Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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8
DISCUSSION
0
null
null
17,452,365
null
There are other approaches to predicting non-coding RNA.
null
56
9,300
0
false
null
null
There are other approaches to predicting non-coding RNA.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
One commonly used method is sequence alignment, e.g.
null
52
9,301
0
false
null
null
One commonly used method is sequence alignment, e.g.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
BLAST (3), Paralign (20) or FASTA (21).
null
39
9,302
0
false
null
null
BLAST (3), Paralign (20) or FASTA (21).
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
Another is based on structure-sensitive Stochastic Context Free Grammars (SCFG) (22) which form the basis of the tRNA prediction program tRNAscan-SE (23) and of Infernal (24), which is used when creating RFAM.
null
209
9,303
0
false
null
null
Another is based on structure-sensitive Stochastic Context Free Grammars (SCFG) (22) which form the basis of the tRNA prediction program tRNAscan-SE (23) and of Infernal (24), which is used when creating RFAM.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
While the sequence alignment methods are very fast, they are not particularly suited for prediction of non-coding RNA (1).
null
122
9,304
0
false
null
null
While the sequence alignment methods are very fast, they are not particularly suited for prediction of non-coding RNA (1).
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
Infernal, however, has a general worst case running time of order O(MN3) , which is prohibitive.
null
96
9,305
0
false
null
null
Infernal, however, has a general worst case running time of order O(MN3) , which is prohibitive.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
The RFAM database (17,18), which includes 5S and the 5β€² domain of 16S, uses BLAST to pre-screen genome sequences, followed by Infernal; despite a more efficient approach than the general SCFG, it does not analyze the entire 16S.
null
228
9,306
0
false
null
null
The RFAM database (17,18), which includes 5S and the 5β€² domain of 16S, uses BLAST to pre-screen genome sequences, followed by Infernal; despite a more efficient approach than the general SCFG, it does not analyze the entire 16S.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
A search for 5S in a 1 Mbp genome using Infernal took 4 hours 45 minutes: almost 1000 times as much as the 16 seconds used by RNAmmer for the much larger 16S model.
null
164
9,307
0
false
null
null
A search for 5S in a 1 Mbp genome using Infernal took 4 hours 45 minutes: almost 1000 times as much as the 16 seconds used by RNAmmer for the much larger 16S model.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
A time-saving approach to SCFGs could be to use the RaveNna (25) package which can convert an RFAM SCFG to an HMM.
null
114
9,308
0
false
null
null
A time-saving approach to SCFGs could be to use the RaveNna (25) package which can convert an RFAM SCFG to an HMM.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
This drastically reduces the running time; however, its usefulness would be limited since no models for the larger rRNAs are available.
null
135
9,309
0
false
null
null
This drastically reduces the running time; however, its usefulness would be limited since no models for the larger rRNAs are available.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
Another factor is that the 5S found by RaveNna (26) which were not already in RFAM were all in organellar sequences, sequences not analyzed by RNAmmer.
null
151
9,310
0
false
null
null
Another factor is that the 5S found by RaveNna (26) which were not already in RFAM were all in organellar sequences, sequences not analyzed by RNAmmer.
true
true
true
true
true
1,481
8
DISCUSSION
0
null
null
17,452,365
null
For further comparisons and comments on these different methods, we refer to (1).
null
81
9,311
0
false
null
null
For further comparisons and comments on these different methods, we refer to (1).
true
true
true
true
true
1,481
9
DISCUSSION
0
null
null
17,452,365
null
The RNAmmer program is available as a traditional HTML-based prediction server at http://www.cbs.dtu.dk/services/RNAmmer as well as through a SOAP-based web service.
null
165
9,312
0
false
null
null
The RNAmmer program is available as a traditional HTML-based prediction server at http://www.cbs.dtu.dk/services/RNAmmer as well as through a SOAP-based web service.
true
true
true
true
true
1,482
9
DISCUSSION
0
null
null
17,452,365
null
It is also available for download through the same site.
null
56
9,313
0
false
null
null
It is also available for download through the same site.
true
true
true
true
true
1,482
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5", "B6", "B7 B8 B9", "B10", "B11", "B12" ]
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
RNA interference (RNAi) is induced by double-stranded RNA (dsRNA) and results in gene silencing through sequence-specific degradation of the target RNA (1).
[ "1", "2–4", "5", "6", "7–9", "10", "11", "12" ]
156
9,314
1
false
RNA interference (RNAi) is induced by double-stranded RNA (dsRNA) and results in gene silencing through sequence-specific degradation of the target RNA.
[ "1" ]
RNA interference (RNAi) is induced by double-stranded RNA (dsRNA) and results in gene silencing through sequence-specific degradation of the target RNA.
true
true
true
true
true
1,483
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4", "B5", "B6", "B7 B8 B9", "B10", "B11", "B12" ]
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
RNAi provides plants and animals a defense mechanism against viruses (2–4) and retrotransposons (5,6).
[ "1", "2–4", "5", "6", "7–9", "10", "11", "12" ]
102
9,315
1
false
RNAi provides plants and animals a defense mechanism against viruses and retrotransposons.
[ "2–4", "5,6" ]
RNAi provides plants and animals a defense mechanism against viruses and retrotransposons.
true
true
true
true
true
1,483
0
INTRODUCTION
1
7–9
[ "B1", "B2 B3 B4", "B5", "B6", "B7 B8 B9", "B10", "B11", "B12" ]
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
The ribonuclease Dicer processes the long dsRNA replication intermediates into small interfering RNAs (siRNAs) of ∼22 nucleotides (nt) (7–9).
[ "1", "2–4", "5", "6", "7–9", "10", "11", "12" ]
141
9,316
1
false
The ribonuclease Dicer processes the long dsRNA replication intermediates into small interfering RNAs (siRNAs) of ∼22 nucleotides (nt).
[ "7–9" ]
The ribonuclease Dicer processes the long dsRNA replication intermediates into small interfering RNAs (siRNAs) of ∼22 nucleotides (nt).
true
true
true
true
true
1,483
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5", "B6", "B7 B8 B9", "B10", "B11", "B12" ]
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
These siRNAs are incorporated into the RNA-induced silencing complex (RISC) that finds complementary RNA sequences, resulting in cleavage of the target RNA (10,11).
[ "1", "2–4", "5", "6", "7–9", "10", "11", "12" ]
164
9,317
0
false
These siRNAs are incorporated into the RNA-induced silencing complex (RISC) that finds complementary RNA sequences, resulting in cleavage of the target RNA.
