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
0
null
null
17,317,681
null
a single vector capable of expression in E. coli, mammalian cell lines (e.g.
null
76
500
0
false
null
null
a single vector capable of expression in E. coli, mammalian cell lines (e.g.
false
true
true
true
false
81
2
DISCUSSION
0
null
null
17,317,681
null
HEK293T cells) and insect cell lines (e.g.
null
42
501
0
false
null
null
HEK293T cells) and insect cell lines (e.g.
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
Sf9 cells).
null
11
502
0
false
null
null
Sf9 cells).
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
By adapting a multi-promoter vector a single cloning step has been used to produce a single vector suitable for expression in E. coli, mammalian and insect cells.
null
162
503
0
false
null
null
By adapting a multi-promoter vector a single cloning step has been used to produce a single vector suitable for expression in E. coli, mammalian and insect cells.
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
The utility of this has been exemplified (Case study III).The expressed proteins must be capable of purification in HTP mode, i.e.
null
130
504
0
false
null
null
The utility of this has been exemplified (Case study III).The expressed proteins must be capable of purification in HTP mode, i.e.
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
they must all be fused to a common affinity purification ‘tag’ which may be removed, if desired, by enzymatic digest prior to crystallization.
null
142
505
0
false
null
null
they must all be fused to a common affinity purification ‘tag’ which may be removed, if desired, by enzymatic digest prior to crystallization.
false
true
true
true
false
81
2
DISCUSSION
0
null
null
17,317,681
null
All vectors, regardless of additional fusion protein expressed, add either an N-terminal or C-terminal His6 tag onto the expressed target protein to facilitate detection and purification.
null
187
506
0
false
null
null
All vectors, regardless of additional fusion protein expressed, add either an N-terminal or C-terminal His6 tag onto the expressed target protein to facilitate detection and purification.
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
The purification of proteins expressed both intracellularly in E. coli and secreted from mammalian cells using a common purification strategy has been exemplified (Case studies I and II).The process should be amenable to automation.
null
232
507
0
false
null
null
The purification of proteins expressed both intracellularly in E. coli and secreted from mammalian cells using a common purification strategy has been exemplified (Case studies I and II).The process should be amenable to automation.
true
true
true
true
true
81
2
DISCUSSION
0
null
null
17,317,681
null
Laboratory automation to carry out liquid handling tasks involved in the various stages of the expression screening experiments in all three hosts has been described.
null
166
508
0
false
null
null
Laboratory automation to carry out liquid handling tasks involved in the various stages of the expression screening experiments in all three hosts has been described.
true
true
true
true
true
81
3
DISCUSSION
0
null
null
17,317,681
null
The ability to clone genes-encoding proteins, or domains thereof, in a rapid and reliable parallel or high-throughput (HTP) fashion.
null
132
509
0
false
null
null
The ability to clone genes-encoding proteins, or domains thereof, in a rapid and reliable parallel or high-throughput (HTP) fashion.
true
true
true
true
true
82
3
DISCUSSION
0
null
null
17,317,681
null
Cloning efficiencies of >90% have been achieved in a parallel 96-well plate format using a generic vector in combination with the In-Fusion™ enzyme.
null
148
510
0
false
null
null
Cloning efficiencies of >90% have been achieved in a parallel 96-well plate format using a generic vector in combination with the In-Fusion™ enzyme.
true
true
true
true
true
82
4
DISCUSSION
0
null
null
17,317,681
null
The ability to accurately determine the final constructs without the addition of extraneous/vector or restriction-site-derived amino acids to the expressed protein.
null
164
511
0
false
null
null
The ability to accurately determine the final constructs without the addition of extraneous/vector or restriction-site-derived amino acids to the expressed protein.
true
true
true
true
true
83
4
DISCUSSION
0
null
null
17,317,681
null
A suite of vectors has been described which make use of In-Fusion™ cloning to precisely engineer the expressed sequence, for example, introducing an N-terminal His6 tag and 3C protease cleavage site to enable removal of the tag during purification.
null
248
512
0
false
null
null
A suite of vectors has been described which make use of In-Fusion™ cloning to precisely engineer the expressed sequence, for example, introducing an N-terminal His6 tag and 3C protease cleavage site to enable removal of the tag during purification.
true
true
true
true
true
83
4
DISCUSSION
0
null
null
17,317,681
null
The utility of this format has been exemplified (Case study I).
null
63
513
0
false
null
null
The utility of this format has been exemplified (Case study I).
true
true
true
true
true
83
5
DISCUSSION
0
null
null
17,317,681
null
The process must be versatile in terms of insert sequence independence.
null
71
514
0
false
null
null
The process must be versatile in terms of insert sequence independence.
true
true
true
true
true
84
5
DISCUSSION
0
null
null
17,317,681
null
Three case studies have been described in which eighty-two expression vectors have been produced from a variety of target genes using the vector system (Case studies I, II, III).
null
178
515
0
false
null
null
Three case studies have been described in which eighty-two expression vectors have been produced from a variety of target genes using the vector system (Case studies I, II, III).
true
true
true
true
true
84
6
DISCUSSION
0
null
null
17,317,681
null
The process would preferably be single-step, to give rapid and cost-effective vector construction.
null
98
516
0
false
null
null
The process would preferably be single-step, to give rapid and cost-effective vector construction.
true
true
true
true
true
85
6
DISCUSSION
0
null
null
17,317,681
null
Vector construction involves a single-step reaction that enables the simple and rapid construction of vectors in parallel using a 96-well plate format.
null
151
517
0
false
null
null
Vector construction involves a single-step reaction that enables the simple and rapid construction of vectors in parallel using a 96-well plate format.
true
true
true
true
true
85
6
DISCUSSION
0
null
null
17,317,681
null
Further, certain PCR products are compatible with multiple fusion vector formats (e.g.
null
86
518
0
false
null
null
Further, certain PCR products are compatible with multiple fusion vector formats (e.g.
true
true
true
true
true
85
6
DISCUSSION
0
null
null
17,317,681
null
N-His, N-His-GST and N-His-MBP—see examples in Case study III) thereby enabling cost-effective use of PCR primers.
null
114
519
0
false
null
null
N-His, N-His-GST and N-His-MBP—see examples in Case study III) thereby enabling cost-effective use of PCR primers.
true
true
true
true
true
85
7
DISCUSSION
0
null
null
17,317,681
null
The constructs should be capable of expressing proteins from multiple hosts, i.e.
null
81
520
0
false
null
null
The constructs should be capable of expressing proteins from multiple hosts, i.e.
