Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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INTRODUCTION
1
5
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
We constructed this database exclusively using our unique dataset of completely sequenced and carefully annotated full-length cDNAs, which was produced by a human annotation meeting, H-Invitational (5,6).
[ "5", "6", "7", "4", "8" ]
204
4,400
0
false
We constructed this database exclusively using our unique dataset of completely sequenced and carefully annotated full-length cDNAs, which was produced by a human annotation meeting, H-Invitational.
[ "5,6" ]
We constructed this database exclusively using our unique dataset of completely sequenced and carefully annotated full-length cDNAs, which was produced by a human annotation meeting, H-Invitational.
true
true
true
true
true
747
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
In H-Invitational, 56 419 cDNA sequences of human genes, which were fully sequenced with a sequence reliability higher than 99% [Phred values greater than 30; (7)] and whose potentially problematic sequences such as vectors and polyA tails were precisely trimmed, were subjected to manual annotation of AS variants.
[ "5", "6", "7", "4", "8" ]
315
4,401
0
false
In H-Invitational, 56 419 cDNA sequences of human genes, which were fully sequenced with a sequence reliability higher than 99% and whose potentially problematic sequences such as vectors and polyA tails were precisely trimmed, were subjected to manual annotation of AS variants.
[ "Phred values greater than 30; (7)" ]
In H-Invitational, 56 419 cDNA sequences of human genes, which were fully sequenced with a sequence reliability higher than 99% and whose potentially problematic sequences such as vectors and polyA tails were precisely trimmed, were subjected to manual annotation of AS variants.
true
true
true
true
true
747
2
INTRODUCTION
1
4
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
These cDNAs were clustered into 24 425 loci and of these, 6877 AS-containing loci, represented by 18 297 AS variants, were identified (4).
[ "5", "6", "7", "4", "8" ]
138
4,402
1
false
These cDNAs were clustered into 24 425 loci and of these, 6877 AS-containing loci, represented by 18 297 AS variants, were identified.
[ "4" ]
These cDNAs were clustered into 24 425 loci and of these, 6877 AS-containing loci, represented by 18 297 AS variants, were identified.
true
true
true
true
true
747
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
As a specialized AS database, H-DBAS enables multifaceted analyses from various viewpoints, comprehensively aiming at elucidating functional consequences of widespread AS in human genes.
[ "5", "6", "7", "4", "8" ]
186
4,403
0
false
As a specialized AS database, H-DBAS enables multifaceted analyses from various viewpoints, comprehensively aiming at elucidating functional consequences of widespread AS in human genes.
[]
As a specialized AS database, H-DBAS enables multifaceted analyses from various viewpoints, comprehensively aiming at elucidating functional consequences of widespread AS in human genes.
true
true
true
true
true
747
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
[Note: We will use the word, β€˜locus’, for the transcript cluster for the purpose of simplicity.
[ "5", "6", "7", "4", "8" ]
95
4,404
0
false
[Note: We will use the word, β€˜locus’, for the transcript cluster for the purpose of simplicity.
[]
[Note: We will use the word, β€˜locus’, for the transcript cluster for the purpose of simplicity.
false
false
true
true
false
747
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
However, the wording might be reconsidered, having observed highly diverse nature of the human transcriptome.
[ "5", "6", "7", "4", "8" ]
109
4,405
0
false
However, the wording might be reconsidered, having observed highly diverse nature of the human transcriptome.
[]
However, the wording might be reconsidered, having observed highly diverse nature of the human transcriptome.
true
true
true
true
true
747
2
INTRODUCTION
1
8
[ "b5", "b6", "b7", "b4", "b8" ]
17,130,147
pmid-15103394|pmid-15860772|pmid-9521921|pmid-16914452|pmid-15273986
Also see the reference (8)].
[ "5", "6", "7", "4", "8" ]
28
4,406
1
false
Also see the reference ].
[ "8" ]
Also see the reference ].
true
true
true
true
true
747
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,631,616
pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a microbial fingerprinting technique capable of discriminating microbial communities quickly and relatively inexpensively (1–3).
[ "1–3", "4", "5" ]
199
4,407
1
false
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a microbial fingerprinting technique capable of discriminating microbial communities quickly and relatively inexpensively.
[ "1–3" ]
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a microbial fingerprinting technique capable of discriminating microbial communities quickly and relatively inexpensively.
true
true
true
true
true
748
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,631,616
pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182
T-RFLP is increasingly used in high-throughput studies of microbial communities in combination with or even in lieu of clone library analysis (4,5).
[ "1–3", "4", "5" ]
148
4,408
0
false
T-RFLP is increasingly used in high-throughput studies of microbial communities in combination with or even in lieu of clone library analysis.
[ "4,5" ]
T-RFLP is increasingly used in high-throughput studies of microbial communities in combination with or even in lieu of clone library analysis.
true
true
true
true
true
748
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,631,616
pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182
Briefly, the method involves PCR amplification of a gene of interest (often 16S rRNA genes) with fluorescent dye-labeled primers, followed by multiple single restriction digests done in parallel.
[ "1–3", "4", "5" ]
195
4,409
0
false
Briefly, the method involves PCR amplification of a gene of interest (often 16S rRNA genes) with fluorescent dye-labeled primers, followed by multiple single restriction digests done in parallel.
[]
Briefly, the method involves PCR amplification of a gene of interest with fluorescent dye-labeled primers, followed by multiple single restriction digests done in parallel.
true
true
true
true
true
748
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,631,616
pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182
The resulting fragments are then separated by capillary electrophoresis with an internal size standard to determine the lengths of the terminal (fluorescently labeled) fragments.
[ "1–3", "4", "5" ]
178
4,410
0
false
The resulting fragments are then separated by capillary electrophoresis with an internal size standard to determine the lengths of the terminal (fluorescently labeled) fragments.
[]
The resulting fragments are then separated by capillary electrophoresis with an internal size standard to determine the lengths of the terminal (fluorescently labeled) fragments.
true
true
true
true
true
748
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,631,616
pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182
Each distinct terminal restriction fragment is considered an operational taxonomic unit (OTU), thus the choice of restriction enzymes can impact the number of OTUs observed in each sample and the calculation of diversity statistics.
