Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
Because of cNAPL's binding to U-rich sequences of chloroplast 5′-UTRs, a more general role for this RNA-binding protein is conceivable, e.g.
[ "78" ]
140
900
0
false
Because of cNAPL's binding to U-rich sequences of chloroplast 5′-UTRs, a more general role for this RNA-binding protein is conceivable, e.g.
[]
Because of cNAPL's binding to U-rich sequences of chloroplast 5′-UTRs, a more general role for this RNA-binding protein is conceivable, e.g.
true
true
true
true
true
154
9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
in translation initiation of several chloroplast transcripts.
[ "78" ]
61
901
0
false
in translation initiation of several chloroplast transcripts.
[]
in translation initiation of several chloroplast transcripts.
false
true
true
true
false
154
9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
Thus, cNAPL might represent a component of the cpRNP complex.
[ "78" ]
61
902
0
false
Thus, cNAPL might represent a component of the cpRNP complex.
[]
Thus, cNAPL might represent a component of the cpRNP complex.
true
true
true
true
true
154
0
INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5" ]
17,652,325
pmid-16989803|pmid-16839875|pmid-16669754|pmid-17011485|pmid-16736022
Protein–RNA complexes (ribonucleoprotein particles, RNPs) play a fundamental role in the control and regulation of gene expression in the eukaryotic cell.
[ "1–5" ]
154
903
0
false
Protein–RNA complexes (ribonucleoprotein particles, RNPs) play a fundamental role in the control and regulation of gene expression in the eukaryotic cell.
[]
Protein–RNA complexes (ribonucleoprotein particles, RNPs) play a fundamental role in the control and regulation of gene expression in the eukaryotic cell.
true
true
true
true
true
155
0
INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5" ]
17,652,325
pmid-16989803|pmid-16839875|pmid-16669754|pmid-17011485|pmid-16736022
They participate in essential cellular processes such as pre-mRNA splicing, rRNA maturation, post-transcriptional control (mRNA stability), RNA export, translation and translational control.
[ "1–5" ]
190
904
0
false
They participate in essential cellular processes such as pre-mRNA splicing, rRNA maturation, post-transcriptional control (mRNA stability), RNA export, translation and translational control.
[]
They participate in essential cellular processes such as pre-mRNA splicing, rRNA maturation, post-transcriptional control (mRNA stability), RNA export, translation and translational control.
true
true
true
true
true
155
0
INTRODUCTION
1
1–5
[ "B1 B2 B3 B4 B5" ]
17,652,325
pmid-16989803|pmid-16839875|pmid-16669754|pmid-17011485|pmid-16736022
In the field of alternative splicing and of translational control by microRNAs, it was recently demonstrated that protein–RNA interactions and their dynamic changes provide a basis for the diverse and complex driving forces behind such processes (1–5).
[ "1–5" ]
252
905
1
false
In the field of alternative splicing and of translational control by microRNAs, it was recently demonstrated that protein–RNA interactions and their dynamic changes provide a basis for the diverse and complex driving forces behind such processes.
[ "1–5" ]
In the field of alternative splicing and of translational control by microRNAs, it was recently demonstrated that protein–RNA interactions and their dynamic changes provide a basis for the diverse and complex driving forces behind such processes.
true
true
true
true
true
155
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10", "B11 B12 B13 B14", "B15", "B16", "B17" ]
17,652,325
pmid-3239801|pmid-2675315|pmid-17076264|pmid-16417469|pmid-16336120|pmid-17368621|pmid-17312397|pmid-15925505|pmid-15691656|pmid-16314460|pmid-17406634|NA
There are various approaches to identifying the proteins involved in these processes.
[ "6", "7", "8–10", "11–14", "15", "16", "17" ]
85
906
0
false
There are various approaches to identifying the proteins involved in these processes.
[]
There are various approaches to identifying the proteins involved in these processes.
true
true
true
true
true
156
1
INTRODUCTION
1
8–10
[ "B6", "B7", "B8 B9 B10", "B11 B12 B13 B14", "B15", "B16", "B17" ]
17,652,325
pmid-3239801|pmid-2675315|pmid-17076264|pmid-16417469|pmid-16336120|pmid-17368621|pmid-17312397|pmid-15925505|pmid-15691656|pmid-16314460|pmid-17406634|NA
One is the overall analysis of the proteins associated with the complexes by mass spectrometry [MALDI-MS (6), Electrospray Ionisation (ESI)-MS (7)], as was recently demonstrated by several proteomic studies of RNP complexes that play fundamental roles in (alternative) splicing (8–10) and siRNA- and miRNA-mediated translational repression (11–14).