true
true
true
true
true
86
7
DISCUSSION
0
null
null
17,317,681
null
a single vector capable of expression in E. coli, mammalian cell lines (e.g.
null
76
521
0
false
null
null
a single vector capable of expression in E. coli, mammalian cell lines (e.g.
false
true
true
true
false
86
7
DISCUSSION
0
null
null
17,317,681
null
HEK293T cells) and insect cell lines (e.g.
null
42
522
0
false
null
null
HEK293T cells) and insect cell lines (e.g.
true
true
true
true
true
86
7
DISCUSSION
0
null
null
17,317,681
null
Sf9 cells).
null
11
523
0
false
null
null
Sf9 cells).
true
true
true
true
true
86
7
DISCUSSION
0
null
null
17,317,681
null
By adapting a multi-promoter vector a single cloning step has been used to produce a single vector suitable for expression in E. coli, mammalian and insect cells.
null
162
524
0
false
null
null
By adapting a multi-promoter vector a single cloning step has been used to produce a single vector suitable for expression in E. coli, mammalian and insect cells.
true
true
true
true
true
86
7
DISCUSSION
0
null
null
17,317,681
null
The utility of this has been exemplified (Case study III).
null
58
525
0
false
null
null
The utility of this has been exemplified (Case study III).
true
true
true
true
true
86
8
DISCUSSION
0
null
null
17,317,681
null
The expressed proteins must be capable of purification in HTP mode, i.e.
null
72
526
0
false
null
null
The expressed proteins must be capable of purification in HTP mode, i.e.
true
true
true
true
true
87
8
DISCUSSION
0
null
null
17,317,681
null
they must all be fused to a common affinity purification ‘tag’ which may be removed, if desired, by enzymatic digest prior to crystallization.
null
142
527
0
false
null
null
they must all be fused to a common affinity purification ‘tag’ which may be removed, if desired, by enzymatic digest prior to crystallization.
false
true
true
true
false
87
8
DISCUSSION
0
null
null
17,317,681
null
All vectors, regardless of additional fusion protein expressed, add either an N-terminal or C-terminal His6 tag onto the expressed target protein to facilitate detection and purification.
null
187
528
0
false
null
null
All vectors, regardless of additional fusion protein expressed, add either an N-terminal or C-terminal His6 tag onto the expressed target protein to facilitate detection and purification.
true
true
true
true
true
87
8
DISCUSSION
0
null
null
17,317,681
null
The purification of proteins expressed both intracellularly in E. coli and secreted from mammalian cells using a common purification strategy has been exemplified (Case studies I and II).
null
187
529
0
false
null
null
The purification of proteins expressed both intracellularly in E. coli and secreted from mammalian cells using a common purification strategy has been exemplified (Case studies I and II).
true
true
true
true
true
87
9
DISCUSSION
0
null
null
17,317,681
pmid-16211504|NA|pmid-2235490|pmid-1362067
The process should be amenable to automation.
null
45
530
0
false
null
null
The process should be amenable to automation.
true
true
true
true
true
88
9
DISCUSSION
0
null
null
17,317,681
pmid-16211504|NA|pmid-2235490|pmid-1362067
Laboratory automation to carry out liquid handling tasks involved in the various stages of the expression screening experiments in all three hosts has been described.
null
166
531
0
false
null
null
Laboratory automation to carry out liquid handling tasks involved in the various stages of the expression screening experiments in all three hosts has been described.
true
true
true
true
true
88
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
DNase I footprinting is a powerful in vitro technique used to identify ligand–DNA interactions at specific DNA sequences (1,2).
[ "1", "2", "3", "4", "5", "6", "7" ]
127
532
0
false
DNase I footprinting is a powerful in vitro technique used to identify ligand–DNA interactions at specific DNA sequences.
[ "1,2" ]
DNase I footprinting is a powerful in vitro technique used to identify ligand–DNA interactions at specific DNA sequences.
true
true
true
true
true
89
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
For the past two decades it has been the fundamental assay used to determine the sequence-selectivity for both proteins and DNA-binding compounds (3,4).
[ "1", "2", "3", "4", "5", "6", "7" ]
152
533
0
false
For the past two decades it has been the fundamental assay used to determine the sequence-selectivity for both proteins and DNA-binding compounds.
[ "3,4" ]
For the past two decades it has been the fundamental assay used to determine the sequence-selectivity for both proteins and DNA-binding compounds.
true
true
true
true
true
89
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
Through manipulations of quantified data, it has become possible to further utilize DNase I footprinting to indirectly measure thermodynamic and kinetic properties of interactions (5,6).
[ "1", "2", "3", "4", "5", "6", "7" ]
186
534
0
false
Through manipulations of quantified data, it has become possible to further utilize DNase I footprinting to indirectly measure thermodynamic and kinetic properties of interactions.
[ "5,6" ]
Through manipulations of quantified data, it has become possible to further utilize DNase I footprinting to indirectly measure thermodynamic and kinetic properties of interactions.
true
true
true
true
true
89
0
INTRODUCTION
1
7
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
Typically it is possible, from one or two footprinting experiments, to locate a ligand's preferential binding sites on a desired short (100–200 bp) target DNA sequence, and characterize the ligand by calculating the binding affinities at such sites (7).
[ "1", "2", "3", "4", "5", "6", "7" ]
253
535
1
false
Typically it is possible, from one or two footprinting experiments, to locate a ligand's preferential binding sites on a desired short target DNA sequence, and characterize the ligand by calculating the binding affinities at such sites.
[ "100–200 bp", "7" ]
Typically it is possible, from one or two footprinting experiments, to locate a ligand's preferential binding sites on a desired short target DNA sequence, and characterize the ligand by calculating the binding affinities at such sites.
true
true
true
true
true
89
1
INTRODUCTION
1
2
[ "B2", "B7", "B8", "B9 B10 B11 B12 B13" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
Unfortunately, as many researchers will testify, DNase I footprinting is a labour-intensive procedure which may take several days to prepare and carry out (2,7,8).
[ "2", "7", "8", "9–13" ]
163
536
0
false
Unfortunately, as many researchers will testify, DNase I footprinting is a labour-intensive procedure which may take several days to prepare and carry out.
[ "2,7,8" ]
Unfortunately, as many researchers will testify, DNase I footprinting is a labour-intensive procedure which may take several days to prepare and carry out.
true
true
true
true
true
90
1
INTRODUCTION
1
2
[ "B2", "B7", "B8", "B9 B10 B11 B12 B13" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
Furthermore, it traditionally involves the undesirable use of radioisotopes and requires tricky ethanol precipitation steps.
