Strand displacement amplification (SDA) utilizes restriction endonucleases to nick double-stranded (ds) DNAs that are extended by nuclease-deficient DNA polymerases.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
The newly synthesized DNA is displaced to serve as a template for antisense DNA synthesis, resulting in exponential amplification of the target DNA (2).
[ "2", "3" ]
152
2,552
1
false
The newly synthesized DNA is displaced to serve as a template for antisense DNA synthesis, resulting in exponential amplification of the target DNA.
[ "2" ]
The newly synthesized DNA is displaced to serve as a template for antisense DNA synthesis, resulting in exponential amplification of the target DNA.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Restriction endonucleases complicate SDA reactions by necessitating the use of modified deoxynucleotides and primers.
[ "2", "3" ]
117
2,553
0
false
Restriction endonucleases complicate SDA reactions by necessitating the use of modified deoxynucleotides and primers.
[]
Restriction endonucleases complicate SDA reactions by necessitating the use of modified deoxynucleotides and primers.
true
true
true
true
true
436
1
INTRODUCTION
1
3
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Similarly, multiply primed rolling circle amplification (RCA) is a complex method for amplifying circular DNAs using random hexamers and Φ29 DNA polymerase (3).
[ "2", "3" ]
160
2,554
1
false
Similarly, multiply primed rolling circle amplification (RCA) is a complex method for amplifying circular DNAs using random hexamers and Φ29 DNA polymerase.
[ "3" ]
Similarly, multiply primed rolling circle amplification (RCA) is a complex method for amplifying circular DNAs using random hexamers and Φ29 DNA polymerase.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Multiply primed RCA can achieve up to 10 000-fold amplification; however, the use of random primers leaves the technique sensitive to contaminating DNAs.
[ "2", "3" ]
153
2,555
0
false
Multiply primed RCA can achieve up to 10 000-fold amplification; however, the use of random primers leaves the technique sensitive to contaminating DNAs.
[]
Multiply primed RCA can achieve up to 10 000-fold amplification; however, the use of random primers leaves the technique sensitive to contaminating DNAs.
true
true
true
true
true
436
1
INTRODUCTION
1
2
[ "b2", "b3" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Although SDA and RCA are described as isothermal amplification systems, both methods require an initial heat denaturation step.
[ "2", "3" ]
127
2,556
0
false
Although SDA and RCA are described as isothermal amplification systems, both methods require an initial heat denaturation step.
[]
Although SDA and RCA are described as isothermal amplification systems, both methods require an initial heat denaturation step.
true
true
true
true
true
436
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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
Recently, a true isothermal DNA amplification technology that incorporates a helicase enzyme into the reaction scheme was reported (4).
[ "4", "4", "4" ]
135
2,557
1
false
Recently, a true isothermal DNA amplification technology that incorporates a helicase enzyme into the reaction scheme was reported.
[ "4" ]
Recently, a true isothermal DNA amplification technology that incorporates a helicase enzyme into the reaction scheme was reported.
true
true
true
true
true
437
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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
Helicase-dependent amplification (HDA) exploits the unwinding activity of a helicase to separate duplex DNA targets during in vitro DNA amplification, eliminating the need for thermocycling (4).
[ "4", "4", "4" ]
194
2,558
1
false
Helicase-dependent amplification (HDA) exploits the unwinding activity of a helicase to separate duplex DNA targets during in vitro DNA amplification, eliminating the need for thermocycling.
[ "4" ]
Helicase-dependent amplification (HDA) exploits the unwinding activity of a helicase to separate duplex DNA targets during in vitro DNA amplification, eliminating the need for thermocycling.
true
true
true
true
true
437
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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
Accessory proteins, like single-stranded DNA-binding (SSB) protein, assist the helicase by preventing reformation of dsDNA.
[ "4", "4", "4" ]
123
2,559
0
false
Accessory proteins, like single-stranded DNA-binding (SSB) protein, assist the helicase by preventing reformation of dsDNA.
[]
Accessory proteins, like single-stranded DNA-binding (SSB) protein, assist the helicase by preventing reformation of dsDNA.
true
true
true
true
true
437
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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
Once the template DNA is separated, specific primers anneal and are extended by an exonuclease-deficient DNA polymerase to yield two replicates of the original DNA; thus, achieving exponential amplification.