[ "6", "7", "8–10", "11–14", "15", "16", "17" ]
348
907
1
false
One is the overall analysis of the proteins associated with the complexes by mass spectrometry, as was recently demonstrated by several proteomic studies of RNP complexes that play fundamental roles in (alternative) splicing and siRNA- and miRNA-mediated translational repression.
[ "MALDI-MS (6), Electrospray Ionisation (ESI)-MS (7)", "8–10", "11–14" ]
One is the overall analysis of the proteins associated with the complexes by mass spectrometry, as was recently demonstrated by several proteomic studies of RNP complexes that play fundamental roles in (alternative) splicing and siRNA- and miRNA-mediated translational repression.
true
true
true
true
true
156
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10", "B11 B12 B13 B14", "B15", "B16", "B17" ]
17,652,325
pmid-3239801|pmid-2675315|pmid-17076264|pmid-16417469|pmid-16336120|pmid-17368621|pmid-17312397|pmid-15925505|pmid-15691656|pmid-16314460|pmid-17406634|NA
However, in proteomic-driven studies, no information is gained regarding the question of which of the identified components interacts directly with RNA.
[ "6", "7", "8–10", "11–14", "15", "16", "17" ]
152
908
0
false
However, in proteomic-driven studies, no information is gained regarding the question of which of the identified components interacts directly with RNA.
[]
However, in proteomic-driven studies, no information is gained regarding the question of which of the identified components interacts directly with RNA.
true
true
true
true
true
156
1
INTRODUCTION
1
15
[ "B6", "B7", "B8 B9 B10", "B11 B12 B13 B14", "B15", "B16", "B17" ]
17,652,325
pmid-3239801|pmid-2675315|pmid-17076264|pmid-16417469|pmid-16336120|pmid-17368621|pmid-17312397|pmid-15925505|pmid-15691656|pmid-16314460|pmid-17406634|NA
A straightforward approach to identify proteins in direct contact to their cognate RNAs is protein–RNA cross-linking combined with MS (15).
[ "6", "7", "8–10", "11–14", "15", "16", "17" ]
139
909
1
false
A straightforward approach to identify proteins in direct contact to their cognate RNAs is protein–RNA cross-linking combined with MS.
[ "15" ]
A straightforward approach to identify proteins in direct contact to their cognate RNAs is protein–RNA cross-linking combined with MS.
true
true
true
true
true
156
1
INTRODUCTION
1
6
[ "B6", "B7", "B8 B9 B10", "B11 B12 B13 B14", "B15", "B16", "B17" ]
17,652,325
pmid-3239801|pmid-2675315|pmid-17076264|pmid-16417469|pmid-16336120|pmid-17368621|pmid-17312397|pmid-15925505|pmid-15691656|pmid-16314460|pmid-17406634|NA
An alternative/additional method for mapping protein–RNA interactions using MS is the dissociation of intact protein–RNA complexes in the mass spectrometer and the analysis of components that are still associated with RNA (16,17).
[ "6", "7", "8–10", "11–14", "15", "16", "17" ]
230
910
0
false
An alternative/additional method for mapping protein–RNA interactions using MS is the dissociation of intact protein–RNA complexes in the mass spectrometer and the analysis of components that are still associated with RNA.
[ "16,17" ]
An alternative/additional method for mapping protein–RNA interactions using MS is the dissociation of intact protein–RNA complexes in the mass spectrometer and the analysis of components that are still associated with RNA.
true
true
true
true
true
156
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
One possibility for protein–RNA cross-linking is the direct UV-irradiation of RNPs at 254 nm (18), based on the natural UV-reactivity of the RNA nucleobases.
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
157
911
1
false
One possibility for protein–RNA cross-linking is the direct UV-irradiation of RNPs at 254 nm, based on the natural UV-reactivity of the RNA nucleobases.