[ "1–3", "4", "5" ]
232
4,411
0
false
Each distinct terminal restriction fragment is considered an operational taxonomic unit (OTU), thus the choice of restriction enzymes can impact the number of OTUs observed in each sample and the calculation of diversity statistics.
[]
Each distinct terminal restriction fragment is considered an operational taxonomic unit (OTU), thus the choice of restriction enzymes can impact the number of OTUs observed in each sample and the calculation of diversity statistics.
true
true
true
true
true
748
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
When analyzing uncharacterized and very diverse bacterial communities, sufficient community discrimination can often be accomplished with multiple randomly-chosen tetrameric restriction enzymes (6).
[ "6", "1–5", "7–26", "1", "2", "17" ]
198
4,412
1
false
When analyzing uncharacterized and very diverse bacterial communities, sufficient community discrimination can often be accomplished with multiple randomly-chosen tetrameric restriction enzymes.
[ "6" ]
When analyzing uncharacterized and very diverse bacterial communities, sufficient community discrimination can often be accomplished with multiple randomly-chosen tetrameric restriction enzymes.
true
true
true
true
true
749
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
However, a brief review of the literature indicates that there is still no standard in even this simplified case.
[ "6", "1–5", "7–26", "1", "2", "17" ]
113
4,413
0
false
However, a brief review of the literature indicates that there is still no standard in even this simplified case.
[]
However, a brief review of the literature indicates that there is still no standard in even this simplified case.
true
true
true
true
true
749
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
We examined 26 papers (1–5,7–26) that were published between 1997 and 2007 and used T-RFLP.
[ "6", "1–5", "7–26", "1", "2", "17" ]
91
4,414
0
false
We examined 26 papers that were published between 1997 and 2007 and used T-RFLP.
[ "1–5,7–26" ]
We examined 26 papers that were published between 1997 and 2007 and used T-RFLP.
true
true
true
true
true
749
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
Of those papers, 38% used universal bacterial primers combined with a single restriction enzyme, but the choice of enzyme was not consistent.
[ "6", "1–5", "7–26", "1", "2", "17" ]
141
4,415
0
false
Of those papers, 38% used universal bacterial primers combined with a single restriction enzyme, but the choice of enzyme was not consistent.
[]
Of those papers, 38% used universal bacterial primers combined with a single restriction enzyme, but the choice of enzyme was not consistent.
true
true
true
true
true
749
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
MspI was used most frequently (four studies), followed by TaqI (two studies), and one study each used AluI, CfoI, HhaI and HaeIII.
[ "6", "1–5", "7–26", "1", "2", "17" ]
130
4,416
0
false
MspI was used most frequently (four studies), followed by TaqI (two studies), and one study each used AluI, CfoI, HhaI and HaeIII.
[]
MspI was used most frequently (four studies), followed by TaqI (two studies), and one study each used AluI, CfoI, HhaI and HaeIII.
true
true
true
true
true
749
1
INTRODUCTION
1
6
[ "B6", "B1 B2 B3 B4 B5", "B7 B8 B9 B10 B11 B12 B13 B14 B15 B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26", "B1", "B2", "B17" ]
17,631,616
pmid-12902276|pmid-9361437|pmid-11243261|pmid-12571013|pmid-19719582|pmid-16957182|pmid-10568840|pmid-10877790|pmid-11233162|NA|pmid-15880891|pmid-19712409|pmid-15767011|pmid-16269735|pmid-15746346|pmid-17064266|pmid-16957219|pmid-17142382|pmid-17041161|pmid-16944345|pmid-17023024|pmid-16957254|pmid-16461676|pmid-17196...
Overall, only three of the 26 papers included a rationalization of enzyme selection (1,2,17).
[ "6", "1–5", "7–26", "1", "2", "17" ]
93
4,417
0
false
Overall, only three of the 26 papers included a rationalization of enzyme selection.
[ "1,2,17" ]
Overall, only three of the 26 papers included a rationalization of enzyme selection.
true
true
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749
2
INTRODUCTION
0
null
null
17,631,616
null
An alternate approach to T-RFLP can be taken if the microbial community has been characterized (by clone library analysis or by prediction from previous studies) or if a particular taxonomic group is being targeted with specific primers.
null
237
4,418
0
false
null
null
An alternate approach to T-RFLP can be taken if the microbial community has been characterized (by clone library analysis or by prediction from previous studies) or if a particular taxonomic group is being targeted with specific primers.
true
true
true
true
true
750
2
INTRODUCTION
0
null
null
17,631,616
null
In this case, a more reasoned choice of restriction enzymes can be conducted.
null
77
4,419
0
false
null
null
In this case, a more reasoned choice of restriction enzymes can be conducted.
true
true
true
true
true
750
2
INTRODUCTION
0
null
null
17,631,616
null
In particular, specific species or microbial taxa of interest to the researcherβ€”particularly closely related taxa that may share some restriction sitesβ€”can often be differentiated if the proper restriction enzymes are selected.
null
227
4,420
0
false
null
null
In particular, specific species or microbial taxa of interest to the researcherβ€”particularly closely related taxa that may share some restriction sitesβ€”can often be differentiated if the proper restriction enzymes are selected.
true
true
true
true
true
750
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
There are, however, few resources available to narrow down the selection process.
[ "27", "28", "29", "30" ]
81
4,421
0
false
There are, however, few resources available to narrow down the selection process.
[]
There are, however, few resources available to narrow down the selection process.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
Over 600 Type II restriction enzymes are commercially available, accounting for 262 distinct specificities (27).
[ "27", "28", "29", "30" ]
112
4,422
1
false
Over 600 Type II restriction enzymes are commercially available, accounting for 262 distinct specificities.
[ "27" ]
Over 600 Type II restriction enzymes are commercially available, accounting for 262 distinct specificities.
true
true
true
true
true
751
3
INTRODUCTION
1
28
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
Existing computer programs for assisting in the choice of restriction enzymes include TAP-TRFLP (28), MiCA Enzyme Resolving Power Analysis (http://mica.ibest.uidaho.edu) and TRF-CUT (29).
[ "27", "28", "29", "30" ]
187
4,423
1
false
Existing computer programs for assisting in the choice of restriction enzymes include TAP-TRFLP, MiCA Enzyme Resolving Power Analysis (http://mica.ibest.uidaho.edu) and TRF-CUT.