[ "4", "4", "4" ]
207
2,560
0
false
Once the template DNA is separated, specific primers anneal and are extended by an exonuclease-deficient DNA polymerase to yield two replicates of the original DNA; thus, achieving exponential amplification.
[]
Once the template DNA is separated, specific primers anneal and are extended by an exonuclease-deficient DNA polymerase to yield two replicates of the original DNA; thus, achieving exponential amplification.
true
true
true
true
true
437
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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 first HDA system reported used the Escherichia coli UvrD helicase and was only able to amplify DNA fragments up to several hundred base pairs in size (4).
[ "4", "4", "4" ]
158
2,561
1
false
The first HDA system reported used the Escherichia coli UvrD helicase and was only able to amplify DNA fragments up to several hundred base pairs in size.
[ "4" ]
The first HDA system reported used the Escherichia coli UvrD helicase and was only able to amplify DNA fragments up to several hundred base pairs in size.
true
true
true
true
true
437
2
INTRODUCTION
1
4
[ "b4", "b4", "b4" ]
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 was suggested that the inefficiency of the UvrD–HDA system at amplifying long target sequences is due to the limited speed (20 bp/s) and processivity (100 bp per binding) of the UvrD helicase.
[ "4", "4", "4" ]
195
2,562
0
false
It was suggested that the inefficiency of the UvrD–HDA system at amplifying long target sequences is due to the limited speed (20 bp/s) and processivity (100 bp per binding) of the UvrD helicase.
[]
It was suggested that the inefficiency of the UvrD–HDA system at amplifying long target sequences is due to the limited speed (20 bp/s) and processivity (100 bp per binding) of the UvrD helicase.
true
true
true
true
true
437
3
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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
In this report, we describe a new helicase-based DNA amplification system that employs a highly processive helicase and selectively uses circular DNA molecules to amplify a very long DNA fragment.
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
196
2,563
0
false
In this report, we describe a new helicase-based DNA amplification system that employs a highly processive helicase and selectively uses circular DNA molecules to amplify a very long DNA fragment.
[]
In this report, we describe a new helicase-based DNA amplification system that employs a highly processive helicase and selectively uses circular DNA molecules to amplify a very long DNA fragment.
true
true
true
true
true
438
3
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 circular helicase-dependent amplification (cHDA) system amplifies circular DNAs using the T7 bacteriophage replication machinery: T7 DNA polymerase (T7 gene 5 protein plus E.coli thioredoxin), T7 helicase (T7 gene 4B protein) and T7 SSB protein (gene 2.5 protein or gp2.5) (5,6).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
283
2,564
0
false
The circular helicase-dependent amplification (cHDA) system amplifies circular DNAs using the T7 bacteriophage replication machinery: T7 DNA polymerase, T7 helicase and T7 SSB protein.
[ "T7 gene 5 protein plus E.coli thioredoxin", "T7 gene 4B protein", "gene 2.5 protein or gp2.5", "5,6" ]
The circular helicase-dependent amplification (cHDA) system amplifies circular DNAs using the T7 bacteriophage replication machinery: T7 DNA polymerase, T7 helicase and T7 SSB protein.
true
true
true
true
true
438
3
INTRODUCTION
1
7
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 T7 DNA polymerase is a non-processive polymerase; however, when it forms a complex with E.coli thioredoxin, DNA synthesis is catalyzed at a speed of >100 nt/s with a processivity >10 kb per binding event (7).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
212
2,565
1
false
The T7 DNA polymerase is a non-processive polymerase; however, when it forms a complex with E.coli thioredoxin, DNA synthesis is catalyzed at a speed of >100 nt/s with a processivity >10 kb per binding event.
[ "7" ]
The T7 DNA polymerase is a non-processive polymerase; however, when it forms a complex with E.coli thioredoxin, DNA synthesis is catalyzed at a speed of >100 nt/s with a processivity >10 kb per binding event.
true
true
true
true
true
438
3
INTRODUCTION
1
8
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 T7 DNA polymerase used in cHDA is T7 Sequenase (USB, Cleveland, OH), which lacks the 3′–5′ exonuclease activity and possesses strand displacement activity (8).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
163
2,566
1
false
The T7 DNA polymerase used in cHDA is T7 Sequenase (USB, Cleveland, OH), which lacks the 3′–5′ exonuclease activity and possesses strand displacement activity.