[ "2", "7", "8", "9–13" ]
124
537
0
false
Furthermore, it traditionally involves the undesirable use of radioisotopes and requires tricky ethanol precipitation steps.
[]
Furthermore, it traditionally involves the undesirable use of radioisotopes and requires tricky ethanol precipitation steps.
true
true
true
true
true
90
1
INTRODUCTION
1
9–13
[ "B2", "B7", "B8", "B9 B10 B11 B12 B13" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
Modifications of the DNase I footprinting protocol have been reported, and these have sought to improve the assay through the removal of radioisotope use and/or ethanol precipitation steps (9–13).
[ "2", "7", "8", "9–13" ]
196
538
1
false
Modifications of the DNase I footprinting protocol have been reported, and these have sought to improve the assay through the removal of radioisotope use and/or ethanol precipitation steps.
[ "9–13" ]
Modifications of the DNase I footprinting protocol have been reported, and these have sought to improve the assay through the removal of radioisotope use and/or ethanol precipitation steps.
true
true
true
true
true
90
1
INTRODUCTION
1
2
[ "B2", "B7", "B8", "B9 B10 B11 B12 B13" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
However, use of these modified assays has not become commonplace, possibly as all describe single-tube methods that ultimately still require significant labour in order to yield data.
[ "2", "7", "8", "9–13" ]
183
539
0
false
However, use of these modified assays has not become commonplace, possibly as all describe single-tube methods that ultimately still require significant labour in order to yield data.
[]
However, use of these modified assays has not become commonplace, possibly as all describe single-tube methods that ultimately still require significant labour in order to yield data.
true
true
true
true
true
90
2
INTRODUCTION
1
14
[ "B14" ]
17,586,817
pmid-7785784|pmid-15701734
For many researchers, including us, the greatest desire is to decrease the data turnover time of DNase I footprinting to maximize productivity.
[ "14" ]
143
540
0
false
For many researchers, including us, the greatest desire is to decrease the data turnover time of DNase I footprinting to maximize productivity.
[]
For many researchers, including us, the greatest desire is to decrease the data turnover time of DNase I footprinting to maximize productivity.
true
true
true
true
true
91
2
INTRODUCTION
1
14
[ "B14" ]
17,586,817
pmid-7785784|pmid-15701734
In the current age of drug discovery and ‘omics’, the need for medium/high-throughput assays is evident, with the same technique performed repeatedly, in order to satisfy large sample sets (14).
[ "14" ]
194
541
1
false
In the current age of drug discovery and ‘omics’, the need for medium/high-throughput assays is evident, with the same technique performed repeatedly, in order to satisfy large sample sets.
[ "14" ]
In the current age of drug discovery and ‘omics’, the need for medium/high-throughput assays is evident, with the same technique performed repeatedly, in order to satisfy large sample sets.
true
true
true
true
true
91
2
INTRODUCTION
1
14
[ "B14" ]
17,586,817
pmid-7785784|pmid-15701734
This is achieved in most experiments by carrying-out reactions in parallel, with the 96-well microtitre plate as the industry standard.
[ "14" ]
135
542
0
false
This is achieved in most experiments by carrying-out reactions in parallel, with the 96-well microtitre plate as the industry standard.
[]
This is achieved in most experiments by carrying-out reactions in parallel, with the 96-well microtitre plate as the industry standard.
true
true
true
true
true
91
2
INTRODUCTION
1
14
[ "B14" ]
17,586,817
pmid-7785784|pmid-15701734
Working in the field of drug design and discovery, it was our own wish to use DNase I footprinting as a screening tool, increasing the throughput such that it could be used to assess libraries of compounds produced by combinatorial methods.
[ "14" ]
240
543
0
false
Working in the field of drug design and discovery, it was our own wish to use DNase I footprinting as a screening tool, increasing the throughput such that it could be used to assess libraries of compounds produced by combinatorial methods.
[]
Working in the field of drug design and discovery, it was our own wish to use DNase I footprinting as a screening tool, increasing the throughput such that it could be used to assess libraries of compounds produced by combinatorial methods.
true
true
true
true
true
91
3
INTRODUCTION
0
null
null
17,586,817
pmid-16942018
Therefore, through scrutiny of every aspect of the standard protocol for DNase I footprinting, we developed a rapid assay that utilizes the 96-well format and gives increased throughput along with decreased risk, error and processing times.
null
240
544
0
false
null
null
Therefore, through scrutiny of every aspect of the standard protocol for DNase I footprinting, we developed a rapid assay that utilizes the 96-well format and gives increased throughput along with decreased risk, error and processing times.
true
true
true
true
true
92
3
INTRODUCTION
0
null
null
17,586,817
pmid-16942018
In the process of developing the method, it also became clear that an equally expedient analysis procedure would be required to handle the large yield of data.
null
159
545
0
false
null
null
In the process of developing the method, it also became clear that an equally expedient analysis procedure would be required to handle the large yield of data.
true
true
true
true
true
92
3
INTRODUCTION
0
null
null
17,586,817
pmid-16942018
To this end, a semi-automated analysis protocol was also designed, tying together gel quantification software with custom-designed programs to produce a single ‘footprinting profile’ for each ligand across several hundred base pairs of sequence.
null
245
546
0
false
null
null
To this end, a semi-automated analysis protocol was also designed, tying together gel quantification software with custom-designed programs to produce a single ‘footprinting profile’ for each ligand across several hundred base pairs of sequence.
true
true
true
true
true
92
3
INTRODUCTION
0
null
null
17,586,817
pmid-16942018
The resultant protocol provides a quick and simple microtitre-based DNase I footprinting assay that is suitable for use as a quantitative screening-tool.
null
153
547
0
false
null
null
The resultant protocol provides a quick and simple microtitre-based DNase I footprinting assay that is suitable for use as a quantitative screening-tool.
true
true
true
true
true
92
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
A rapid 96-well DNase I footprinting screen was developed that gives readily comparable quantitative binding data for multiple test agents over long sequences of DNA.
[ "2", "7", "8" ]
166
548
0
false
A rapid 96-well DNase I footprinting screen was developed that gives readily comparable quantitative binding data for multiple test agents over long sequences of DNA.
[]
A rapid 96-well DNase I footprinting screen was developed that gives readily comparable quantitative binding data for multiple test agents over long sequences of DNA.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
By increasing substantially the throughput of footprinting, we have demonstrated the suitability of this assay as a screening tool relevant in the current age of drug discovery.
[ "2", "7", "8" ]
177
549
0
false
By increasing substantially the throughput of footprinting, we have demonstrated the suitability of this assay as a screening tool relevant in the current age of drug discovery.