[ "28", "29" ]
Existing computer programs for assisting in the choice of restriction enzymes include TAP-TRFLP, MiCA Enzyme Resolving Power Analysis (http://mica.ibest.uidaho.edu) and TRF-CUT.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
These programs perform in silico restriction digestions of a predefined sequence database or user-provided sequences, but these results must still be manually examined to determine which enzymes are best suited to discriminate that set of sequences.
[ "27", "28", "29", "30" ]
249
4,424
0
false
These programs perform in silico restriction digestions of a predefined sequence database or user-provided sequences, but these results must still be manually examined to determine which enzymes are best suited to discriminate that set of sequences.
[]
These programs perform in silico restriction digestions of a predefined sequence database or user-provided sequences, but these results must still be manually examined to determine which enzymes are best suited to discriminate that set of sequences.
true
true
true
true
true
751
3
INTRODUCTION
1
30
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
CLEAVER (30), a stand alone program, provides the above features as well as the ability to assign sequences to taxonomic groups at multiple levels and to search for enzymes that cut one group but not another group.
[ "27", "28", "29", "30" ]
214
4,425
1
false
CLEAVER, a stand alone program, provides the above features as well as the ability to assign sequences to taxonomic groups at multiple levels and to search for enzymes that cut one group but not another group.
[ "30" ]
CLEAVER, a stand alone program, provides the above features as well as the ability to assign sequences to taxonomic groups at multiple levels and to search for enzymes that cut one group but not another group.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
However, it is limited to comparing only two groups at once.
[ "27", "28", "29", "30" ]
60
4,426
0
false
However, it is limited to comparing only two groups at once.
[]
However, it is limited to comparing only two groups at once.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
Restriction Endonuclease Picker (REPK) addresses this gap by finding enzymes that are able to discriminate an unlimited number of user-designated sequence groups on the basis of their terminal restriction fragment lengths.
[ "27", "28", "29", "30" ]
222
4,427
0
false
Restriction Endonuclease Picker (REPK) addresses this gap by finding enzymes that are able to discriminate an unlimited number of user-designated sequence groups on the basis of their terminal restriction fragment lengths.
[]
Restriction Endonuclease Picker (REPK) addresses this gap by finding enzymes that are able to discriminate an unlimited number of user-designated sequence groups on the basis of their terminal restriction fragment lengths.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
If no single enzyme can discriminate all groups, REPK reports sets of four restriction enzymes that together are able to differentiate the groups of interest.
[ "27", "28", "29", "30" ]
158
4,428
0
false
If no single enzyme can discriminate all groups, REPK reports sets of four restriction enzymes that together are able to differentiate the groups of interest.
[]
If no single enzyme can discriminate all groups, REPK reports sets of four restriction enzymes that together are able to differentiate the groups of interest.
true
true
true
true
true
751
3
INTRODUCTION
1
27
[ "B27", "B28", "B29", "B30" ]
17,631,616
pmid-17202163|pmid-10919828|pmid-15746378|pmid-16787976
An important component of REPK is this ability to specify the taxonomic rank of sequences to be differentiated, which is particularly useful in the case where a diverse microbial community has been characterized by clone library analysis or there is an existing database of several subgroups of sequences that amplify wi...
[ "27", "28", "29", "30" ]
349
4,429
0
false
An important component of REPK is this ability to specify the taxonomic rank of sequences to be differentiated, which is particularly useful in the case where a diverse microbial community has been characterized by clone library analysis or there is an existing database of several subgroups of sequences that amplify wi...
[]
An important component of REPK is this ability to specify the taxonomic rank of sequences to be differentiated, which is particularly useful in the case where a diverse microbial community has been characterized by clone library analysis or there is an existing database of several subgroups of sequences that amplify wi...
true
true
true
true
true
751
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
The discovery of naturally occurring RNA enzymes (ribozymes) (1,2) has postulated so-called the RNA world where RNAs could have served both genetic and catalytic roles (3).
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
172
4,430
1
false
The discovery of naturally occurring RNA enzymes (ribozymes) has postulated so-called the RNA world where RNAs could have served both genetic and catalytic roles.
[ "1,2", "3" ]
The discovery of naturally occurring RNA enzymes (ribozymes) has postulated so-called the RNA world where RNAs could have served both genetic and catalytic roles.
true
true
true
true
true
752
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
This notion has motivated us to not only search more ribozymes from nature (in vivo) but also artificially generate ribozymes in vitro with a wide variety of catalytic functions.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
178
4,431
0
false
This notion has motivated us to not only search more ribozymes from nature (in vivo) but also artificially generate ribozymes in vitro with a wide variety of catalytic functions.
[]
This notion has motivated us to not only search more ribozymes from nature (in vivo) but also artificially generate ribozymes in vitro with a wide variety of catalytic functions.
true
true
true
true
true
752
0
INTRODUCTION
1
6
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Representative examples include phosphoryl transfer (4,5), acylation (6), alkylation (7,8), Diels-Alder (9), aldol (10) and redox (11) reactions.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
145
4,432
1
false
Representative examples include phosphoryl transfer, acylation, alkylation, Diels-Alder, aldol and redox reactions.
[ "4,5", "6", "7,8", "9", "10", "11" ]
Representative examples include phosphoryl transfer, acylation, alkylation, Diels-Alder, aldol and redox reactions.
true
true
true
true
true
752
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Among them, in vitro selection of ribozymes that utilize nucleotide triphosphates (NTPs) has been of great interest since NTPs are playing diverse but essential roles in biological systems.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
189
4,433
0
false
Among them, in vitro selection of ribozymes that utilize nucleotide triphosphates (NTPs) has been of great interest since NTPs are playing diverse but essential roles in biological systems.
[]
Among them, in vitro selection of ribozymes that utilize nucleotide triphosphates (NTPs) has been of great interest since NTPs are playing diverse but essential roles in biological systems.
true
true
true
true
true
752
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
ATP, for example, is one of the building blocks of RNA and at the same time serves an energy or a phosphate source as well as in cofactors.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
139
4,434
0
false
ATP, for example, is one of the building blocks of RNA and at the same time serves an energy or a phosphate source as well as in cofactors.