[ "8" ]
The T7 DNA polymerase used in cHDA is T7 Sequenase (USB, Cleveland, OH), which lacks the 3′–5′ exonuclease activity and possesses strand displacement activity.
true
true
true
true
true
438
3
INTRODUCTION
1
9
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 T7 gene 4 encodes two forms of the helicase, a 63 kDa (gene 4A) and a 56 kDa (gene 4B) protein (9).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
103
2,567
1
false
The T7 gene 4 encodes two forms of the helicase, a 63 kDa (gene 4A) and a 56 kDa (gene 4B) protein.
[ "9" ]
The T7 gene 4 encodes two forms of the helicase, a 63 kDa (gene 4A) and a 56 kDa (gene 4B) protein.
true
true
true
true
true
438
3
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 translation of the 56 kDa protein is initiated at an internal initiation codon (Met64) that is in frame with the coding sequence of gene 4A.
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
144
2,568
0
false
The translation of the 56 kDa protein is initiated at an internal initiation codon that is in frame with the coding sequence of gene 4A.
[ "Met64" ]
The translation of the 56 kDa protein is initiated at an internal initiation codon that is in frame with the coding sequence of gene 4A.
true
true
true
true
true
438
3
INTRODUCTION
1
10
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 T7 4A protein displays both helicase and primase activities (10); whereas, the T7 4B protein only exhibits a 5′–3′ helicase activity (11–15).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
145
2,569
1
false
The T7 4A protein displays both helicase and primase activities ; whereas, the T7 4B protein only exhibits a 5′–3′ helicase activity.
[ "10", "11–15" ]
The T7 4A protein displays both helicase and primase activities ; whereas, the T7 4B protein only exhibits a 5′–3′ helicase activity.
true
true
true
true
true
438
3
INTRODUCTION
1
16
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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
Either form is highly processive, traveling an average of 75 kb of single-stranded DNA (ssDNA) before dissociating (16).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
120
2,570
1
false
Either form is highly processive, traveling an average of 75 kb of single-stranded DNA (ssDNA) before dissociating.
[ "16" ]
Either form is highly processive, traveling an average of 75 kb of single-stranded DNA (ssDNA) before dissociating.
true
true
true
true
true
438
3
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 T7 gene 2.5 encodes a SSB protein that is able to bind ∼7 nt per monomer (17,18).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
85
2,571
0
false
The T7 gene 2.5 encodes a SSB protein that is able to bind ∼7 nt per monomer.
[ "17,18" ]
The T7 gene 2.5 encodes a SSB protein that is able to bind ∼7 nt per monomer.
true
true
true
true
true
438
3
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b15", "b16", "b17", "b18", "b19", "b21" ]
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 Gp2.5 protein stimulates DNA polymerase activity and increases the efficiency of RNA primer synthesis by physically interacting with the T7 DNA polymerase and T7 gene 4 helicase (19–21).
[ "5", "6", "7", "8", "9", "10", "11", "15", "16", "17", "18", "19", "21" ]
190
2,572
0
false
The Gp2.5 protein stimulates DNA polymerase activity and increases the efficiency of RNA primer synthesis by physically interacting with the T7 DNA polymerase and T7 gene 4 helicase.
[ "19–21" ]
The Gp2.5 protein stimulates DNA polymerase activity and increases the efficiency of RNA primer synthesis by physically interacting with the T7 DNA polymerase and T7 gene 4 helicase.
true
true
true
true
true
438
4
INTRODUCTION
0
null
null
16,893,951
null
In cHDA, a modified T7 replisome amplifies circular DNA templates in vitro.
null
75
2,573
0
false
null
null
In cHDA, a modified T7 replisome amplifies circular DNA templates in vitro.
true
true
true
true
true
439
4
INTRODUCTION
0
null
null
16,893,951
null
Amplification requires two specific primers and a complete replisome, including T7 Sequenase, T7 helicase and T7 SSB.
null
117
2,574
0
false
null
null
Amplification requires two specific primers and a complete replisome, including T7 Sequenase, T7 helicase and T7 SSB.
true
true
true
true
true
439
4
INTRODUCTION
0
null
null
16,893,951
null
The cHDA platform can amplify not only the entire circular DNA template, but also a specific target sequence defined by two primers and, thus, plasmid amplification and screening can be simultaneously performed.
null
211
2,575
0
false
null
null
The cHDA platform can amplify not only the entire circular DNA template, but also a specific target sequence defined by two primers and, thus, plasmid amplification and screening can be simultaneously performed.
true
true
true
true
true
439
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
HDA exploits the cell's replication machinery to mimic the process of duplicating genomic DNA in vivo.