[ "18" ]
One possibility for protein–RNA cross-linking is the direct UV-irradiation of RNPs at 254 nm, based on the natural UV-reactivity of the RNA nucleobases.
true
true
true
true
true
157
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
Upon excitation, a covalent bond between a nucleobase and an amino-acid side chain of a protein is formed.
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
106
912
0
false
Upon excitation, a covalent bond between a nucleobase and an amino-acid side chain of a protein is formed.
[]
Upon excitation, a covalent bond between a nucleobase and an amino-acid side chain of a protein is formed.
true
true
true
true
true
157
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
This approach has several advantages over site-specific labelling (19,20) or over using heterobifunctional reagents [e.g.
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
121
913
0
false
This approach has several advantages over site-specific labelling or over using heterobifunctional reagents [e.g.
[ "19,20" ]
This approach has several advantages over site-specific labelling or over using heterobifunctional reagents [e.g.
true
true
true
true
true
157
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
(21,22)]: (i) It can be applied directly to any native protein–RNA complex isolated from cells without reconstituting particles carrying site-specific cross-linkers (which can lead to a heterogeneous population and/or can reduce the yield of complexes for interaction studies).
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
277
914
0
false
]: (i) It can be applied directly to any native protein–RNA complex isolated from cells without reconstituting particles carrying site-specific cross-linkers (which can lead to a heterogeneous population and/or can reduce the yield of complexes for interaction studies).
[ "21,22" ]
]: (i) It can be applied directly to any native protein–RNA complex isolated from cells without reconstituting particles carrying site-specific cross-linkers (which can lead to a heterogeneous population and/or can reduce the yield of complexes for interaction studies).
false
false
true
true
false
157
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
(ii) Zero-length cross-links have been proven to have a very high specificity, as demonstrated recently by the 3D structures of co-crystallized RNA–protein complexes (23,24).
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
174
915
0
false
(ii) Zero-length cross-links have been proven to have a very high specificity, as demonstrated recently by the 3D structures of co-crystallized RNA–protein complexes.
[ "23,24" ]
(ii) Zero-length cross-links have been proven to have a very high specificity, as demonstrated recently by the 3D structures of co-crystallized RNA–protein complexes.
false
false
true
true
false
157
2
INTRODUCTION
1
25
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
The site of contact identified in this way always reflects a structural (and functional) RNA interaction domain within or very close to the RNA-binding domain of the protein (25).
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
179
916
1
false
The site of contact identified in this way always reflects a structural (and functional) RNA interaction domain within or very close to the RNA-binding domain of the protein.
[ "25" ]
The site of contact identified in this way always reflects a structural (and functional) RNA interaction domain within or very close to the RNA-binding domain of the protein.
true
true
true
true
true
157
2
INTRODUCTION
1
21
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
(iii) It obviates extensive probing experiments, in contrast to comparable protein–RNA cross-linking studies using heterobifunctional reagents, in which the optimal probing conditions have to be carefully adjusted (21).
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
219
917
1
false
(iii) It obviates extensive probing experiments, in contrast to comparable protein–RNA cross-linking studies using heterobifunctional reagents, in which the optimal probing conditions have to be carefully adjusted.
[ "21" ]
(iii) It obviates extensive probing experiments, in contrast to comparable protein–RNA cross-linking studies using heterobifunctional reagents, in which the optimal probing conditions have to be carefully adjusted.
false
false
true
true
false
157
2
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24", "B25", "B21" ]
17,652,325
pmid-7815187|pmid-10208813|pmid-14624009|pmid-16875836|pmid-15567411|pmid-11226169|pmid-17412961|pmid-12374753|pmid-16875836
No inter- or intramolecular protein–protein cross-links are generated (at least as reported so far), which reduces the number of putatively cross-linked species within the mass spectra and simplifies their interpretation.
[ "18", "19", "20", "21", "22", "23", "24", "25", "21" ]
221
918
0
false
No inter- or intramolecular protein–protein cross-links are generated (at least as reported so far), which reduces the number of putatively cross-linked species within the mass spectra and simplifies their interpretation.