[]
ATP, for example, is one of the building blocks of RNA and at the same time serves an energy or a phosphate source as well as in cofactors.
true
true
true
true
true
752
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Because of their potential biological significance, tremendous efforts have been made to evolve NTP-utilizing ribozymes from an RNA pool of random sequences.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
157
4,435
0
false
Because of their potential biological significance, tremendous efforts have been made to evolve NTP-utilizing ribozymes from an RNA pool of random sequences.
[]
Because of their potential biological significance, tremendous efforts have been made to evolve NTP-utilizing ribozymes from an RNA pool of random sequences.
true
true
true
true
true
752
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6", "B7", "B8", "B9", "B10", "B11" ]
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Indeed, it has been thus far reported that ribozymes catalyze three types of chemistry with nucleotide substrates.
[ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11" ]
114
4,436
0
false
Indeed, it has been thus far reported that ribozymes catalyze three types of chemistry with nucleotide substrates.
[]
Indeed, it has been thus far reported that ribozymes catalyze three types of chemistry with nucleotide substrates.
true
true
true
true
true
752
1
INTRODUCTION
1
4
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
The first example is ribozymes that use ATP as a phosphate source.
[ "4", "12", "13–15", "16", "17", "16" ]
66
4,437
0
false
The first example is ribozymes that use ATP as a phosphate source.
[]
The first example is ribozymes that use ATP as a phosphate source.
true
true
true
true
true
753
1
INTRODUCTION
1
4
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
Polynucleotide kinase ribozymes (4,12) are capable of catalyzing 5β€²- or 2β€²-phosphoryl transfer reaction.
[ "4", "12", "13–15", "16", "17", "16" ]
104
4,438
0
false
Polynucleotide kinase ribozymes are capable of catalyzing 5β€²- or 2β€²-phosphoryl transfer reaction.
[ "4,12" ]
Polynucleotide kinase ribozymes are capable of catalyzing 5β€²- or 2β€²-phosphoryl transfer reaction.
true
true
true
true
true
753
1
INTRODUCTION
1
13–15
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
The second example is a 5β€²-capping ribozyme (13–15), which utilizes GDP (as well as GMP or GTP) to form a 5′–5β€² phosphoanhydride bond that is analogous to the 5β€²-cap structure of mRNA.
[ "4", "12", "13–15", "16", "17", "16" ]
184
4,439
1
false
The second example is a 5β€²-capping ribozyme, which utilizes GDP (as well as GMP or GTP) to form a 5′–5β€² phosphoanhydride bond that is analogous to the 5β€²-cap structure of mRNA.
[ "13–15" ]
The second example is a 5β€²-capping ribozyme, which utilizes GDP (as well as GMP or GTP) to form a 5′–5β€² phosphoanhydride bond that is analogous to the 5β€²-cap structure of mRNA.
true
true
true
true
true
753
1
INTRODUCTION
1
4
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
The third example is those that can elongate their own or other oligonucleotide chain by NTPs (16,17).
[ "4", "12", "13–15", "16", "17", "16" ]
102
4,440
0
false
The third example is those that can elongate their own or other oligonucleotide chain by NTPs.
[ "16,17" ]
The third example is those that can elongate their own or other oligonucleotide chain by NTPs.
true
true
true
true
true
753
1
INTRODUCTION
1
4
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
Earlier ribozymes of this kind were isolated as those capable of ligating an oligonucleotide to its own 5β€²-end.
[ "4", "12", "13–15", "16", "17", "16" ]
111
4,441
0
false
Earlier ribozymes of this kind were isolated as those capable of ligating an oligonucleotide to its own 5β€²-end.
[]
Earlier ribozymes of this kind were isolated as those capable of ligating an oligonucleotide to its own 5β€²-end.
true
true
true
true
true
753
1
INTRODUCTION
1
16
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
One of these ribozymes, called Class I ligase ribozyme, was further evolved using various ingenious strategies and successfully turned into an RNA polymerase ribozyme (16).
[ "4", "12", "13–15", "16", "17", "16" ]
172
4,442
1
false
One of these ribozymes, called Class I ligase ribozyme, was further evolved using various ingenious strategies and successfully turned into an RNA polymerase ribozyme.
[ "16" ]
One of these ribozymes, called Class I ligase ribozyme, was further evolved using various ingenious strategies and successfully turned into an RNA polymerase ribozyme.
true
true
true
true
true
753
1
INTRODUCTION
1
4
[ "B4", "B12", "B13 B14 B15", "B16", "B17", "B16" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
Significantly, this ribozyme is able to add multiple nucleotides to the 3β€²-end of a substrate RNA according to the external template sequence in trans; thus, its 5β€²β†’3β€² polymerization function is analogous to the naturally occurring counterparts.
[ "4", "12", "13–15", "16", "17", "16" ]
245
4,443
0
false
Significantly, this ribozyme is able to add multiple nucleotides to the 3β€²-end of a substrate RNA according to the external template sequence in trans; thus, its 5β€²β†’3β€² polymerization function is analogous to the naturally occurring counterparts.
[]
Significantly, this ribozyme is able to add multiple nucleotides to the 3β€²-end of a substrate RNA according to the external template sequence in trans; thus, its 5β€²β†’3β€² polymerization function is analogous to the naturally occurring counterparts.
true
true
true
true
true
753
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
Most of earlier demonstrations described above have dealt with chemistry where the selection strategy could be rather easily devised; i.e.
[ "4", "5", "12", "18" ]
138
4,444
0
false
Most of earlier demonstrations described above have dealt with chemistry where the selection strategy could be rather easily devised; i.e.
[]
Most of earlier demonstrations described above have dealt with chemistry where the selection strategy could be rather easily devised; i.e.
true
true
true
true
true
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
a selection method allowed ones to fish out desired ribozymes with only one possible function or with a dominant function competing with other potential reactions to occur.
[ "4", "5", "12", "18" ]
172
4,445
0
false
a selection method allowed ones to fish out desired ribozymes with only one possible function or with a dominant function competing with other potential reactions to occur.
[]
a selection method allowed ones to fish out desired ribozymes with only one possible function or with a dominant function competing with other potential reactions to occur.
false
true
true
true
false
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
However, this does not mean that the ribozyme chemistry using NTPs or other nucleotide phosphates is limited to these reactions.