[ "22", "4", "5", "6", "16" ]
102
2,576
0
false
HDA exploits the cell's replication machinery to mimic the process of duplicating genomic DNA in vivo.
[]
HDA exploits the cell's replication machinery to mimic the process of duplicating genomic DNA in vivo.
true
true
true
true
true
440
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
During DNA replication, a helicase unwinds DNA to provide single-stranded templates for polymerase-dependent DNA synthesis (22).
[ "22", "4", "5", "6", "16" ]
128
2,577
1
false
During DNA replication, a helicase unwinds DNA to provide single-stranded templates for polymerase-dependent DNA synthesis.
[ "22" ]
During DNA replication, a helicase unwinds DNA to provide single-stranded templates for polymerase-dependent DNA synthesis.
true
true
true
true
true
440
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
Similarly, HDA reactions rely on the coordinated activities of helicase, SSB proteins and DNA polymerase to amplify DNA.
[ "22", "4", "5", "6", "16" ]
120
2,578
0
false
Similarly, HDA reactions rely on the coordinated activities of helicase, SSB proteins and DNA polymerase to amplify DNA.
[]
Similarly, HDA reactions rely on the coordinated activities of helicase, SSB proteins and DNA polymerase to amplify DNA.
true
true
true
true
true
440
0
DISCUSSION
1
4
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
Helicase melts the DNA template and SSB proteins coordinate replication, allowing DNA polymerase to extend annealed primers (4).
[ "22", "4", "5", "6", "16" ]
128
2,579
1
false
Helicase melts the DNA template and SSB proteins coordinate replication, allowing DNA polymerase to extend annealed primers.
[ "4" ]
Helicase melts the DNA template and SSB proteins coordinate replication, allowing DNA polymerase to extend annealed primers.
true
true
true
true
true
440
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
A new HDA platform, cHDA, has been developed using the replicative machinery of bacteriophage T7 that can replicate its 40 kb genome in one initiation event (5,6).
[ "22", "4", "5", "6", "16" ]
163
2,580
0
false
A new HDA platform, cHDA, has been developed using the replicative machinery of bacteriophage T7 that can replicate its 40 kb genome in one initiation event.
[ "5,6" ]
A new HDA platform, cHDA, has been developed using the replicative machinery of bacteriophage T7 that can replicate its 40 kb genome in one initiation event.
true
true
true
true
true
440
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
The cHDA system uses a modified T7 replisome, composed of T7 Sequenase, 4B helicase and Gp2.5 SSB protein, to perform helicase-dependent and strand-displacement amplification.
[ "22", "4", "5", "6", "16" ]
175
2,581
0
false
The cHDA system uses a modified T7 replisome, composed of T7 Sequenase, 4B helicase and Gp2.5 SSB protein, to perform helicase-dependent and strand-displacement amplification.
[]
The cHDA system uses a modified T7 replisome, composed of T7 Sequenase, 4B helicase and Gp2.5 SSB protein, to perform helicase-dependent and strand-displacement amplification.
true
true
true
true
true
440
0
DISCUSSION
1
16
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
The T7 helicase, like other replicative helicases, displays a rapid translocation rate and high processivity, traveling 75 kb at a rate of 130 nt/s on ssDNA before dissociating (16).
[ "22", "4", "5", "6", "16" ]
182
2,582
1
false
The T7 helicase, like other replicative helicases, displays a rapid translocation rate and high processivity, traveling 75 kb at a rate of 130 nt/s on ssDNA before dissociating.