[]
By increasing substantially the throughput of footprinting, we have demonstrated the suitability of this assay as a screening tool relevant in the current age of drug discovery.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
A typical radioisotope DNase I footprinting experiment might be able to assess up to a maximum of two ligands over 100 bp of DNA, whilst requiring approximately 3–4 days to proceed from an unlabelled DNA template to an analysable gel image (2,7,8).
[ "2", "7", "8" ]
248
550
0
false
A typical radioisotope DNase I footprinting experiment might be able to assess up to a maximum of two ligands over 100 bp of DNA, whilst requiring approximately 3–4 days to proceed from an unlabelled DNA template to an analysable gel image.
[ "2,7,8" ]
A typical radioisotope DNase I footprinting experiment might be able to assess up to a maximum of two ligands over 100 bp of DNA, whilst requiring approximately 3–4 days to proceed from an unlabelled DNA template to an analysable gel image.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
The 96-well format screen described herein permits the assessment of 12 ligands over 500 bp of DNA (or six ligands over 1 kb) in as little as two days, along with a greatly decreased proportion of user-time spent on difficult liquid-handling steps, which could ultimately be programmed to be carried-out by a benchtop robot system.
[ "2", "7", "8" ]
331
551
0
false
The 96-well format screen described herein permits the assessment of 12 ligands over 500 bp of DNA (or six ligands over 1 kb) in as little as two days, along with a greatly decreased proportion of user-time spent on difficult liquid-handling steps, which could ultimately be programmed to be carried-out by a benchtop robot system.
[]
The 96-well format screen described herein permits the assessment of 12 ligands over 500 bp of DNA (or six ligands over 1 kb) in as little as two days, along with a greatly decreased proportion of user-time spent on difficult liquid-handling steps, which could ultimately be programmed to be carried-out by a benchtop robot system.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
This represents up to a 30-fold increase in data yield within a significantly shortened timescale.
[ "2", "7", "8" ]
98
552
0
false
This represents up to a 30-fold increase in data yield within a significantly shortened timescale.
[]
This represents up to a 30-fold increase in data yield within a significantly shortened timescale.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
Indeed, within our lab, the screen is routinely used to assess 12 compounds over 500 bp every 24 h, using only one automated sequencer.
[ "2", "7", "8" ]
135
553
0
false
Indeed, within our lab, the screen is routinely used to assess 12 compounds over 500 bp every 24 h, using only one automated sequencer.
[]
Indeed, within our lab, the screen is routinely used to assess 12 compounds over 500 bp every 24 h, using only one automated sequencer.
true
true
true
true
true
93
0
DISCUSSION
1
2
[ "B2", "B7", "B8" ]
17,586,817
pmid-212715|pmid-15333913|pmid-9407524|pmid-11265303|pmid-3773731|pmid-9013649|pmid-11494863|pmid-15333913|pmid-11494863|pmid-11529207
The described assay has the further advantage of producing quantifiable, linearly-separated band intensities collected in real-time and does not require such unreliable steps as ethanol precipitation and the transfer of an electrophoresis gel to blotting paper.
[ "2", "7", "8" ]
261
554
0
false
The described assay has the further advantage of producing quantifiable, linearly-separated band intensities collected in real-time and does not require such unreliable steps as ethanol precipitation and the transfer of an electrophoresis gel to blotting paper.
[]
The described assay has the further advantage of producing quantifiable, linearly-separated band intensities collected in real-time and does not require such unreliable steps as ethanol precipitation and the transfer of an electrophoresis gel to blotting paper.
true
true
true
true
true
93
1
DISCUSSION
1
9–13
[ "B9 B10 B11 B12 B13", "B30", "B31", "B32", "B33", "B34" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
As with other previously described modifications to DNase I footprinting (9–13), useful improvements are afforded by the introduction of an automated DNA sequencing system and the omission of radioisotope use—although in a well-equipped laboratory it would be perfectly reasonable to use the 96-well procedure with radiolabelled DNA.
[ "9–13", "30", "31", "32", "33", "34" ]
333
555
1
false
As with other previously described modifications to DNase I footprinting, useful improvements are afforded by the introduction of an automated DNA sequencing system and the omission of radioisotope use—although in a well-equipped laboratory it would be perfectly reasonable to use the 96-well procedure with radiolabelled DNA.
[ "9–13" ]
As with other previously described modifications to DNase I footprinting, useful improvements are afforded by the introduction of an automated DNA sequencing system and the omission of radioisotope use—although in a well-equipped laboratory it would be perfectly reasonable to use the 96-well procedure with radiolabelled DNA.
true
true
true
true
true
94
1
DISCUSSION
1
30
[ "B9 B10 B11 B12 B13", "B30", "B31", "B32", "B33", "B34" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
Despite the relative expense of automated DNA sequencing systems, their versatility allows them to be used for many other applications, notably DNA sequencing (30), AFLP analysis, (31) electrophoretic mobility shift assays (32) and in vivo footprinting (33).
[ "9–13", "30", "31", "32", "33", "34" ]
258
556
1
false
Despite the relative expense of automated DNA sequencing systems, their versatility allows them to be used for many other applications, notably DNA sequencing, AFLP analysis, electrophoretic mobility shift assays and in vivo footprinting.
[ "30", "31", "32", "33" ]
Despite the relative expense of automated DNA sequencing systems, their versatility allows them to be used for many other applications, notably DNA sequencing, AFLP analysis, electrophoretic mobility shift assays and in vivo footprinting.
true
true
true
true
true
94
1
DISCUSSION
1
34
[ "B9 B10 B11 B12 B13", "B30", "B31", "B32", "B33", "B34" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
Additionally, the dye labels utilized are considerably safer, have long lifetimes and are low in cost (34).
[ "9–13", "30", "31", "32", "33", "34" ]
107
557
1
false
Additionally, the dye labels utilized are considerably safer, have long lifetimes and are low in cost.
[ "34" ]
Additionally, the dye labels utilized are considerably safer, have long lifetimes and are low in cost.
true
true
true
true
true
94
1
DISCUSSION
1
9–13
[ "B9 B10 B11 B12 B13", "B30", "B31", "B32", "B33", "B34" ]
17,586,817
pmid-15333913|pmid-11494863|pmid-11529207|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-8190649|NA|pmid-9266087|pmid-11084866|pmid-11465496|pmid-11217851|pmid-11233604|pmid-11730013|pmid-11017053|pmid-8738322
It is also common to find that such systems are available for communal use in many research environments, and although fluorescent sequencing systems are more common than the LI-COR infrared system described here, continual improvement in the fluorescent dyes and optics used by automated sequencing systems should no longer prevent such fluorophores being used as an alternative to radioisotopes in exactly the same method described here.