[ "4", "5", "12", "18" ]
128
4,446
0
false
However, this does not mean that the ribozyme chemistry using NTPs or other nucleotide phosphates is limited to these reactions.
[]
However, this does not mean that the ribozyme chemistry using NTPs or other nucleotide phosphates is limited to these reactions.
true
true
true
true
true
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
For example, phosphoryl transfer to the 3β€²-hydroxyl or 5β€²-triphosphate (5β€²-ppp), and the 5β€²-nucleotidyl transfer (3β€²β†’5β€² extension) could be catalyzed by RNA using ATP (or other NTPs) as a substrate.
[ "4", "5", "12", "18" ]
198
4,447
0
false
For example, phosphoryl transfer to the 3β€²-hydroxyl or 5β€²-triphosphate, and the 5β€²-nucleotidyl transfer could be catalyzed by RNA using ATP (or other NTPs) as a substrate.
[ "5β€²-ppp", "3β€²β†’5β€² extension" ]
For example, phosphoryl transfer to the 3β€²-hydroxyl or 5β€²-triphosphate, and the 5β€²-nucleotidyl transfer could be catalyzed by RNA using ATP (or other NTPs) as a substrate.
true
true
true
true
true
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
In principle, RNA sequences that catalyze one of these reactions can be selected by a conventional strategy that yielded kinase ribozymes using ATP-Ξ³S as a substrate (4,5,12,18); yet, no ribozyme with such functions has been reported.
[ "4", "5", "12", "18" ]
234
4,448
0
false
In principle, RNA sequences that catalyze one of these reactions can be selected by a conventional strategy that yielded kinase ribozymes using ATP-Ξ³S as a substrate ; yet, no ribozyme with such functions has been reported.
[ "4,5,12,18" ]
In principle, RNA sequences that catalyze one of these reactions can be selected by a conventional strategy that yielded kinase ribozymes using ATP-Ξ³S as a substrate ; yet, no ribozyme with such functions has been reported.
true
true
true
true
true
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
Therefore, a challenge is how ribozymes that catalyze unreported reactions are isolated and identified from a random RNA pool competing with those catalyzing other reactions reported previously.
[ "4", "5", "12", "18" ]
194
4,449
0
false
Therefore, a challenge is how ribozymes that catalyze unreported reactions are isolated and identified from a random RNA pool competing with those catalyzing other reactions reported previously.
[]
Therefore, a challenge is how ribozymes that catalyze unreported reactions are isolated and identified from a random RNA pool competing with those catalyzing other reactions reported previously.
true
true
true
true
true
754
2
INTRODUCTION
1
4
[ "B4", "B5", "B12", "B18" ]
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
Accordingly, the selection strategy should be the most critical factor toward the success.
[ "4", "5", "12", "18" ]
90
4,450
0
false
Accordingly, the selection strategy should be the most critical factor toward the success.
[]
Accordingly, the selection strategy should be the most critical factor toward the success.
true
true
true
true
true
754
3
INTRODUCTION
0
null
null
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
To isolate ribozymes capable of catalyzing the above reactions, we developed a strategy involving three layers of selection constraints to enrich 5β€²-ppp-dependent catalytic species in a random RNA pool.
null
202
4,451
0
false
null
null
To isolate ribozymes capable of catalyzing the above reactions, we developed a strategy involving three layers of selection constraints to enrich 5β€²-ppp-dependent catalytic species in a random RNA pool.
true
true
true
true
true
755
3
INTRODUCTION
0
null
null
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
Executing this selection indeed yielded a novel RNA sequence that catalyzes one of the above reactions: 3β€²β†’5β€² nucleotide extension.
null
131
4,452
0
false
null
null
Executing this selection indeed yielded a novel RNA sequence that catalyzes one of the above reactions: 3β€²β†’5β€² nucleotide extension.
true
true
true
true
true
755
3
INTRODUCTION
0
null
null
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
We report here selection and characterization of this ribozyme that shows intriguing promiscuous recognition to purine nucleotides.
null
131
4,453
0
false
null
null
We report here selection and characterization of this ribozyme that shows intriguing promiscuous recognition to purine nucleotides.
true
true
true
true
true
755
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Here we have shown in vitro selection of a novel ribozyme C06 that catalyzes the 5β€²-nucleotidyl transfer reaction forming the 2′–5β€² phosphodiester bond (Figure 4E).
null
164
4,454
0
false
null
null
Here we have shown in vitro selection of a novel ribozyme C06 that catalyzes the 5β€²-nucleotidyl transfer reaction forming the 2′–5β€² phosphodiester bond (Figure 4E).
true
true
true
true
true
756
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
The C06 sequence was found in pool 14-I as a minor population compared to possible internal kinases (Figure 2B).
null
112
4,455
0
false
null
null
The C06 sequence was found in pool 14-I as a minor population compared to possible internal kinases (Figure 2B).
true
true
true
true
true
756
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Finding of such a sequence was made possible by executing selection under the layers of selection criteria and the careful sequence comparison in two pools at the round 14 generated by the procedures involving 5β€²-ppp or 5β€²-OH RNA for the selection.
null
248
4,456
0
false
null
null
Finding of such a sequence was made possible by executing selection under the layers of selection criteria and the careful sequence comparison in two pools at the round 14 generated by the procedures involving 5β€²-ppp or 5β€²-OH RNA for the selection.
true
true
true
true
true
756
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Especially, the latter counterselection strategy facilitated the confirmation of the desired activity without checking all clones for their activities.
null
151
4,457
0
false
null
null
Especially, the latter counterselection strategy facilitated the confirmation of the desired activity without checking all clones for their activities.
true
true
true
true
true
756
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
The 5β€²-nucleotidyl transfer reaction is considered as a 3β€²β†’5β€² mononucleotide extension, and thus no natural counterpart is known to exist in the present enzyme world.
null
166
4,458
0
false
null
null
The 5β€²-nucleotidyl transfer reaction is considered as a 3β€²β†’5β€² mononucleotide extension, and thus no natural counterpart is known to exist in the present enzyme world.
true
true
true
true
true
756
0
DISCUSSION
0
null
null
17,567,602
pmid-6297745|pmid-6197186|NA|pmid-7521014|pmid-16274247|pmid-11459506|pmid-7723823|pmid-8849775|pmid-9288965|pmid-16125106|pmid-12910259
Nonetheless, an RNA molecule reported here is able to perform such a unique chemistry in cis as well as in trans.
null
113
4,459
0
false
null
null
Nonetheless, an RNA molecule reported here is able to perform such a unique chemistry in cis as well as in trans.
true
true
true
true
true
756
1
DISCUSSION
1
17
[ "B17" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
Joyce et al.