[ "16" ]
The T7 helicase, like other replicative helicases, displays a rapid translocation rate and high processivity, traveling 75 kb at a rate of 130 nt/s on ssDNA before dissociating.
true
true
true
true
true
440
0
DISCUSSION
1
22
[ "b22", "b4", "b5", "b6", "b16" ]
16,893,951
NA|NA|pmid-15247927|pmid-8156591|pmid-9651583|pmid-12206763
Using circular DNA as a template, the cHDA sytem is able to amplify both a target region defined by specific primers and the entire circular template harboring the target DNA.
[ "22", "4", "5", "6", "16" ]
175
2,583
0
false
Using circular DNA as a template, the cHDA sytem is able to amplify both a target region defined by specific primers and the entire circular template harboring the target DNA.
[]
Using circular DNA as a template, the cHDA sytem is able to amplify both a target region defined by specific primers and the entire circular template harboring the target DNA.
true
true
true
true
true
440
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Based on the results from this study, the amplification mechanism of cHDA was postulated to be a helicase-dependent RCA, as illustrated in Figure 10.
[ "10" ]
149
2,584
0
false
Based on the results from this study, the amplification mechanism of cHDA was postulated to be a helicase-dependent RCA, as illustrated in Figure 10.
[]
Based on the results from this study, the amplification mechanism of cHDA was postulated to be a helicase-dependent RCA, as illustrated in Figure 10.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Amplification is initiated by the annealing of a forward primer to a single-stranded circle or to one of the two circular strands of the plasmid.
[ "10" ]
145
2,585
0
false
Amplification is initiated by the annealing of a forward primer to a single-stranded circle or to one of the two circular strands of the plasmid.
[]
Amplification is initiated by the annealing of a forward primer to a single-stranded circle or to one of the two circular strands of the plasmid.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
For simplicity, the primer is shown as annealed to a single-stranded circle in Step 1 of Figure 10.
[ "10" ]
99
2,586
0
false
For simplicity, the primer is shown as annealed to a single-stranded circle in Step 1 of Figure 10.
[]
For simplicity, the primer is shown as annealed to a single-stranded circle in Step 1 of Figure 10.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
The primer is extended by the T7 replisome, which includes the T7 Sequenase, T7 gp4B helicase and T7 gp2.5
[ "10" ]
106
2,587
0
false
The primer is extended by the T7 replisome, which includes the T7 Sequenase, T7 gp4B helicase and T7 gp2.5
[]
The primer is extended by the T7 replisome, which includes the T7 Sequenase, T7 gp4B helicase and T7 gp2.5
true
true
false
true
false
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
SSB protein; The SSB protein is omitted from the figure to simplify the diagram.
[ "10" ]
80
2,588
0
false
SSB protein; The SSB protein is omitted from the figure to simplify the diagram.
[]
SSB protein; The SSB protein is omitted from the figure to simplify the diagram.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
When replication reaches the 5′ end of the newly synthesized strand, helicase binds to the 5′ end and the replisome begins strand displacement synthesis around the circular template (Step 2).
[ "10" ]
191
2,589
0
false
When replication reaches the 5′ end of the newly synthesized strand, helicase binds to the 5′ end and the replisome begins strand displacement synthesis around the circular template (Step 2).
[]
When replication reaches the 5′ end of the newly synthesized strand, helicase binds to the 5′ end and the replisome begins strand displacement synthesis around the circular template (Step 2).
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
The displaced tail grows and provides multiple sites for reverse primers to anneal and to be extended by T7 replisomes (Step 3).
[ "10" ]
128
2,590
0
false
The displaced tail grows and provides multiple sites for reverse primers to anneal and to be extended by T7 replisomes (Step 3).
[]
The displaced tail grows and provides multiple sites for reverse primers to anneal and to be extended by T7 replisomes (Step 3).
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Primer extension continues until the replisome reaches the duplex ahead, and begins strand displacement synthesis, releasing ssDNA products, which carry one or more sites for forward primers to bind (Step 4).
[ "10" ]
208
2,591
0
false
Primer extension continues until the replisome reaches the duplex ahead, and begins strand displacement synthesis, releasing ssDNA products, which carry one or more sites for forward primers to bind (Step 4).
[]
Primer extension continues until the replisome reaches the duplex ahead, and begins strand displacement synthesis, releasing ssDNA products, which carry one or more sites for forward primers to bind (Step 4).