[ "9–13", "30", "31", "32", "33", "34" ]
439
558
0
false
It is also common to find that such systems are available for communal use in many research environments, and although fluorescent sequencing systems are more common than the LI-COR infrared system described here, continual improvement in the fluorescent dyes and optics used by automated sequencing systems should no longer prevent such fluorophores being used as an alternative to radioisotopes in exactly the same method described here.
[]
It is also common to find that such systems are available for communal use in many research environments, and although fluorescent sequencing systems are more common than the LI-COR infrared system described here, continual improvement in the fluorescent dyes and optics used by automated sequencing systems should no longer prevent such fluorophores being used as an alternative to radioisotopes in exactly the same method described here.
true
true
true
true
true
94
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
Ultimately, the optimization of the practical steps for the DNase I footprinting screen were less challenging than the development of the analysis procedure.
[ "25" ]
157
559
0
false
Ultimately, the optimization of the practical steps for the DNase I footprinting screen were less challenging than the development of the analysis procedure.
[]
Ultimately, the optimization of the practical steps for the DNase I footprinting screen were less challenging than the development of the analysis procedure.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
As many features of the screen were novel, no commercially available programs were suitable for the entire analysis.
[ "25" ]
116
560
0
false
As many features of the screen were novel, no commercially available programs were suitable for the entire analysis.
[]
As many features of the screen were novel, no commercially available programs were suitable for the entire analysis.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
The final analysis system is, in effect, a hybrid between existing image analysis software and our own programs, and as such some degree of user-input is still required, in order to transfer data between steps and to make occasional informed judgements.
[ "25" ]
253
561
0
false
The final analysis system is, in effect, a hybrid between existing image analysis software and our own programs, and as such some degree of user-input is still required, in order to transfer data between steps and to make occasional informed judgements.
[]
The final analysis system is, in effect, a hybrid between existing image analysis software and our own programs, and as such some degree of user-input is still required, in order to transfer data between steps and to make occasional informed judgements.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
Nevertheless, one advantage of a semi-automated procedure over a fully automated procedure is that it allows the user to monitor the analysis at several stages and in greater depth (25).
[ "25" ]
186
562
1
false
Nevertheless, one advantage of a semi-automated procedure over a fully automated procedure is that it allows the user to monitor the analysis at several stages and in greater depth.
[ "25" ]
Nevertheless, one advantage of a semi-automated procedure over a fully automated procedure is that it allows the user to monitor the analysis at several stages and in greater depth.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
With the DNase I footprinting screen in particular, the use of a semi-automated procedure allowed us to overcome the difficulty of having a wide range of band intensities within each lane (due to the inherent non-uniform cleavage of DNA by DNase I).
[ "25" ]
249
563
0
false
With the DNase I footprinting screen in particular, the use of a semi-automated procedure allowed us to overcome the difficulty of having a wide range of band intensities within each lane (due to the inherent non-uniform cleavage of DNA by DNase I).
[]
With the DNase I footprinting screen in particular, the use of a semi-automated procedure allowed us to overcome the difficulty of having a wide range of band intensities within each lane (due to the inherent non-uniform cleavage of DNA by DNase I).
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
By allowing the user to monitor the differential cleavage outputs, it became possible to ensure that the desired ‘score’ data gave an accurate description of the initial gel image data without compromising on the speed of analysis.
[ "25" ]
231
564
0
false
By allowing the user to monitor the differential cleavage outputs, it became possible to ensure that the desired ‘score’ data gave an accurate description of the initial gel image data without compromising on the speed of analysis.
[]
By allowing the user to monitor the differential cleavage outputs, it became possible to ensure that the desired ‘score’ data gave an accurate description of the initial gel image data without compromising on the speed of analysis.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
A further advantage of the semi-automated procedure is that it introduces flexibility to the analysis.
[ "25" ]
102
565
0
false
A further advantage of the semi-automated procedure is that it introduces flexibility to the analysis.
[]
A further advantage of the semi-automated procedure is that it introduces flexibility to the analysis.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
With only minor modifications, our programs can be adjusted to analyse gel images of different dimensions (length, width, and number of lanes) or even to analyse electrophoresis results from alternative sequencing systems and from conventional radioisotope footprinting.
[ "25" ]
270
566
0
false
With only minor modifications, our programs can be adjusted to analyse gel images of different dimensions (length, width, and number of lanes) or even to analyse electrophoresis results from alternative sequencing systems and from conventional radioisotope footprinting.
[]
With only minor modifications, our programs can be adjusted to analyse gel images of different dimensions (length, width, and number of lanes) or even to analyse electrophoresis results from alternative sequencing systems and from conventional radioisotope footprinting.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
Indeed, the whole design of our 96-well DNase I footprinting screen is intentionally modular, in order to permit the user to adapt the protocol to suit their needs.
[ "25" ]
164
567
0
false
Indeed, the whole design of our 96-well DNase I footprinting screen is intentionally modular, in order to permit the user to adapt the protocol to suit their needs.
[]
Indeed, the whole design of our 96-well DNase I footprinting screen is intentionally modular, in order to permit the user to adapt the protocol to suit their needs.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
For example, a researcher wanting to screen a mutant library of transcription factors on several promoters could perform the DNase I footprinting in 96-well format (incubating with proteinase K before sample clean-up, in order to remove the protein content) before resolving the gel images using standard radioisotope electrophoresis over several days.
[ "25" ]
352
568
0
false
For example, a researcher wanting to screen a mutant library of transcription factors on several promoters could perform the DNase I footprinting in 96-well format (incubating with proteinase K before sample clean-up, in order to remove the protein content) before resolving the gel images using standard radioisotope electrophoresis over several days.
[]
For example, a researcher wanting to screen a mutant library of transcription factors on several promoters could perform the DNase I footprinting in 96-well format (incubating with proteinase K before sample clean-up, in order to remove the protein content) before resolving the gel images using standard radioisotope electrophoresis over several days.
true
true
true
true
true
95
2
DISCUSSION
1
25
[ "B25" ]
17,586,817
pmid-7785784|pmid-15701734
The subsequent data could then be processed rapidly using the semi-automated procedure providing the user with readily-comparable profiles of how each mutation effects transcription factor binding.
[ "25" ]
197
569
0
false
The subsequent data could then be processed rapidly using the semi-automated procedure providing the user with readily-comparable profiles of how each mutation effects transcription factor binding.