[ "10,11" ]
These siRNAs are incorporated into the RNA-induced silencing complex (RISC) that finds complementary RNA sequences, resulting in cleavage of the target RNA.
true
true
true
true
true
1,483
0
INTRODUCTION
1
12
[ "B1", "B2 B3 B4", "B5", "B6", "B7 B8 B9", "B10", "B11", "B12" ]
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
The central catalytic component of RISC is an Argonaute protein, which contains the signature domains PAZ and PIWI responsible for binding the siRNA strand (12).
[ "1", "2–4", "5", "6", "7–9", "10", "11", "12" ]
161
9,318
1
false
The central catalytic component of RISC is an Argonaute protein, which contains the signature domains PAZ and PIWI responsible for binding the siRNA strand.
[ "12" ]
The central catalytic component of RISC is an Argonaute protein, which contains the signature domains PAZ and PIWI responsible for binding the siRNA strand.
true
true
true
true
true
1,483
1
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
Transfection of synthetic siRNAs into cells or intracellular expression of short hairpin RNAs (shRNAs), which are processed into siRNA duplexes by Dicer, are powerful tools to suppress gene expression (13–15).
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
209
9,319
1
false
Transfection of synthetic siRNAs into cells or intracellular expression of short hairpin RNAs (shRNAs), which are processed into siRNA duplexes by Dicer, are powerful tools to suppress gene expression.
[ "13–15" ]
Transfection of synthetic siRNAs into cells or intracellular expression of short hairpin RNAs (shRNAs), which are processed into siRNA duplexes by Dicer, are powerful tools to suppress gene expression.
true
true
true
true
true
1,484
1
INTRODUCTION
1
16
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
Randomly selected siRNAs against a target show a large variation in their efficacy (16).
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
88
9,320
1
false
Randomly selected siRNAs against a target show a large variation in their efficacy.
[ "16" ]
Randomly selected siRNAs against a target show a large variation in their efficacy.
true
true
true
true
true
1,484
1
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
Empirical rules on siRNA duplex features have been reported and improve design of effective siRNAs.
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
99
9,321
0
false
Empirical rules on siRNA duplex features have been reported and improve design of effective siRNAs.
[]
Empirical rules on siRNA duplex features have been reported and improve design of effective siRNAs.
true
true
true
true
true
1,484
1
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
The asymmetry rule for siRNA duplex ends requires that the 5β€² end of the antisense strand forms a less stable end with its complement than the 5β€² end of the sense strand (17,18).
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
178
9,322
0
false
The asymmetry rule for siRNA duplex ends requires that the 5β€² end of the antisense strand forms a less stable end with its complement than the 5β€² end of the sense strand.
[ "17,18" ]
The asymmetry rule for siRNA duplex ends requires that the 5β€² end of the antisense strand forms a less stable end with its complement than the 5β€² end of the sense strand.
true
true
true
true
true
1,484
1
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
Related to this rule is the described requirement of high A/U content at the 5β€² end of the antisense strand and high G/C at the 5β€² end of the sense strand (19,20).
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
163
9,323
0
false
Related to this rule is the described requirement of high A/U content at the 5β€² end of the antisense strand and high G/C at the 5β€² end of the sense strand.
[ "19,20" ]
Related to this rule is the described requirement of high A/U content at the 5β€² end of the antisense strand and high G/C at the 5β€² end of the sense strand.
true
true
true
true
true
1,484
1
INTRODUCTION
1
13–15
[ "B13 B14 B15", "B16", "B17", "B18", "B19", "B20", "B19", "B21 B22 B23" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
In addition, a number of position-specific nucleotides, an unstructured guide-RNA, and an accessible target site have been reported to positively effect siRNA efficiency (19,21–23).
[ "13–15", "16", "17", "18", "19", "20", "19", "21–23" ]
181
9,324
0
false
In addition, a number of position-specific nucleotides, an unstructured guide-RNA, and an accessible target site have been reported to positively effect siRNA efficiency.
[ "19,21–23" ]
In addition, a number of position-specific nucleotides, an unstructured guide-RNA, and an accessible target site have been reported to positively effect siRNA efficiency.
true
true
true
true
true
1,484
2
INTRODUCTION
1
24
[ "B24", "B25 B26 B27 B28", "B29 B30 B31 B32 B33 B34", "B31", "B35", "B36", "B34", "B37" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
RNAi can be used as a therapeutic strategy against human pathogenic viruses such as HIV-1 (24).
[ "24", "25–28", "29–34", "31", "35", "36", "34", "37" ]
95
9,325
1
false
RNAi can be used as a therapeutic strategy against human pathogenic viruses such as HIV-1.
[ "24" ]
RNAi can be used as a therapeutic strategy against human pathogenic viruses such as HIV-1.
true
true
true
true
true
1,485
2
INTRODUCTION
1
25–28
[ "B24", "B25 B26 B27 B28", "B29 B30 B31 B32 B33 B34", "B31", "B35", "B36", "B34", "B37" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
HIV-1 replication can be inhibited transiently by transfection of synthetic siRNAs targeting viral RNA sequences or cellular co-factors (25–28).
[ "24", "25–28", "29–34", "31", "35", "36", "34", "37" ]
144
9,326
1
false
HIV-1 replication can be inhibited transiently by transfection of synthetic siRNAs targeting viral RNA sequences or cellular co-factors.
[ "25–28" ]
HIV-1 replication can be inhibited transiently by transfection of synthetic siRNAs targeting viral RNA sequences or cellular co-factors.
true
true
true
true
true
1,485
2
INTRODUCTION
1
29–34
[ "B24", "B25 B26 B27 B28", "B29 B30 B31 B32 B33 B34", "B31", "B35", "B36", "B34", "B37" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
Furthermore, long-term inhibition of HIV-1 replication has been demonstrated in transduced cell lines stably expressing antiviral siRNAs or shRNAs (29–34).
[ "24", "25–28", "29–34", "31", "35", "36", "34", "37" ]
155
9,327
1
false
Furthermore, long-term inhibition of HIV-1 replication has been demonstrated in transduced cell lines stably expressing antiviral siRNAs or shRNAs.
[ "29–34" ]
Furthermore, long-term inhibition of HIV-1 replication has been demonstrated in transduced cell lines stably expressing antiviral siRNAs or shRNAs.
true
true
true
true
true
1,485
2
INTRODUCTION
1
24
[ "B24", "B25 B26 B27 B28", "B29 B30 B31 B32 B33 B34", "B31", "B35", "B36", "B34", "B37" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
However, HIV-1 escape variants with nucleotide substitutions or deletions in the siRNA target sequence do emerge after prolonged culturing (31,35,36).