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
The forward primers are extended by T7 replisomes, resulting in the synthesis of dsDNA products and release of ssDNA for the next round of strand displacement synthesis (Step 5).
[ "10" ]
178
2,592
0
false
The forward primers are extended by T7 replisomes, resulting in the synthesis of dsDNA products and release of ssDNA for the next round of strand displacement synthesis (Step 5).
[]
The forward primers are extended by T7 replisomes, resulting in the synthesis of dsDNA products and release of ssDNA for the next round of strand displacement synthesis (Step 5).
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Multiple rounds of strand displacement synthesis by the T7 replisome produce a specific product defined by two primers and concatemers of the circular DNA template.
[ "10" ]
164
2,593
0
false
Multiple rounds of strand displacement synthesis by the T7 replisome produce a specific product defined by two primers and concatemers of the circular DNA template.
[]
Multiple rounds of strand displacement synthesis by the T7 replisome produce a specific product defined by two primers and concatemers of the circular DNA template.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
The larger products increase in size by the unit size of the circular template present in the concatamers.
[ "10" ]
106
2,594
0
false
The larger products increase in size by the unit size of the circular template present in the concatamers.
[]
The larger products increase in size by the unit size of the circular template present in the concatamers.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Based on published studies on T7 replication [reviewed in (10)], we can speculate the role of each T7 protein in the cHDA system: during the amplification process, helicases unwind duplex DNA ahead of the DNA polymerase; SSB protein stabilizes the transient ssDNAs unwound by the helicase by preventing the reassociation...
[ "10" ]
424
2,595
0
false
Based on published studies on T7 replication, we can speculate the role of each T7 protein in the cHDA system: during the amplification process, helicases unwind duplex DNA ahead of the DNA polymerase; SSB protein stabilizes the transient ssDNAs unwound by the helicase by preventing the reassociation of duble-stranded ...
[ "reviewed in (10)" ]
Based on published studies on T7 replication, we can speculate the role of each T7 protein in the cHDA system: during the amplification process, helicases unwind duplex DNA ahead of the DNA polymerase; SSB protein stabilizes the transient ssDNAs unwound by the helicase by preventing the reassociation of duble-stranded ...
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
When cHDA is used with a double-stranded circular DNA as a template, the same reaction is carried out on the complementary strand of the circle, beginning with a reverse primer annealed to the template.
[ "10" ]
202
2,596
0
false
When cHDA is used with a double-stranded circular DNA as a template, the same reaction is carried out on the complementary strand of the circle, beginning with a reverse primer annealed to the template.
[]
When cHDA is used with a double-stranded circular DNA as a template, the same reaction is carried out on the complementary strand of the circle, beginning with a reverse primer annealed to the template.
true
true
true
true
true
441
1
DISCUSSION
1
10
[ "b10" ]
16,893,951
pmid-1309614|pmid-11381035|pmid-6344999
Therefore, ssDNA products generated from the forward primers can anneal to the ssDNA produced from the reverse primers, which may be an additional source for generating dsDNA products.
[ "10" ]
184
2,597
0
false
Therefore, ssDNA products generated from the forward primers can anneal to the ssDNA produced from the reverse primers, which may be an additional source for generating dsDNA products.
[]
Therefore, ssDNA products generated from the forward primers can anneal to the ssDNA produced from the reverse primers, which may be an additional source for generating dsDNA products.
true
true
true
true
true
441
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
Amplification by cHDA is dependent on the presence and specific interaction of the SSB protein, helicase and T7 Sequenase.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
122
2,598
0
false
Amplification by cHDA is dependent on the presence and specific interaction of the SSB protein, helicase and T7 Sequenase.
[]
Amplification by cHDA is dependent on the presence and specific interaction of the SSB protein, helicase and T7 Sequenase.
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
Without the T7 helicase and/or SSB protein, no product is observed with only the T7 Sequenase.
[ "23", "12", "24", "19", "20", "25", "24", "26", "29" ]
94
2,599
0
false
Without the T7 helicase and/or SSB protein, no product is observed with only the T7 Sequenase.
[]
Without the T7 helicase and/or SSB protein, no product is observed with only the T7 Sequenase.
true
true
true
true
true
442