[]
The subsequent data could then be processed rapidly using the semi-automated procedure providing the user with readily-comparable profiles of how each mutation effects transcription factor binding.
true
true
true
true
true
95
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
The 30-fold increase in throughput afforded by the 96-well DNase I footprinting assay allows, for the first time, the use of DNase I footprinting as a screening tool for assessing the DNA-binding properties of ligands, DNA-binding proteins and potentially therapeutic test agents.
[ "19" ]
280
570
0
false
The 30-fold increase in throughput afforded by the 96-well DNase I footprinting assay allows, for the first time, the use of DNase I footprinting as a screening tool for assessing the DNA-binding properties of ligands, DNA-binding proteins and potentially therapeutic test agents.
[]
The 30-fold increase in throughput afforded by the 96-well DNase I footprinting assay allows, for the first time, the use of DNase I footprinting as a screening tool for assessing the DNA-binding properties of ligands, DNA-binding proteins and potentially therapeutic test agents.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
In our lab, we have found it possible to work at a capacity that allows as many as 42 compounds to be characterized per week against a 500 bp DNA target when using the 56 concentration range described here.
[ "19" ]
206
571
0
false
In our lab, we have found it possible to work at a capacity that allows as many as 42 compounds to be characterized per week against a 500 bp DNA target when using the 56 concentration range described here.
[]
In our lab, we have found it possible to work at a capacity that allows as many as 42 compounds to be characterized per week against a 500 bp DNA target when using the 56 concentration range described here.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
The power of the assay is illustrated by the results described here, obtained using the PBD-polypyrrole series.
[ "19" ]
111
572
0
false
The power of the assay is illustrated by the results described here, obtained using the PBD-polypyrrole series.
[]
The power of the assay is illustrated by the results described here, obtained using the PBD-polypyrrole series.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
The full series was characterized—including full analysis over 700 bp of DNA and preparation of labelled DNA—in a total time of just three days.
[ "19" ]
144
573
0
false
The full series was characterized—including full analysis over 700 bp of DNA and preparation of labelled DNA—in a total time of just three days.
[]
The full series was characterized—including full analysis over 700 bp of DNA and preparation of labelled DNA—in a total time of just three days.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
By comparison, our previous characterization that included analysis of the series (over 200 bp of DNA) took more than four weeks to achieve (19).
[ "19" ]
145
574
1
false
By comparison, our previous characterization that included analysis of the series (over 200 bp of DNA) took more than four weeks to achieve.
[ "19" ]
By comparison, our previous characterization that included analysis of the series (over 200 bp of DNA) took more than four weeks to achieve.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
By comparing the ‘score’ profiles of a large number of compounds, differences in binding-site size, sequence-selectivity and affinity can all be determined with ease.
[ "19" ]
166
575
0
false
By comparing the ‘score’ profiles of a large number of compounds, differences in binding-site size, sequence-selectivity and affinity can all be determined with ease.
[]
By comparing the ‘score’ profiles of a large number of compounds, differences in binding-site size, sequence-selectivity and affinity can all be determined with ease.
true
true
true
true
true
96
3
DISCUSSION
1
19
[ "B19" ]
17,586,817
pmid-16942018
In research programs to design novel drugs, these data are invaluable for selecting lead compounds, directing further synthesis and in determining the nature of drug–DNA interactions.
[ "19" ]
183
576
0
false
In research programs to design novel drugs, these data are invaluable for selecting lead compounds, directing further synthesis and in determining the nature of drug–DNA interactions.
[]
In research programs to design novel drugs, these data are invaluable for selecting lead compounds, directing further synthesis and in determining the nature of drug–DNA interactions.
true
true
true
true
true
96
0
INTRODUCTION
1
1
[ "B1" ]
17,264,124
pmid-11529427
Meiotic recombination is critical for sexual reproduction, since it is essential for the viability of gametes and their genetic diversity.
[ "1" ]
138
577
0
false
Meiotic recombination is critical for sexual reproduction, since it is essential for the viability of gametes and their genetic diversity.
[]
Meiotic recombination is critical for sexual reproduction, since it is essential for the viability of gametes and their genetic diversity.
true
true
true
true
true
97
0
INTRODUCTION
1
1
[ "B1" ]
17,264,124
pmid-11529427
In meiosis, recombination between homologous chromosomes is initiated by programmed double-stranded DNA breaks (DSBs), which are transiently and meiotically introduced at recombination initiation sites, after the completion of premeiotic DNA replication.
[ "1" ]
254
578
0
false
In meiosis, recombination between homologous chromosomes is initiated by programmed double-stranded DNA breaks (DSBs), which are transiently and meiotically introduced at recombination initiation sites, after the completion of premeiotic DNA replication.
[]
In meiosis, recombination between homologous chromosomes is initiated by programmed double-stranded DNA breaks (DSBs), which are transiently and meiotically introduced at recombination initiation sites, after the completion of premeiotic DNA replication.
true
true
true
true
true
97
0
INTRODUCTION
1
1
[ "B1" ]
17,264,124
pmid-11529427
In the yeast Saccharomyces cerevisiae, ten genes (SPO11, MEI4, MER2/REC107, REC102, SKI8/REC103, REC104, REC114, MRE11, RAD50 and XRS2) are required for meiotic DSB formation, in addition to two genes for meiosis-specific RNA splicing (MER1 and MRE2) (1).
[ "1" ]
255
579
1
false
In the yeast Saccharomyces cerevisiae, ten genes are required for meiotic DSB formation, in addition to two genes for meiosis-specific RNA splicing.
[ "SPO11, MEI4, MER2/REC107, REC102, SKI8/REC103, REC104, REC114, MRE11, RAD50 and XRS2", "MER1 and MRE2", "1" ]
In the yeast Saccharomyces cerevisiae, ten genes are required for meiotic DSB formation, in addition to two genes for meiosis-specific RNA splicing.
true
true
true
true
true
97
0
INTRODUCTION
1
1
[ "B1" ]
17,264,124
pmid-11529427
Null mutations of these genes result in defective meiotic recombination and spore inviability.
[ "1" ]
94
580
0
false
Null mutations of these genes result in defective meiotic recombination and spore inviability.
[]
Null mutations of these genes result in defective meiotic recombination and spore inviability.
true
true
true
true
true
97
1
INTRODUCTION
1
2
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
Spo11, an evolutionarily conserved protein, is the catalytic component of meiotic DNA cleavage, and many studies suggest that Spo11 cleaves DNA via a topoisomerase-like transesterification reaction, forming intermediates by linking to the 5′ ends of the DNA strands (2,3).