[ "24", "25–28", "29–34", "31", "35", "36", "34", "37" ]
150
9,328
0
false
However, HIV-1 escape variants with nucleotide substitutions or deletions in the siRNA target sequence do emerge after prolonged culturing.
[ "31,35,36" ]
However, HIV-1 escape variants with nucleotide substitutions or deletions in the siRNA target sequence do emerge after prolonged culturing.
true
true
true
true
true
1,485
2
INTRODUCTION
1
24
[ "B24", "B25 B26 B27 B28", "B29 B30 B31 B32 B33 B34", "B31", "B35", "B36", "B34", "B37" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
The emergence of RNAi-resistant variants may be blocked by a combination-shRNA therapy, which simultaneously targets multiple conserved viral RNA sequences (34,37).
[ "24", "25–28", "29–34", "31", "35", "36", "34", "37" ]
164
9,329
0
false
The emergence of RNAi-resistant variants may be blocked by a combination-shRNA therapy, which simultaneously targets multiple conserved viral RNA sequences.
[ "34,37" ]
The emergence of RNAi-resistant variants may be blocked by a combination-shRNA therapy, which simultaneously targets multiple conserved viral RNA sequences.
true
true
true
true
true
1,485
3
INTRODUCTION
1
36
[ "B36", "B59", "B38" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
We demonstrated that HIV-1 can also become resistant against RNAi by placing the target sequence in a stable RNA structure, which prevents binding of the siRNA (36).
[ "36", "59", "38" ]
165
9,330
1
false
We demonstrated that HIV-1 can also become resistant against RNAi by placing the target sequence in a stable RNA structure, which prevents binding of the siRNA.
[ "36" ]
We demonstrated that HIV-1 can also become resistant against RNAi by placing the target sequence in a stable RNA structure, which prevents binding of the siRNA.
true
true
true
true
true
1,486
3
INTRODUCTION
1
59
[ "B36", "B59", "B38" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
We also suggested that such structure-based target occlusion occurs in the RNA genomes of lentiviral vectors with a shRNA-cassette (59).
[ "36", "59", "38" ]
136
9,331
1
false
We also suggested that such structure-based target occlusion occurs in the RNA genomes of lentiviral vectors with a shRNA-cassette.
[ "59" ]
We also suggested that such structure-based target occlusion occurs in the RNA genomes of lentiviral vectors with a shRNA-cassette.
true
true
true
true
true
1,486
3
INTRODUCTION
1
36
[ "B36", "B59", "B38" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
By inserting these cassettes, the target sequence will automatically be present in the vector genome, and self-targeting by the shRNA should reduce the lentiviral production level.
[ "36", "59", "38" ]
180
9,332
0
false
By inserting these cassettes, the target sequence will automatically be present in the vector genome, and self-targeting by the shRNA should reduce the lentiviral production level.
[]
By inserting these cassettes, the target sequence will automatically be present in the vector genome, and self-targeting by the shRNA should reduce the lentiviral production level.
true
true
true
true
true
1,486
3
INTRODUCTION
1
36
[ "B36", "B59", "B38" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
However, since the target sequence in the genome is also located in this perfect shRNA hairpin, it is protected against RNAi, ensuring a normal vector titer.
[ "36", "59", "38" ]
157
9,333
0
false
However, since the target sequence in the genome is also located in this perfect shRNA hairpin, it is protected against RNAi, ensuring a normal vector titer.
[]
However, since the target sequence in the genome is also located in this perfect shRNA hairpin, it is protected against RNAi, ensuring a normal vector titer.
true
true
true
true
true
1,486
3
INTRODUCTION
1
38
[ "B36", "B59", "B38" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
Indeed, when the target in the lentiviral genome is unstructured, the titer is significantly reduced by the shRNA (38).
[ "36", "59", "38" ]
119
9,334
1
false
Indeed, when the target in the lentiviral genome is unstructured, the titer is significantly reduced by the shRNA.
[ "38" ]
Indeed, when the target in the lentiviral genome is unstructured, the titer is significantly reduced by the shRNA.
true
true
true
true
true
1,486
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The inhibitory effect of target RNA structure on RNAi efficiency has been described in several studies (23,39,40).
[ "23", "39", "40", "41", "42", "43" ]
114
9,335
0
false
The inhibitory effect of target RNA structure on RNAi efficiency has been described in several studies.
[ "23,39,40" ]
The inhibitory effect of target RNA structure on RNAi efficiency has been described in several studies.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
These studies compared the efficiency of different siRNAs on a fixed target, and found a correlation between target availability and RNAi efficiency.
[ "23", "39", "40", "41", "42", "43" ]
149
9,336
0
false
These studies compared the efficiency of different siRNAs on a fixed target, and found a correlation between target availability and RNAi efficiency.
[]
These studies compared the efficiency of different siRNAs on a fixed target, and found a correlation between target availability and RNAi efficiency.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Schubert et al.
[ "23", "39", "40", "41", "42", "43" ]
15
9,337
0
false
Schubert et al.
[]
Schubert et al.
true
true
true
true
true
1,487
4
INTRODUCTION
1
41
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
suggested that the local free energy of base pairing in the target region determines RNAi efficiency (41).
[ "23", "39", "40", "41", "42", "43" ]
106
9,338
1
false
suggested that the local free energy of base pairing in the target region determines RNAi efficiency.
[ "41" ]
suggested that the local free energy of base pairing in the target region determines RNAi efficiency.
false
true
true
true
false
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Ideally, one should test this concept by a mutational analysis of one target instead of comparing different siRNAs with intrinsically different RNAi efficacies.
[ "23", "39", "40", "41", "42", "43" ]
160
9,339
0
false
Ideally, one should test this concept by a mutational analysis of one target instead of comparing different siRNAs with intrinsically different RNAi efficacies.
[]
Ideally, one should test this concept by a mutational analysis of one target instead of comparing different siRNAs with intrinsically different RNAi efficacies.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
In this scenario, mutations that affect the RNA structure should not affect the target sequence itself, such that the same siRNA inhibitor can be used.
[ "23", "39", "40", "41", "42", "43" ]
151
9,340
0
false
In this scenario, mutations that affect the RNA structure should not affect the target sequence itself, such that the same siRNA inhibitor can be used.