[ "17" ]
12
4,460
0
false
Joyce et al.
[]
Joyce et al.
true
true
true
true
true
757
1
DISCUSSION
1
17
[ "B17" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
have reported a ribozyme capable of catalyzing both 5β€²- and 3β€²-nucleotidyl transfer reactions (17).
[ "17" ]
99
4,461
1
false
have reported a ribozyme capable of catalyzing both 5β€²- and 3β€²-nucleotidyl transfer reactions.
[ "17" ]
have reported a ribozyme capable of catalyzing both 5β€²- and 3β€²-nucleotidyl transfer reactions.
false
true
true
true
false
757
1
DISCUSSION
1
17
[ "B17" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
This ribozyme, called E278-19, is a variant of Class
[ "17" ]
52
4,462
0
false
This ribozyme, called E278-19, is a variant of Class
[]
This ribozyme, called E278-19, is a variant of Class
true
true
false
true
false
757
1
DISCUSSION
1
17
[ "B17" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
I ligase ribozyme isolated by a continuous in vitro evolution procedure aimed at evolving 5β€²β†’3β€² mono- or di-nucleotide extension.
[ "17" ]
129
4,463
0
false
I ligase ribozyme isolated by a continuous in vitro evolution procedure aimed at evolving 5β€²β†’3β€² mono- or di-nucleotide extension.
[]
I ligase ribozyme isolated by a continuous in vitro evolution procedure aimed at evolving 5β€²β†’3β€² mono- or di-nucleotide extension.
true
true
true
true
true
757
1
DISCUSSION
1
17
[ "B17" ]
17,567,602
pmid-7521014|pmid-7578148|pmid-9184134|pmid-17044717|pmid-16973893|pmid-11358999|pmid-12031665|pmid-11358999|pmid-12031665
Thus, the 3β€²β†’5β€² nucleotidyl transfer activity was coincidently discovered in the collection of ligase or polymerase ribozymes, but it certainly kept the same signatures as the parental class I ligase ribozyme, where the incoming nucleotide formed a base pair with the template nucleotide and the 3′–5β€² phosphodiester lin...
[ "17" ]
339
4,464
0
false
Thus, the 3β€²β†’5β€² nucleotidyl transfer activity was coincidently discovered in the collection of ligase or polymerase ribozymes, but it certainly kept the same signatures as the parental class I ligase ribozyme, where the incoming nucleotide formed a base pair with the template nucleotide and the 3′–5β€² phosphodiester lin...
[]
Thus, the 3β€²β†’5β€² nucleotidyl transfer activity was coincidently discovered in the collection of ligase or polymerase ribozymes, but it certainly kept the same signatures as the parental class I ligase ribozyme, where the incoming nucleotide formed a base pair with the template nucleotide and the 3′–5β€² phosphodiester lin...
true
true
true
true
true
757
2
DISCUSSION
0
null
null
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
In contrast, C06 and its miniaturized variant M4 promiscuously recognize the incoming purine nucleotides for the 3β€²β†’5β€² extension (Figure 5).
null
140
4,465
0
false
null
null
In contrast, C06 and its miniaturized variant M4 promiscuously recognize the incoming purine nucleotides for the 3β€²β†’5β€² extension (Figure 5).
true
true
true
true
true
758
2
DISCUSSION
0
null
null
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
Although it has not been ruled out if a nucleotide templating to the incoming purine nucleotide resides in the active site, the observed promiscuous activity toward various purine bases suggests that specific hydrogen bonding to purine bases is very unlikely.
null
259
4,466
0
false
null
null
Although it has not been ruled out if a nucleotide templating to the incoming purine nucleotide resides in the active site, the observed promiscuous activity toward various purine bases suggests that specific hydrogen bonding to purine bases is very unlikely.
true
true
true
true
true
758
2
DISCUSSION
0
null
null
17,567,602
pmid-7521014|pmid-16274247|pmid-7578148|pmid-16790565
We rather think that the incoming substrate is guided by base-stacking interactions to the active site of ribozyme and somehow the ribozyme 5β€²-Ξ±-phosphate is projected to the 2β€²-OH of the incoming nucleotide for the nucleophilic attack.
null
236
4,467
0
false
null
null
We rather think that the incoming substrate is guided by base-stacking interactions to the active site of ribozyme and somehow the ribozyme 5β€²-Ξ±-phosphate is projected to the 2β€²-OH of the incoming nucleotide for the nucleophilic attack.
true
true
true
true
true
758
3
DISCUSSION
1
22
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
Even though we cannot identify a direct counterpart enzyme in the contemporary protein world, terminal deoxyribonucleotide transferase (TdT) catalyzes a similar reaction.
[ "22", "23", "23", "3", "24" ]
170
4,468
0
false
Even though we cannot identify a direct counterpart enzyme in the contemporary protein world, terminal deoxyribonucleotide transferase (TdT) catalyzes a similar reaction.
[]
Even though we cannot identify a direct counterpart enzyme in the contemporary protein world, terminal deoxyribonucleotide transferase (TdT) catalyzes a similar reaction.
true
true
true
true
true
759
3
DISCUSSION
1
22
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
This enzyme can add nucleotide(s) to the 3β€²-end of DNA in a template-independent manner.
[ "22", "23", "23", "3", "24" ]
88
4,469
0
false
This enzyme can add nucleotide(s) to the 3β€²-end of DNA in a template-independent manner.
[]
This enzyme can add nucleotide(s) to the 3β€²-end of DNA in a template-independent manner.
true
true
true
true
true
759
3
DISCUSSION
1
22
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
Also TdT is well-known to have a preference to dG over other deoxyribonucleotides even though it basically has a promiscuous ability to accept nucleotide substrates (22).