[ "2", "3", "4", "5", "6", "7" ]
272
581
0
false
Spo11, an evolutionarily conserved protein, is the catalytic component of meiotic DNA cleavage, and many studies suggest that Spo11 cleaves DNA via a topoisomerase-like transesterification reaction, forming intermediates by linking to the 5′ ends of the DNA strands.
[ "2,3" ]
Spo11, an evolutionarily conserved protein, is the catalytic component of meiotic DNA cleavage, and many studies suggest that Spo11 cleaves DNA via a topoisomerase-like transesterification reaction, forming intermediates by linking to the 5′ ends of the DNA strands.
true
true
true
true
true
98
1
INTRODUCTION
1
4
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
These intermediates are then further processed via asymmetric endonucleolytic cleavage that is likely mediated by one or more other endonucleases (4).
[ "2", "3", "4", "5", "6", "7" ]
150
582
1
false
These intermediates are then further processed via asymmetric endonucleolytic cleavage that is likely mediated by one or more other endonucleases.
[ "4" ]
These intermediates are then further processed via asymmetric endonucleolytic cleavage that is likely mediated by one or more other endonucleases.
true
true
true
true
true
98
1
INTRODUCTION
1
2
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
Importantly, Spo11 shares structural similarity with the A subunit of topoisomerase 6 (Top6A) that has been found only in the archaeon Sulfolobus shibatae.
[ "2", "3", "4", "5", "6", "7" ]
155
583
0
false
Importantly, Spo11 shares structural similarity with the A subunit of topoisomerase 6 that has been found only in the archaeon Sulfolobus shibatae.
[ "Top6A" ]
Importantly, Spo11 shares structural similarity with the A subunit of topoisomerase 6 that has been found only in the archaeon Sulfolobus shibatae.
true
true
true
true
true
98
1
INTRODUCTION
1
5
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
Top6A has ATP-dependent DNA relaxation activity in vitro and forms a heterotetramer with Top6B (5).
[ "2", "3", "4", "5", "6", "7" ]
99
584
1
false
Top6A has ATP-dependent DNA relaxation activity in vitro and forms a heterotetramer with Top6B.
[ "5" ]
Top6A has ATP-dependent DNA relaxation activity in vitro and forms a heterotetramer with Top6B.
true
true
true
true
true
98
1
INTRODUCTION
1
6
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
Crystallized Top6A of Methanococcus jannaschii forms a U-shaped dimer with a putative DNA interaction channel (6).
[ "2", "3", "4", "5", "6", "7" ]
114
585
1
false
Crystallized Top6A of Methanococcus jannaschii forms a U-shaped dimer with a putative DNA interaction channel.
[ "6" ]
Crystallized Top6A of Methanococcus jannaschii forms a U-shaped dimer with a putative DNA interaction channel.
true
true
true
true
true
98
1
INTRODUCTION
1
2
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
To date, whether or not this dimer is similar to the Spo11 complex has not been determined, since it has proved difficult to purify functional Spo11 protein.
[ "2", "3", "4", "5", "6", "7" ]
157
586
0
false
To date, whether or not this dimer is similar to the Spo11 complex has not been determined, since it has proved difficult to purify functional Spo11 protein.
[]
To date, whether or not this dimer is similar to the Spo11 complex has not been determined, since it has proved difficult to purify functional Spo11 protein.
true
true
true
true
true
98
1
INTRODUCTION
1
7
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
In S. cerevisiae, the heterozygous combination of various DSB-defective spo11 mutant alleles and SPO11-3HA results in a partial dominant negative phenotype with respect to DSB formation, although the SPO11-3HA/SPO11-3HA homozygous diploid strain has a wild-type level of DSB formation, suggesting that Spo11 functions in dimeric or multimeric form (7).
[ "2", "3", "4", "5", "6", "7" ]
352
587
1
false
In S. cerevisiae, the heterozygous combination of various DSB-defective spo11 mutant alleles and SPO11-3HA results in a partial dominant negative phenotype with respect to DSB formation, although the SPO11-3HA/SPO11-3HA homozygous diploid strain has a wild-type level of DSB formation, suggesting that Spo11 functions in dimeric or multimeric form.
[ "7" ]
In S. cerevisiae, the heterozygous combination of various DSB-defective spo11 mutant alleles and SPO11-3HA results in a partial dominant negative phenotype with respect to DSB formation, although the SPO11-3HA/SPO11-3HA homozygous diploid strain has a wild-type level of DSB formation, suggesting that Spo11 functions in dimeric or multimeric form.
true
true
true
true
true
98
1
INTRODUCTION
1
2
[ "B2", "B3", "B4", "B5", "B6", "B7" ]
17,264,124
pmid-9121560|pmid-9039264|pmid-16107854|pmid-12596227|pmid-10545127|pmid-11809802
The difficulties experienced in purifying soluble Spo11 led us to investigate the interaction between Spo11 subunits in vivo.
[ "2", "3", "4", "5", "6", "7" ]
125
588
0
false
The difficulties experienced in purifying soluble Spo11 led us to investigate the interaction between Spo11 subunits in vivo.
[]
The difficulties experienced in purifying soluble Spo11 led us to investigate the interaction between Spo11 subunits in vivo.
true
true
true
true
true
98
2
INTRODUCTION
1
1
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
Regulation of Spo11 endonucleolytic activity can be envisaged to occur in at least two ways.
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
92
589
0
false
Regulation of Spo11 endonucleolytic activity can be envisaged to occur in at least two ways.
[]
Regulation of Spo11 endonucleolytic activity can be envisaged to occur in at least two ways.
true
true
true
true
true
99
2
INTRODUCTION
1
1
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
In the first model, cleavage activity of Spo11 might be activated or facilitated by other proteins.
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
99
590
0
false
In the first model, cleavage activity of Spo11 might be activated or facilitated by other proteins.
[]
In the first model, cleavage activity of Spo11 might be activated or facilitated by other proteins.
true
true
true
true
true
99
2
INTRODUCTION
1
1
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
In S. cerevisiae, at least nine other proteins are known to be required for DSB formation, but their role remains poorly understood; genetic and/or physical studies indicate that they interact with each other (1).
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
213
591
1
false
In S. cerevisiae, at least nine other proteins are known to be required for DSB formation, but their role remains poorly understood; genetic and/or physical studies indicate that they interact with each other.
[ "1" ]
In S. cerevisiae, at least nine other proteins are known to be required for DSB formation, but their role remains poorly understood; genetic and/or physical studies indicate that they interact with each other.
true
true
true
true
true
99
2
INTRODUCTION
1
8
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
Ski8 interacts directly with Spo11, and this interaction, in addition to the interaction of Spo11 with Rec102 and Rec104, is essential for DNA cleavage (8), suggesting that these proteins form a complex with Spo11 to activate the cleavage reaction.