[]
In this scenario, mutations that affect the RNA structure should not affect the target sequence itself, such that the same siRNA inhibitor can be used.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
In this study, we set out to determine the exact hairpin stability at which RNAi suppression occurs by systematically destabilizing a 21-base pair (bp) hairpin structure that occludes the complete target sequence.
[ "23", "39", "40", "41", "42", "43" ]
213
9,341
0
false
In this study, we set out to determine the exact hairpin stability at which RNAi suppression occurs by systematically destabilizing a 21-base pair (bp) hairpin structure that occludes the complete target sequence.
[]
In this study, we set out to determine the exact hairpin stability at which RNAi suppression occurs by systematically destabilizing a 21-base pair (bp) hairpin structure that occludes the complete target sequence.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
We monitored the effects on siRNA binding in vitro and RNAi efficiency in vivo.
[ "23", "39", "40", "41", "42", "43" ]
79
9,342
0
false
We monitored the effects on siRNA binding in vitro and RNAi efficiency in vivo.
[]
We monitored the effects on siRNA binding in vitro and RNAi efficiency in vivo.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The 3β€² end of the mRNA target sequence is initially recognized by bases 2–5 of the antisense/guide strand siRNA, therefore named the β€˜seed’ sequence (42,43).
[ "23", "39", "40", "41", "42", "43" ]
157
9,343
0
false
The 3β€² end of the mRNA target sequence is initially recognized by bases 2–5 of the antisense/guide strand siRNA, therefore named the β€˜seed’ sequence.
[ "42,43" ]
The 3β€² end of the mRNA target sequence is initially recognized by bases 2–5 of the antisense/guide strand siRNA, therefore named the β€˜seed’ sequence.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Thus, one may expect a more prominent effect of an accessible target 3β€² end, which primed us to address positional effects when destabilizing the target hairpin.
[ "23", "39", "40", "41", "42", "43" ]
161
9,344
0
false
Thus, one may expect a more prominent effect of an accessible target 3β€² end, which primed us to address positional effects when destabilizing the target hairpin.
[]
Thus, one may expect a more prominent effect of an accessible target 3β€² end, which primed us to address positional effects when destabilizing the target hairpin.
true
true
true
true
true
1,487
4
INTRODUCTION
1
23
[ "B23", "B39", "B40", "B41", "B42", "B43" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The results demonstrate a clear correlation between the overall stability of the target hairpin and RNAi efficiency, but positional effects were also apparent.
[ "23", "39", "40", "41", "42", "43" ]
159
9,345
0
false
The results demonstrate a clear correlation between the overall stability of the target hairpin and RNAi efficiency, but positional effects were also apparent.
[]
The results demonstrate a clear correlation between the overall stability of the target hairpin and RNAi efficiency, but positional effects were also apparent.
true
true
true
true
true
1,487
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
It has been proposed that RNAi efficiency is influenced by the local RNA structure of the targeted sequence.
null
108
9,346
0
false
null
null
It has been proposed that RNAi efficiency is influenced by the local RNA structure of the targeted sequence.
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
We investigated this phenomenon in detail by placement of the target sequence in a perfect hairpin structure (Ξ”G = βˆ’36.6 kcal/mol), which indeed resisted RNAi.
null
159
9,347
0
false
null
null
We investigated this phenomenon in detail by placement of the target sequence in a perfect hairpin structure (Ξ”G = βˆ’36.6 kcal/mol), which indeed resisted RNAi.
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
Subsequently we destabilized this tight target structure resulting in a gradual exposure of the target sequence.
null
112
9,348
0
false
null
null
Subsequently we destabilized this tight target structure resulting in a gradual exposure of the target sequence.
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
Destabilization of the hairpin structure has little effect on RNAi activity until a threshold is reached (Ξ”G β‰ˆ βˆ’30 kcal/mol).
null
125
9,349
0
false
null
null
Destabilization of the hairpin structure has little effect on RNAi activity until a threshold is reached (Ξ”G β‰ˆ βˆ’30 kcal/mol).
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
Beyond this threshold we demonstrate an inverse correlation between hairpin stability and RNAi-mediated inhibition.
null
115
9,350
0
false
null
null
Beyond this threshold we demonstrate an inverse correlation between hairpin stability and RNAi-mediated inhibition.
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
Maximal RNAi efficiency was observed with hairpins of Ξ”G β‰₯ βˆ’15 kcal/mol.
null
72
9,351
0
false
null
null
Maximal RNAi efficiency was observed with hairpins of Ξ”G β‰₯ βˆ’15 kcal/mol.
true
true
true
true
true
1,488
0
DISCUSSION
0
null
null
17,576,691
pmid-9486653|pmid-11423650|pmid-11459066|pmid-16554838|pmid-15817569|pmid-10535732|pmid-11157775|pmid-10749213|pmid-10778853|pmid-11253050|pmid-12230974|pmid-16009129
In vitro binding experiments suggested that the increase of RNAi-mediated inhibition is due to efficient siRNA binding to the destabilized target RNA hairpins.
null
159
9,352
0
false
null
null
In vitro binding experiments suggested that the increase of RNAi-mediated inhibition is due to efficient siRNA binding to the destabilized target RNA hairpins.
true
true
true
true
true
1,488
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
When we introduced position-specific mutations in the target hairpin, we observed RNAi efficiencies that deviate from this trend.
[ "43", "46", "47", "48", "36" ]
129
9,353
0
false
When we introduced position-specific mutations in the target hairpin, we observed RNAi efficiencies that deviate from this trend.
[]
When we introduced position-specific mutations in the target hairpin, we observed RNAi efficiencies that deviate from this trend.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
Hairpins with an opened 5β€² end or central part of the target sequence show less RNAi activity than predicted based on their overall stability.
[ "43", "46", "47", "48", "36" ]
142
9,354
0
false
Hairpins with an opened 5β€² end or central part of the target sequence show less RNAi activity than predicted based on their overall stability.
[]
Hairpins with an opened 5β€² end or central part of the target sequence show less RNAi activity than predicted based on their overall stability.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
In contrast, hairpins with an opened 3β€² end are more susceptible to RNAi than expected.
[ "43", "46", "47", "48", "36" ]
87
9,355
0
false
In contrast, hairpins with an opened 3β€² end are more susceptible to RNAi than expected.
[]
In contrast, hairpins with an opened 3β€² end are more susceptible to RNAi than expected.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
These results are consistent with the current notion that the 3β€² region of the target is initially recognized and bound by the RISC/siRNA complex (43).