[ "22", "23", "23", "3", "24" ]
170
4,470
1
false
Also TdT is well-known to have a preference to dG over other deoxyribonucleotides even though it basically has a promiscuous ability to accept nucleotide substrates.
[ "22" ]
Also TdT is well-known to have a preference to dG over other deoxyribonucleotides even though it basically has a promiscuous ability to accept nucleotide substrates.
true
true
true
true
true
759
3
DISCUSSION
1
23
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
TdT apparently uses base-stacking interaction at least for its second nucleotidyl transfer step (23).
[ "22", "23", "23", "3", "24" ]
101
4,471
1
false
TdT apparently uses base-stacking interaction at least for its second nucleotidyl transfer step.
[ "23" ]
TdT apparently uses base-stacking interaction at least for its second nucleotidyl transfer step.
true
true
true
true
true
759
3
DISCUSSION
1
22
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
Although TdT shares some of key features of M4, distinct differences exist regarding directionality and substrate specificity of the nucleotidyl transfer event.
[ "22", "23", "23", "3", "24" ]
160
4,472
0
false
Although TdT shares some of key features of M4, distinct differences exist regarding directionality and substrate specificity of the nucleotidyl transfer event.
[]
Although TdT shares some of key features of M4, distinct differences exist regarding directionality and substrate specificity of the nucleotidyl transfer event.
true
true
true
true
true
759
3
DISCUSSION
1
23
[ "B22", "B23", "B23", "B3", "B24" ]
17,567,602
pmid-6301484|pmid-8524303|pmid-8524303|NA|pmid-14700631
As TdT plays an indispensable role in enhancing the diversity of the immunoglobulin repertoire (23), we can imagine a beneficial role of terminal nucleotide transfer at either end of RNA in the RNA world with regard to a genetic diversity, where the recombination could have been the primary source to achieve an evoluti...
[ "22", "23", "23", "3", "24" ]
344
4,473
1
false
As TdT plays an indispensable role in enhancing the diversity of the immunoglobulin repertoire, we can imagine a beneficial role of terminal nucleotide transfer at either end of RNA in the RNA world with regard to a genetic diversity, where the recombination could have been the primary source to achieve an evolution or...
[ "23", "3,24" ]
As TdT plays an indispensable role in enhancing the diversity of the immunoglobulin repertoire, we can imagine a beneficial role of terminal nucleotide transfer at either end of RNA in the RNA world with regard to a genetic diversity, where the recombination could have been the primary source to achieve an evolution or...
true
true
true
true
true
759
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
During the course of mutation studies, we found that indispensable motifs in M4 reside in the regions of the 5β€²-overhang, P2–P3 junction and L3 loop (Figures 3 and 6A).
[ "25–28", "25", "26", "27", "28", "30" ]
168
4,474
0
false
During the course of mutation studies, we found that indispensable motifs in M4 reside in the regions of the 5β€²-overhang, P2–P3 junction and L3 loop (Figures 3 and 6A).
[]
During the course of mutation studies, we found that indispensable motifs in M4 reside in the regions of the 5β€²-overhang, P2–P3 junction and L3 loop (Figures 3 and 6A).
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Since M4 catalyzes essentially the same chemistry as RNA ligase ribozymes except for the directionality of extension, it is of interest to compare the secondary structure of M4 with those of reported ligase ribozymes.
[ "25–28", "25", "26", "27", "28", "30" ]
217
4,475
0
false
Since M4 catalyzes essentially the same chemistry as RNA ligase ribozymes except for the directionality of extension, it is of interest to compare the secondary structure of M4 with those of reported ligase ribozymes.
[]
Since M4 catalyzes essentially the same chemistry as RNA ligase ribozymes except for the directionality of extension, it is of interest to compare the secondary structure of M4 with those of reported ligase ribozymes.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Four representative ligases are selected for comparison; Bartel's class II ligase, Ellington's L1 ligase, Joyce's R3C and cytidine-free ligases (Figure 6B–E) (25–28), all of which form a 2′–5β€² phosphodiester linkages like M4 ribozyme.
[ "25–28", "25", "26", "27", "28", "30" ]
234
4,476
1
false
Four representative ligases are selected for comparison; Bartel's class II ligase, Ellington's L1 ligase, Joyce's R3C and cytidine-free ligases (Figure 6B–E), all of which form a 2′–5β€² phosphodiester linkages like M4 ribozyme.
[ "25–28" ]
Four representative ligases are selected for comparison; Bartel's class II ligase, Ellington's L1 ligase, Joyce's R3C and cytidine-free ligases, all of which form a 2′–5β€² phosphodiester linkages like M4 ribozyme.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
These four ligases share the structural features of 5β€²-overhang and internal guide sequence for the incoming oligonucleotide.
[ "25–28", "25", "26", "27", "28", "30" ]
125
4,477
0
false
These four ligases share the structural features of 5β€²-overhang and internal guide sequence for the incoming oligonucleotide.
[]
These four ligases share the structural features of 5β€²-overhang and internal guide sequence for the incoming oligonucleotide.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
An obvious similarity found in all ribozymes including M4 is that the junction domain likely consisting of a part of catalytic core is dominated with A and G, occasionally containing U (note that G is dominated at the 5β€²-end because the consecutive Gs generally give higher transcription efficiency and therefore such RN...
[ "25–28", "25", "26", "27", "28", "30" ]
364
4,478
0
false
An obvious similarity found in all ribozymes including M4 is that the junction domain likely consisting of a part of catalytic core is dominated with A and G, occasionally containing U (note that G is dominated at the 5β€²-end because the consecutive Gs generally give higher transcription efficiency and therefore such RN...
[]
An obvious similarity found in all ribozymes including M4 is that the junction domain likely consisting of a part of catalytic core is dominated with A and G, occasionally containing U.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
This suggests that such AG-rich motifs are suitable for composing the tertiary space where 5β€²-Ξ±-phosphate is positioned to the 2β€²-OH of the incoming nucleotide.
[ "25–28", "25", "26", "27", "28", "30" ]
160
4,479
0
false
This suggests that such AG-rich motifs are suitable for composing the tertiary space where 5β€²-Ξ±-phosphate is positioned to the 2β€²-OH of the incoming nucleotide.