[]
No inter- or intramolecular protein–protein cross-links are generated (at least as reported so far), which reduces the number of putatively cross-linked species within the mass spectra and simplifies their interpretation.
true
true
true
true
true
157
3
INTRODUCTION
0
null
null
17,652,325
null
However, combining protein–RNA cross-linking with mass spectrometry encounters several challenges: (i) because the yield in UV cross-linking is low(er), a purification strategy must be established that separates the cross-linked species from the excess of non-crosslinked species.
null
280
919
0
false
null
null
However, combining protein–RNA cross-linking with mass spectrometry encounters several challenges: (i) because the yield in UV cross-linking is low(er), a purification strategy must be established that separates the cross-linked species from the excess of non-crosslinked species.
true
true
true
true
true
158
3
INTRODUCTION
0
null
null
17,652,325
null
(ii) MS per se must be adapted, since the peptide and RNA moieties of the cross-linked conjugates show divergent physico-chemical properties in the analysis.
null
157
920
0
false
null
null
(ii) MS per se must be adapted, since the peptide and RNA moieties of the cross-linked conjugates show divergent physico-chemical properties in the analysis.
false
false
true
true
false
158
3
INTRODUCTION
0
null
null
17,652,325
null
(iii) Enrichment and/or down-scaling strategies are required, both to reduce the amount of starting material (and thus to allow the study of material directly isolated from cells) and to increase the intensity of the peaks from (low-abundance) protein–RNA cross-links in MS.
null
274
921
0
false
null
null
(iii) Enrichment and/or down-scaling strategies are required, both to reduce the amount of starting material (and thus to allow the study of material directly isolated from cells) and to increase the intensity of the peaks from (low-abundance) protein–RNA cross-links in MS.
false
false
true
true
false
158
4
INTRODUCTION
1
15
[ "B15", "B16", "B15" ]
17,652,325
pmid-16314460|pmid-17406634|pmid-16314460
In recent years, we have established a strategy for the purification and subsequent MALDI-Time-of-Flight (MALDI-ToF)
[ "15", "26", "15" ]
116
922
0
false
In recent years, we have established a strategy for the purification and subsequent MALDI-Time-of-Flight (MALDI-ToF)
[]
In recent years, we have established a strategy for the purification and subsequent MALDI-Time-of-Flight (MALDI-ToF)
true
true
false
true
false
159
4
INTRODUCTION
1
15
[ "B15", "B16", "B15" ]
17,652,325
pmid-16314460|pmid-17406634|pmid-16314460
MS analysis of cross-linked peptide–oligoribonucleotides derived from UV-irradiated native and reconstituted ribonucleoprotein particles (15,26 and below).
[ "15", "26", "15" ]
155
923
0
false
MS analysis of cross-linked peptide–oligoribonucleotides derived from UV-irradiated native and reconstituted ribonucleoprotein particles.
[ "15,26 and below" ]
MS analysis of cross-linked peptide–oligoribonucleotides derived from UV-irradiated native and reconstituted ribonucleoprotein particles.
true
true
true
true
true
159
4
INTRODUCTION
1
15
[ "B15", "B16", "B15" ]
17,652,325
pmid-16314460|pmid-17406634|pmid-16314460
It comprises: digestion of the protein moiety of cross-linked RNPs with endoproteinases, removal of the excess of non-crosslinked peptides by size-exclusion chromatography, hydrolysis of RNA-containing fractions with RNases and subsequent fractionation of the resulting mixtures on a microbore liquid-chromatography (LC) system.
[ "15", "26", "15" ]
328
924
0
false
It comprises: digestion of the protein moiety of cross-linked RNPs with endoproteinases, removal of the excess of non-crosslinked peptides by size-exclusion chromatography, hydrolysis of RNA-containing fractions with RNases and subsequent fractionation of the resulting mixtures on a microbore liquid-chromatography (LC) system.
[]
It comprises: digestion of the protein moiety of cross-linked RNPs with endoproteinases, removal of the excess of non-crosslinked peptides by size-exclusion chromatography, hydrolysis of RNA-containing fractions with RNases and subsequent fractionation of the resulting mixtures on a microbore liquid-chromatography (LC) system.
true
true
true
true
true
159
4
INTRODUCTION
1
15
[ "B15", "B16", "B15" ]
17,652,325
pmid-16314460|pmid-17406634|pmid-16314460
Fractions that showed an absorbance at 220 nm (peptide moiety) and 254 nm (RNA moiety) were considered to contain cross-linked species and were subsequently analysed by MALDI-MS and -MS/MS using 2,5-dihydroxybenzoic acid (DHB) and/or 2,4,6-trihydroxyacetophenone (THAP) as matrices (15).