[ "43", "46", "47", "48", "36" ]
151
9,356
1
false
These results are consistent with the current notion that the 3β€² region of the target is initially recognized and bound by the RISC/siRNA complex.
[ "43" ]
These results are consistent with the current notion that the 3β€² region of the target is initially recognized and bound by the RISC/siRNA complex.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
This model is supported by structural data on RISC bound to the siRNA strand.
[ "43", "46", "47", "48", "36" ]
77
9,357
0
false
This model is supported by structural data on RISC bound to the siRNA strand.
[]
This model is supported by structural data on RISC bound to the siRNA strand.
true
true
true
true
true
1,489
1
DISCUSSION
1
46
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
The 3β€² end of the siRNA is recognized and bound in a pocket by the PAZ domain of the Argonaute protein (46).
[ "43", "46", "47", "48", "36" ]
108
9,358
1
false
The 3β€² end of the siRNA is recognized and bound in a pocket by the PAZ domain of the Argonaute protein.
[ "46" ]
The 3β€² end of the siRNA is recognized and bound in a pocket by the PAZ domain of the Argonaute protein.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
The 5β€² end of the siRNA is anchored at the PIWI domain of Argonaute and these 5β€² nucleotides are readily accessible for base pairing to complementary 3β€² nucleotides of the target RNA (47,48).
[ "43", "46", "47", "48", "36" ]
191
9,359
0
false
The 5β€² end of the siRNA is anchored at the PIWI domain of Argonaute and these 5β€² nucleotides are readily accessible for base pairing to complementary 3β€² nucleotides of the target RNA.
[ "47,48" ]
The 5β€² end of the siRNA is anchored at the PIWI domain of Argonaute and these 5β€² nucleotides are readily accessible for base pairing to complementary 3β€² nucleotides of the target RNA.
true
true
true
true
true
1,489
1
DISCUSSION
1
43
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
The importance of the target 3β€² end was also revealed in experiments that selected for viruses that resist RNAi-mediated inhibition.
[ "43", "46", "47", "48", "36" ]
132
9,360
0
false
The importance of the target 3β€² end was also revealed in experiments that selected for viruses that resist RNAi-mediated inhibition.
[]
The importance of the target 3β€² end was also revealed in experiments that selected for viruses that resist RNAi-mediated inhibition.
true
true
true
true
true
1,489
1
DISCUSSION
1
36
[ "B43", "B46", "B47", "B48", "B36" ]
17,576,691
pmid-11910072|pmid-11373684|pmid-11981566|pmid-11937629|pmid-14567918|pmid-14567917|pmid-14758366|pmid-14769950|pmid-14758366|pmid-16258545|pmid-12604614|pmid-12888501|pmid-15170178|pmid-15156196|pmid-15800629|pmid-15800628|pmid-15687388
We described a unique HIV-1 escape variant that acquired a mutation outside the 19-nt target, which forces the RNA into an alternative structure that occludes the 3β€² end of the target (36).
[ "43", "46", "47", "48", "36" ]
189
9,361
1
false
We described a unique HIV-1 escape variant that acquired a mutation outside the 19-nt target, which forces the RNA into an alternative structure that occludes the 3β€² end of the target.
[ "36" ]
We described a unique HIV-1 escape variant that acquired a mutation outside the 19-nt target, which forces the RNA into an alternative structure that occludes the 3β€² end of the target.
true
true
true
true
true
1,489
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
Besides the in vivo RNAi measurements, we also tested the different RNA targets for their ability to interact with the siRNA in vitro.
[ "49" ]
134
9,362
0
false
Besides the in vivo RNAi measurements, we also tested the different RNA targets for their ability to interact with the siRNA in vitro.
[]
Besides the in vivo RNAi measurements, we also tested the different RNA targets for their ability to interact with the siRNA in vitro.
true
true
true
true
true
1,490
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
The overall Ξ”G effect of stable target hairpins is confirmed in this simplified in vitro setting, demonstrating that RNAi resistance is due to the inability of the siRNA to interact with the base-paired stem of the hairpin.
[ "49" ]
223
9,363
0
false
The overall Ξ”G effect of stable target hairpins is confirmed in this simplified in vitro setting, demonstrating that RNAi resistance is due to the inability of the siRNA to interact with the base-paired stem of the hairpin.
[]
The overall Ξ”G effect of stable target hairpins is confirmed in this simplified in vitro setting, demonstrating that RNAi resistance is due to the inability of the siRNA to interact with the base-paired stem of the hairpin.
true
true
true
true
true
1,490
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
We realize that the siRNA does not act by itself in vivo as it is part of RISC, of which the helicase activity may affect local structure in the target RNA (49).
[ "49" ]
161
9,364
1
false
We realize that the siRNA does not act by itself in vivo as it is part of RISC, of which the helicase activity may affect local structure in the target RNA.
[ "49" ]
We realize that the siRNA does not act by itself in vivo as it is part of RISC, of which the helicase activity may affect local structure in the target RNA.
true
true
true
true
true
1,490
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
In fact, we observed an interesting discrepancy between the in vivo and in vitro results for the 5β€²/center/3β€²-destabilized hairpins.
[ "49" ]
132
9,365
0
false
In fact, we observed an interesting discrepancy between the in vivo and in vitro results for the 5β€²/center/3β€²-destabilized hairpins.
[]
In fact, we observed an interesting discrepancy between the in vivo and in vitro results for the 5β€²/center/3β€²-destabilized hairpins.
true
true
true
true
true
1,490
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
We observed that an accessible 3β€² target is key for RNAi activity, but this effect was not seen in vitro.
[ "49" ]
105
9,366
0
false
We observed that an accessible 3β€² target is key for RNAi activity, but this effect was not seen in vitro.
[]
We observed that an accessible 3β€² target is key for RNAi activity, but this effect was not seen in vitro.
true
true
true
true
true
1,490
2
DISCUSSION
1
49
[ "B49" ]
17,576,691
NA|pmid-12186906|pmid-12087358|pmid-11981565|pmid-12042777|pmid-12842429|pmid-15006606|pmid-14963165|pmid-14581533|pmid-15831707|pmid-16959541|pmid-14963165|pmid-14557638|pmid-15687388|pmid-16959541|pmid-15195925|pmid-11701122
This result may indicate an important contribution of RISC in the siRNA-target RNA annealing step.