[]
This suggests that such AG-rich motifs are suitable for composing the tertiary space where 5β€²-Ξ±-phosphate is positioned to the 2β€²-OH of the incoming nucleotide.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
On the other hand, a significant difference between M4 and these ribozymes is that M4 lacks the internal guide sequence for specific base pairing.
[ "25–28", "25", "26", "27", "28", "30" ]
146
4,480
0
false
On the other hand, a significant difference between M4 and these ribozymes is that M4 lacks the internal guide sequence for specific base pairing.
[]
On the other hand, a significant difference between M4 and these ribozymes is that M4 lacks the internal guide sequence for specific base pairing.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Probably, the P2–P3 junction and L3 region would be located in close proximity, creating a 3D space for bringing the incoming purine nucleotides to the active site via base-stacking interactions.
[ "25–28", "25", "26", "27", "28", "30" ]
195
4,481
0
false
Probably, the P2–P3 junction and L3 region would be located in close proximity, creating a 3D space for bringing the incoming purine nucleotides to the active site via base-stacking interactions.
[]
Probably, the P2–P3 junction and L3 region would be located in close proximity, creating a 3D space for bringing the incoming purine nucleotides to the active site via base-stacking interactions.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Figure 6.Proposed secondary structures of M4 ribozyme and ligases.
[ "25–28", "25", "26", "27", "28", "30" ]
66
4,482
0
false
Figure 6.Proposed secondary structures of M4 ribozyme and ligases.
[]
Figure 6.Proposed secondary structures of M4 ribozyme and ligases.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(A) M4 from this study.
[ "25–28", "25", "26", "27", "28", "30" ]
23
4,483
0
false
(A) M4 from this study.
[]
(A) M4 from this study.
false
false
true
true
false
760
4
DISCUSSION
1
25
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(B) Bartel's class II ligase ribozyme (25).
[ "25–28", "25", "26", "27", "28", "30" ]
43
4,484
1
false
(B) Bartel's class II ligase ribozyme.
[ "25" ]
(B) Bartel's class II ligase ribozyme.
false
false
true
true
false
760
4
DISCUSSION
1
26
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(C) Ellington's L1 ligase ribozyme (26).
[ "25–28", "25", "26", "27", "28", "30" ]
40
4,485
1
false
(C) Ellington's L1 ligase ribozyme.
[ "26" ]
(C) Ellington's L1 ligase ribozyme.
false
false
true
true
false
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively (27,28).
[ "25–28", "25", "26", "27", "28", "30" ]
80
4,486
0
false
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively.
[ "27,28" ]
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively.
false
false
true
true
false
760
4
DISCUSSION
1
30
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(F) Siverman's 7S11 RNA ligase DNA enzyme (30).
[ "25–28", "25", "26", "27", "28", "30" ]
47
4,487
1
false
(F) Siverman's 7S11 RNA ligase DNA enzyme.
[ "30" ]
(F) Siverman's 7S11 RNA ligase DNA enzyme.
false
false
true
true
false
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Bases likely involved in catalysis are shown.
[ "25–28", "25", "26", "27", "28", "30" ]
45
4,488
0
false
Bases likely involved in catalysis are shown.
[]
Bases likely involved in catalysis are shown.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
[ "25–28", "25", "26", "27", "28", "30" ]
101
4,489
0
false
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
[]
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
true
true
true
true
true
760
4
DISCUSSION
1
25–28
[ "B25 B26 B27 B28", "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
[ "25–28", "25", "26", "27", "28", "30" ]
132
4,490
0
false
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
[]
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
true
true
true
true
true
760
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Proposed secondary structures of M4 ribozyme and ligases.
[ "25", "26", "27", "28", "30" ]
57
4,491
0
false
Proposed secondary structures of M4 ribozyme and ligases.
[]
Proposed secondary structures of M4 ribozyme and ligases.
true
true
true
true
true
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(A) M4 from this study.
[ "25", "26", "27", "28", "30" ]
23
4,492
0
false
(A) M4 from this study.
[]
(A) M4 from this study.
false
false
true
true
false
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(B) Bartel's class II ligase ribozyme (25).
[ "25", "26", "27", "28", "30" ]
43
4,493
1
false
(B) Bartel's class II ligase ribozyme.
[ "25" ]
(B) Bartel's class II ligase ribozyme.
false
false
true
true
false
761
5
DISCUSSION
1
26
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(C) Ellington's L1 ligase ribozyme (26).
[ "25", "26", "27", "28", "30" ]
40
4,494
1
false
(C) Ellington's L1 ligase ribozyme.
[ "26" ]
(C) Ellington's L1 ligase ribozyme.
false
false
true
true
false
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively (27,28).
[ "25", "26", "27", "28", "30" ]
80
4,495
0
false
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively.
[ "27,28" ]
(D) and (E) Joyce's R3C and cytidine-free ligase ribozyme, respectively.
false
false
true
true
false
761
5
DISCUSSION
1
30
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
(F) Siverman's 7S11 RNA ligase DNA enzyme (30).
[ "25", "26", "27", "28", "30" ]
47
4,496
1
false
(F) Siverman's 7S11 RNA ligase DNA enzyme.
[ "30" ]
(F) Siverman's 7S11 RNA ligase DNA enzyme.
false
false
true
true
false
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Bases likely involved in catalysis are shown.
[ "25", "26", "27", "28", "30" ]
45
4,497
0
false
Bases likely involved in catalysis are shown.
[]
Bases likely involved in catalysis are shown.
true
true
true
true
true
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
[ "25", "26", "27", "28", "30" ]
101
4,498
0
false
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
[]
Other parts of ribozyme sequences are shown in solid line; DNA parts are shown in thicker solid line.
true
true
true
true
true
761
5
DISCUSSION
1
25
[ "B25", "B26", "B27", "B28", "B30" ]
17,567,602
pmid-7618102|pmid-11345430|pmid-11333020|pmid-10580507|pmid-14758353
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
[ "25", "26", "27", "28", "30" ]
132
4,499
0
false
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
[]
The hydroxyl nucleophile of incoming purine (R) or oligonucleotide substrate (dashed lines) attacks the Ξ±-phosphate on the ribozyme.
true
true
true
true
true
761