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
248
592
1
false
Ski8 interacts directly with Spo11, and this interaction, in addition to the interaction of Spo11 with Rec102 and Rec104, is essential for DNA cleavage, suggesting that these proteins form a complex with Spo11 to activate the cleavage reaction.
[ "8" ]
Ski8 interacts directly with Spo11, and this interaction, in addition to the interaction of Spo11 with Rec102 and Rec104, is essential for DNA cleavage, suggesting that these proteins form a complex with Spo11 to activate the cleavage reaction.
true
true
true
true
true
99
2
INTRODUCTION
1
8–10
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
Mer2/Rec107, Mei4 and Rec114 interact with each other, and contact Xrs2 of the Mre11/Rad50/Xrs2 complex, which is required for DSB formation and repair, raising the additional question of how DSB formation is coupled to single-strand end processing (8–10).
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
256
593
1
false
Mer2/Rec107, Mei4 and Rec114 interact with each other, and contact Xrs2 of the Mre11/Rad50/Xrs2 complex, which is required for DSB formation and repair, raising the additional question of how DSB formation is coupled to single-strand end processing.
[ "8–10" ]
Mer2/Rec107, Mei4 and Rec114 interact with each other, and contact Xrs2 of the Mre11/Rad50/Xrs2 complex, which is required for DSB formation and repair, raising the additional question of how DSB formation is coupled to single-strand end processing.
true
true
true
true
true
99
2
INTRODUCTION
1
11
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
Overexpression of Rec114 in S. cerevisiae is known to inhibit meiotic DSB formation, suggesting that Rec114 is a key regulator of meiotic DSB formation (11), but the molecular basis of this effect has not yet been elucidated.
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
225
594
1
false
Overexpression of Rec114 in S. cerevisiae is known to inhibit meiotic DSB formation, suggesting that Rec114 is a key regulator of meiotic DSB formation, but the molecular basis of this effect has not yet been elucidated.
[ "11" ]
Overexpression of Rec114 in S. cerevisiae is known to inhibit meiotic DSB formation, suggesting that Rec114 is a key regulator of meiotic DSB formation, but the molecular basis of this effect has not yet been elucidated.
true
true
true
true
true
99
2
INTRODUCTION
1
12–14
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
Some additional factors, including histone acetyltransferases and chromatin-remodeling factors, are involved in meiotic alteration of local chromatin structure at DSB sites (12–14), which is a prerequisite for meiotic DSB cleavage.
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
231
595
1
false
Some additional factors, including histone acetyltransferases and chromatin-remodeling factors, are involved in meiotic alteration of local chromatin structure at DSB sites, which is a prerequisite for meiotic DSB cleavage.
[ "12–14" ]
Some additional factors, including histone acetyltransferases and chromatin-remodeling factors, are involved in meiotic alteration of local chromatin structure at DSB sites, which is a prerequisite for meiotic DSB cleavage.
true
true
true
true
true
99
2
INTRODUCTION
1
15
[ "B1", "B8", "B8 B9 B10", "B11", "B12 B13 B14", "B15", "B15 B16 B17" ]
17,264,124
pmid-11529427|pmid-14992724|pmid-14992724|pmid-14967146|pmid-16783010|pmid-10526232|pmid-9799249|pmid-9435246|pmid-14988732|pmid-11231124|pmid-11231124|pmid-16814718|pmid-16698922|pmid-11805049|pmid-12897161|pmid-15044957
DSB formation is temporally correlated with DNA replication (15), and is also controlled by cell cycle regulators, since inactivation of the S cyclins Clb5-Clb6, CDK and Hsk1 kinasae (S. pombe homolog of CDC7) eliminates DSB formation (15–17).
[ "1", "8", "8–10", "11", "12–14", "15", "15–17" ]
243
596
1
false
DSB formation is temporally correlated with DNA replication, and is also controlled by cell cycle regulators, since inactivation of the S cyclins Clb5-Clb6, CDK and Hsk1 kinasae (S. pombe homolog of CDC7) eliminates DSB formation.
[ "15", "15–17" ]
DSB formation is temporally correlated with DNA replication, and is also controlled by cell cycle regulators, since inactivation of the S cyclins Clb5-Clb6, CDK and Hsk1 kinasae (S. pombe homolog of CDC7) eliminates DSB formation.
true
true
true
true
true
99
3
INTRODUCTION
1
9
[ "B9", "B18", "B19" ]
17,264,124
pmid-14967146|pmid-9144217|pmid-11027339
An alternative but not mutually exclusive model to explain the regulation of Spo11 activity is to invoke chromosomal features (chromatin or higher order chromosome structures) defining permissive or nonpermissive chromosomal domains for DSB formation.
[ "9", "18", "19" ]
251
597
0
false
An alternative but not mutually exclusive model to explain the regulation of Spo11 activity is to invoke chromosomal features (chromatin or higher order chromosome structures) defining permissive or nonpermissive chromosomal domains for DSB formation.
[]
An alternative but not mutually exclusive model to explain the regulation of Spo11 activity is to invoke chromosomal features (chromatin or higher order chromosome structures) defining permissive or nonpermissive chromosomal domains for DSB formation.
true
true
true
true
true
100
3
INTRODUCTION
1
9
[ "B9", "B18", "B19" ]
17,264,124
pmid-14967146|pmid-9144217|pmid-11027339
Genome-wide studies have shown that DSB regions are not randomly distributed, but are rather distributed nonrandomly in DSB-hot and DSB-cold domains (9,18,19).
[ "9", "18", "19" ]
159
598
0
false
Genome-wide studies have shown that DSB regions are not randomly distributed, but are rather distributed nonrandomly in DSB-hot and DSB-cold domains.
[ "9,18,19" ]
Genome-wide studies have shown that DSB regions are not randomly distributed, but are rather distributed nonrandomly in DSB-hot and DSB-cold domains.
true
true
true
true
true
100
3
INTRODUCTION
1
9
[ "B9", "B18", "B19" ]
17,264,124
pmid-14967146|pmid-9144217|pmid-11027339
Whether this reflects the regulation of Spo11 binding or cleavage is not known.
[ "9", "18", "19" ]
79
599
0
false
Whether this reflects the regulation of Spo11 binding or cleavage is not known.
[]
Whether this reflects the regulation of Spo11 binding or cleavage is not known.
true
true
true
true
true
100