[ "49" ]
98
9,367
0
false
This result may indicate an important contribution of RISC in the siRNA-target RNA annealing step.
[]
This result may indicate an important contribution of RISC in the siRNA-target RNA annealing step.
true
true
true
true
true
1,490
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
Thus, target RNA structure is an important factor when selecting a suitable target sequence, as it can have a negative effect on RNAi efficiency.
[ "31", "40", "50", "31", "51", "39", "36" ]
145
9,368
0
false
Thus, target RNA structure is an important factor when selecting a suitable target sequence, as it can have a negative effect on RNAi efficiency.
[]
Thus, target RNA structure is an important factor when selecting a suitable target sequence, as it can have a negative effect on RNAi efficiency.
true
true
true
true
true
1,491
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
For instance, it has been shown that the TAR hairpin of the HIV-1 genome is an unsuitable target because of its tight structure (31,40,50).
[ "31", "40", "50", "31", "51", "39", "36" ]
139
9,369
0
false
For instance, it has been shown that the TAR hairpin of the HIV-1 genome is an unsuitable target because of its tight structure.
[ "31,40,50" ]
For instance, it has been shown that the TAR hairpin of the HIV-1 genome is an unsuitable target because of its tight structure.
true
true
true
true
true
1,491
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
On the other hand, it is obvious that an accessible sequence does not automatically make a good siRNA target (31), as the matching siRNA may not meet the criteria of an effective siRNA (51).
[ "31", "40", "50", "31", "51", "39", "36" ]
190
9,370
1
false
On the other hand, it is obvious that an accessible sequence does not automatically make a good siRNA target, as the matching siRNA may not meet the criteria of an effective siRNA.
[ "31", "51" ]
On the other hand, it is obvious that an accessible sequence does not automatically make a good siRNA target, as the matching siRNA may not meet the criteria of an effective siRNA.
true
true
true
true
true
1,491
3
DISCUSSION
1
39
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
It has been proposed to include a calculation of the amount of hydrogen bonds within the target sequence as a parameter for efficient target sequences (39).
[ "31", "40", "50", "31", "51", "39", "36" ]
156
9,371
1
false
It has been proposed to include a calculation of the amount of hydrogen bonds within the target sequence as a parameter for efficient target sequences.
[ "39" ]
It has been proposed to include a calculation of the amount of hydrogen bonds within the target sequence as a parameter for efficient target sequences.
true
true
true
true
true
1,491
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
We provide a Ξ”G threshold at which an hairpin RNA structure becomes inaccessible, and we differentiate between different target positions.
[ "31", "40", "50", "31", "51", "39", "36" ]
138
9,372
0
false
We provide a Ξ”G threshold at which an hairpin RNA structure becomes inaccessible, and we differentiate between different target positions.
[]
We provide a Ξ”G threshold at which an hairpin RNA structure becomes inaccessible, and we differentiate between different target positions.
true
true
true
true
true
1,491
3
DISCUSSION
1
36
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
When designing antiviral siRNAs one may also consider ways to obstruct viral escape via folding of an alternative target RNA structure (36).
[ "31", "40", "50", "31", "51", "39", "36" ]
140
9,373
1
false
When designing antiviral siRNAs one may also consider ways to obstruct viral escape via folding of an alternative target RNA structure.
[ "36" ]
When designing antiviral siRNAs one may also consider ways to obstruct viral escape via folding of an alternative target RNA structure.
true
true
true
true
true
1,491
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
The local RNA region should be screened for the absence of alternative foldings that occlude the 3β€² end of the target and that can be selected by one or two mutations.
[ "31", "40", "50", "31", "51", "39", "36" ]
167
9,374
0
false
The local RNA region should be screened for the absence of alternative foldings that occlude the 3β€² end of the target and that can be selected by one or two mutations.
[]
The local RNA region should be screened for the absence of alternative foldings that occlude the 3β€² end of the target and that can be selected by one or two mutations.
true
true
true
true
true
1,491
3
DISCUSSION
1
31
[ "B31", "B40", "B50", "B31", "B51", "B39", "B36" ]
17,576,691
pmid-15687388|NA|pmid-16948865|pmid-14963165|pmid-14762201|pmid-15852021|pmid-14963165|pmid-15143318|pmid-15110788|pmid-15687388
If not available, the genetic threshold for structure-based escape might prove too high, even for a fast evolving virus like HIV-1.
[ "31", "40", "50", "31", "51", "39", "36" ]
131
9,375
0
false
If not available, the genetic threshold for structure-based escape might prove too high, even for a fast evolving virus like HIV-1.
[]
If not available, the genetic threshold for structure-based escape might prove too high, even for a fast evolving virus like HIV-1.
true
true
true
true
true
1,491
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
RNA structure-mediated resistance against RNAi is in fact beneficial when expressing highly structured shRNAs or miRNAs in cells.
[ "52", "53", "54", "55", "56", "57", "58" ]
129
9,376
0
false
RNA structure-mediated resistance against RNAi is in fact beneficial when expressing highly structured shRNAs or miRNAs in cells.
[]
RNA structure-mediated resistance against RNAi is in fact beneficial when expressing highly structured shRNAs or miRNAs in cells.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
For instance, the incorporation of shRNA cassettes in a lentiviral vector is potentially problematic, because the shRNA will target the viral RNA genome during vector production, thus reducing the titer.
[ "52", "53", "54", "55", "56", "57", "58" ]
203
9,377
0
false
For instance, the incorporation of shRNA cassettes in a lentiviral vector is potentially problematic, because the shRNA will target the viral RNA genome during vector production, thus reducing the titer.
[]
For instance, the incorporation of shRNA cassettes in a lentiviral vector is potentially problematic, because the shRNA will target the viral RNA genome during vector production, thus reducing the titer.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Such self-targeting has not been reported (52,53), we think because the target is not accessible as part of the perfectly base-paired shRNA hairpin.
[ "52", "53", "54", "55", "56", "57", "58" ]
148
9,378
0
false
Such self-targeting has not been reported, we think because the target is not accessible as part of the perfectly base-paired shRNA hairpin.
[ "52,53" ]
Such self-targeting has not been reported, we think because the target is not accessible as part of the perfectly base-paired shRNA hairpin.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The apparent absence of such self-targeting is particularly important for the development of multi-shRNA lentiviral vectors without titer reduction.
[ "52", "53", "54", "55", "56", "57", "58" ]
148
9,379
0
false
The apparent absence of such self-targeting is particularly important for the development of multi-shRNA lentiviral vectors without titer reduction.
[]
The apparent absence of such self-targeting is particularly important for the development of multi-shRNA lentiviral vectors without titer reduction.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
However, placing many tight RNA structures in the vector genome may negatively influence the titer by other means.
[ "52", "53", "54", "55", "56", "57", "58" ]
114
9,380
0
false
However, placing many tight RNA structures in the vector genome may negatively influence the titer by other means.
[]
However, placing many tight RNA structures in the vector genome may negatively influence the titer by other means.
true
true
true
true
true
1,492
4
DISCUSSION
1
54
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
For instance, reverse transcription is very sensitive to excessively stable RNA structure (54) and RNA polymerase II transcription may pause at sites where the RNA products folds stable hairpin structures (55).
[ "52", "53", "54", "55", "56", "57", "58" ]
210
9,381
1
false
For instance, reverse transcription is very sensitive to excessively stable RNA structure and RNA polymerase II transcription may pause at sites where the RNA products folds stable hairpin structures.
[ "54", "55" ]
For instance, reverse transcription is very sensitive to excessively stable RNA structure and RNA polymerase II transcription may pause at sites where the RNA products folds stable hairpin structures.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
We did indeed observe that four shRNA cassettes reduce the lentiviral vector titer (ter Brake, unpublished data).
[ "52", "53", "54", "55", "56", "57", "58" ]
113
9,382
0
false
We did indeed observe that four shRNA cassettes reduce the lentiviral vector titer (ter Brake, unpublished data).
[]
We did indeed observe that four shRNA cassettes reduce the lentiviral vector titer (ter Brake, unpublished data).
true
true
true
true
true
1,492
4
DISCUSSION
1
56
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Destabilizing the introduced shRNAs may avoid such vector problems, and provide additional benefits for cloning and sequencing of inverted repeat sequences (56).
[ "52", "53", "54", "55", "56", "57", "58" ]
161
9,383
1
false
Destabilizing the introduced shRNAs may avoid such vector problems, and provide additional benefits for cloning and sequencing of inverted repeat sequences.
[ "56" ]
Destabilizing the introduced shRNAs may avoid such vector problems, and provide additional benefits for cloning and sequencing of inverted repeat sequences.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
In our target model system, we mutated the antisense strand of the shRNA hairpin, leaving the sense target sequence intact.
[ "52", "53", "54", "55", "56", "57", "58" ]
123
9,384
0
false
In our target model system, we mutated the antisense strand of the shRNA hairpin, leaving the sense target sequence intact.
[]
In our target model system, we mutated the antisense strand of the shRNA hairpin, leaving the sense target sequence intact.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
In the case of a true shRNA expression cassette, modifications will be made in the sense (target) strand to leave the guide/antisense siRNA strand unaltered.
[ "52", "53", "54", "55", "56", "57", "58" ]
157
9,385
0
false
In the case of a true shRNA expression cassette, modifications will be made in the sense (target) strand to leave the guide/antisense siRNA strand unaltered.
[]
In the case of a true shRNA expression cassette, modifications will be made in the sense (target) strand to leave the guide/antisense siRNA strand unaltered.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The obvious advantage will be reduced complementarity between the target and the siRNA inhibitor.
[ "52", "53", "54", "55", "56", "57", "58" ]
97
9,386
0
false
The obvious advantage will be reduced complementarity between the target and the siRNA inhibitor.
[]
The obvious advantage will be reduced complementarity between the target and the siRNA inhibitor.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
The impact of such mutations on self-targeting is likely to depend on the position and type of mismatches that are introduced (57,58).
[ "52", "53", "54", "55", "56", "57", "58" ]
134
9,387
0
false
The impact of such mutations on self-targeting is likely to depend on the position and type of mismatches that are introduced.
[ "57,58" ]
The impact of such mutations on self-targeting is likely to depend on the position and type of mismatches that are introduced.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
It is therefore impossible to make general rules for shRNA design and destabilization as each hairpin RNA structure will have its unique characteristics as target and effector in the RNAi mechanism.
[ "52", "53", "54", "55", "56", "57", "58" ]
198
9,388
0
false
It is therefore impossible to make general rules for shRNA design and destabilization as each hairpin RNA structure will have its unique characteristics as target and effector in the RNAi mechanism.
[]
It is therefore impossible to make general rules for shRNA design and destabilization as each hairpin RNA structure will have its unique characteristics as target and effector in the RNAi mechanism.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Here we demonstrate a Ξ”G window for shRNA-Pol destabilization without activating RNAi self-targeting, which may provide a guideline for other shRNAs.
[ "52", "53", "54", "55", "56", "57", "58" ]
149
9,389
0
false
Here we demonstrate a Ξ”G window for shRNA-Pol destabilization without activating RNAi self-targeting, which may provide a guideline for other shRNAs.
[]
Here we demonstrate a Ξ”G window for shRNA-Pol destabilization without activating RNAi self-targeting, which may provide a guideline for other shRNAs.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
Positional effects should be considered, and hairpins may be destabilized to Ξ”G = βˆ’25 kcal/mol as long as the target 3β€² end remains base-paired.
[ "52", "53", "54", "55", "56", "57", "58" ]
144
9,390
0
false
Positional effects should be considered, and hairpins may be destabilized to Ξ”G = βˆ’25 kcal/mol as long as the target 3β€² end remains base-paired.
[]
Positional effects should be considered, and hairpins may be destabilized to Ξ”G = βˆ’25 kcal/mol as long as the target 3β€² end remains base-paired.
true
true
true
true
true
1,492
4
DISCUSSION
1
52
[ "B52", "B53", "B54", "B55", "B56", "B57", "B58" ]
17,576,691
pmid-12888501|pmid-15110788|pmid-14762201|pmid-15843020|pmid-15014042|pmid-15170178|pmid-14738896|pmid-14670130|pmid-11058109|pmid-6322106|pmid-15241778|pmid-15781493|pmid-16113241
It is too early to define more general guidelines for structured RNA motifs other than the man-made, perfectly base-paired shRNA hairpins, as natural RNA structures differ significantly in their topology and architecture.
[ "52", "53", "54", "55", "56", "57", "58" ]
221
9,391
0
false
It is too early to define more general guidelines for structured RNA motifs other than the man-made, perfectly base-paired shRNA hairpins, as natural RNA structures differ significantly in their topology and architecture.
[]
It is too early to define more general guidelines for structured RNA motifs other than the man-made, perfectly base-paired shRNA hairpins, as natural RNA structures differ significantly in their topology and architecture.
true
true
true
true
true
1,492
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B5 B6 B7", "B8", "B9", "B3", "B4" ]
17,311,812
pmid-2124274|pmid-1645868|pmid-15152202|pmid-16064056|pmid-9217051|pmid-7947755|pmid-8197162|pmid-8768071|pmid-10688366|pmid-15152202|pmid-16064056
Like most retroviruses, the human immunodeficiency virus type I (HIV-1) selectively packages two copies of its RNA genome (1–4).
[ "1–4", "5–7", "8", "9", "3", "4" ]
128
9,392
1
false
Like most retroviruses, the human immunodeficiency virus type I (HIV-1) selectively packages two copies of its RNA genome.
[ "1–4" ]
Like most retroviruses, the human immunodeficiency virus type I selectively packages two copies of its RNA genome.
true
true
true
true
true
1,493
0
INTRODUCTION
1
5–7
[ "B1 B2 B3 B4", "B5 B6 B7", "B8", "B9", "B3", "B4" ]
17,311,812
pmid-2124274|pmid-1645868|pmid-15152202|pmid-16064056|pmid-9217051|pmid-7947755|pmid-8197162|pmid-8768071|pmid-10688366|pmid-15152202|pmid-16064056
The two copies are held together as a non-covalent dimer at the dimer linkage structure (DLS) (5–7) in the 5β€²-leader RNA (8,9).
[ "1–4", "5–7", "8", "9", "3", "4" ]
127
9,393
1
false
The two copies are held together as a non-covalent dimer at the dimer linkage structure (DLS) in the 5β€²-leader RNA.
[ "5–7", "8,9" ]
The two copies are held together as a non-covalent dimer at the dimer linkage structure (DLS) in the 5β€²-leader RNA.
true
true
true
true
true
1,493
0
INTRODUCTION
1
1–4
[ "B1 B2 B3 B4", "B5 B6 B7", "B8", "B9", "B3", "B4" ]
17,311,812
pmid-2124274|pmid-1645868|pmid-15152202|pmid-16064056|pmid-9217051|pmid-7947755|pmid-8197162|pmid-8768071|pmid-10688366|pmid-15152202|pmid-16064056
The RNA dimer has been shown to exert advantageous roles in reverse transcription, including in promoting recombination and generation of drug-resistant strains and its formation has been linked to packaging of the genomic RNA and viral maturation (3,4).
[ "1–4", "5–7", "8", "9", "3", "4" ]
254
9,394
0
false
The RNA dimer has been shown to exert advantageous roles in reverse transcription, including in promoting recombination and generation of drug-resistant strains and its formation has been linked to packaging of the genomic RNA and viral maturation.
[ "3,4" ]
The RNA dimer has been shown to exert advantageous roles in reverse transcription, including in promoting recombination and generation of drug-resistant strains and its formation has been linked to packaging of the genomic RNA and viral maturation.
true
true
true
true
true
1,493
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
Stem loop1 (SL1) is a highly conserved 35-nt hairpin in the HIV-1 5β€²-leader RNA (Figure 1A) and a key component of the DLS structure (6,7,10).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
142
9,395
0
false
Stem loop1 is a highly conserved 35-nt hairpin in the HIV-1 5β€²-leader RNA and a key component of the DLS structure.
[ "SL1", "Figure 1A", "6,7,10" ]
Stem loop1 is a highly conserved 35-nt hairpin in the HIV-1 5β€²-leader RNA and a key component of the DLS structure.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
SL1 contains a self-complementary GC-rich apical loop that promotes dimerization of the HIV-1 genome by forming metastable kissing dimers that are held together by intermolecular base-pairing (Figure 1B) (1,2,6,7).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
214
9,396
0
false
SL1 contains a self-complementary GC-rich apical loop that promotes dimerization of the HIV-1 genome by forming metastable kissing dimers that are held together by intermolecular base-pairing.
[ "Figure 1B", "1,2,6,7" ]
SL1 contains a self-complementary GC-rich apical loop that promotes dimerization of the HIV-1 genome by forming metastable kissing dimers that are held together by intermolecular base-pairing.
true
true
true
true
true
1,494
1
INTRODUCTION
1
6
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
During viral maturation, the metastable kissing dimer undergoes a transition into a more stable dimer in which the two genome copies are more strongly associated (11,12).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
170
9,397
0
false
During viral maturation, the metastable kissing dimer undergoes a transition into a more stable dimer in which the two genome copies are more strongly associated.
[ "11,12" ]
During viral maturation, the metastable kissing dimer undergoes a transition into a more stable dimer in which the two genome copies are more strongly associated.
true
true
true
true
true
1,494
1
INTRODUCTION
1
13
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
This transition occurs following the proteolytic release of the N-terminus domain of nucleocapsid (NC) protein from the Gag precursor (13).
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
139
9,398
1
false
This transition occurs following the proteolytic release of the N-terminus domain of nucleocapsid (NC) protein from the Gag precursor.
[ "13" ]
This transition occurs following the proteolytic release of the N-terminus domain of nucleocapsid (NC) protein from the Gag precursor.
true
true
true
true
true
1,494
1
INTRODUCTION
1
14
[ "B6", "B7", "B10", "B1", "B2", "B6", "B7", "B11", "B12", "B13", "B14", "B15", "B16", "B41" ]
17,311,812
pmid-7947755|pmid-8197162|pmid-8955907|pmid-2124274|pmid-1645868|pmid-7947755|pmid-8197162|pmid-8350405|pmid-8035501|pmid-11533179|pmid-10400801|pmid-8083960|pmid-9223458|pmid-16603544|pmid-12225748|pmid-12225748|pmid-8709210
The processing of Gag has also been shown to be dependent on formation of the RNA dimer (14) and on interactions with the HIV-1 RNA genome (15,16), indicating that maturation of viral proteins and RNA are tightly coupled events.
[ "6", "7", "10", "1", "2", "6", "7", "11", "12", "13", "14", "15", "16", "41" ]
228
9,399
1
false
The processing of Gag has also been shown to be dependent on formation of the RNA dimer and on interactions with the HIV-1 RNA genome, indicating that maturation of viral proteins and RNA are tightly coupled events.
[ "14", "15,16" ]
The processing of Gag has also been shown to be dependent on formation of the RNA dimer and on interactions with the HIV-1 RNA genome, indicating that maturation of viral proteins and RNA are tightly coupled events.
true
true
true
true
true
1,494