[ "15", "26", "15" ]
287
925
1
false
Fractions that showed an absorbance at 220 nm (peptide moiety) and 254 nm (RNA moiety) were considered to contain cross-linked species and were subsequently analysed by MALDI-MS and -MS/MS using 2,5-dihydroxybenzoic acid (DHB) and/or 2,4,6-trihydroxyacetophenone (THAP) as matrices.
[ "15" ]
Fractions that showed an absorbance at 220 nm (peptide moiety) and 254 nm (RNA moiety) were considered to contain cross-linked species and were subsequently analysed by MALDI-MS and -MS/MS using 2,5-dihydroxybenzoic acid (DHB) and/or 2,4,6-trihydroxyacetophenone (THAP) as matrices.
true
true
true
true
true
159
5
INTRODUCTION
0
null
null
17,652,325
null
On the basis of this work, we report here a down-scaling/enrichment strategy of cross-linked peptide–RNA oligonucleotide species from low amounts of starting material (≤50 pmol) obtained from UV-irradiated RNPs.
null
211
926
0
false
null
null
On the basis of this work, we report here a down-scaling/enrichment strategy of cross-linked peptide–RNA oligonucleotide species from low amounts of starting material (≤50 pmol) obtained from UV-irradiated RNPs.
true
true
true
true
true
160
5
INTRODUCTION
0
null
null
17,652,325
null
The novel approach comprises enrichment of peptide–RNA cross-links by immobilized metal-ion affinity chromatography (IMAC) from capillary RP-HPLC fractions combined with treatment of the enriched species with calf intestinal alkaline phosphatase (CIP) to exclude false positives and the subsequent MS analysis by MALDI-ToF mass spectrometry.
null
341
927
0
false
null
null
The novel approach comprises enrichment of peptide–RNA cross-links by immobilized metal-ion affinity chromatography (IMAC) from capillary RP-HPLC fractions combined with treatment of the enriched species with calf intestinal alkaline phosphatase (CIP) to exclude false positives and the subsequent MS analysis by MALDI-ToF mass spectrometry.
true
true
true
true
true
160
6
INTRODUCTION
1
26
[ "B26", "B24", "B25", "B27", "B28", "B15", "B29", "B30", "B31" ]
17,652,325
pmid-16201866|pmid-17412961|pmid-12374753|NA|NA|pmid-16314460|pmid-11006293|pmid-17349801|pmid-16495236
In feasibility studies, we successfully applied this strategy to the detection of several peptide–RNA oligonucleotide heteroconjugates derived from (i) UV-irradiated partial complexes of the human minor spliceosome (26), i.e.
[ "26", "24", "25", "27", "28", "15", "29", "30", "31" ]
225
928
1
false
In feasibility studies, we successfully applied this strategy to the detection of several peptide–RNA oligonucleotide heteroconjugates derived from (i) UV-irradiated partial complexes of the human minor spliceosome, i.e.
[ "26" ]
In feasibility studies, we successfully applied this strategy to the detection of several peptide–RNA oligonucleotide heteroconjugates derived from (i) UV-irradiated partial complexes of the human minor spliceosome, i.e.
true
true
true
true
true
161
6
INTRODUCTION
1
27
[ "B26", "B24", "B25", "B27", "B28", "B15", "B29", "B30", "B31" ]
17,652,325
pmid-16201866|pmid-17412961|pmid-12374753|NA|NA|pmid-16314460|pmid-11006293|pmid-17349801|pmid-16495236
[15.5K-61K-U4atac snRNA] complexes (24,25), and (ii) from UV-irradiated native U1 small nuclear ribonucleoprotein (snRNP) particles (27) of the human major spliceosome (28) that had been studied before (15,29,30).
[ "26", "24", "25", "27", "28", "15", "29", "30", "31" ]
213
929
1
false
complexes, and (ii) from UV-irradiated native U1 small nuclear ribonucleoprotein (snRNP) particles of the human major spliceosome that had been studied before.
[ "15.5K-61K-U4atac snRNA", "24,25", "27", "28", "15,29,30" ]
complexes, and (ii) from UV-irradiated native U1 small nuclear ribonucleoprotein (snRNP) particles of the human major spliceosome that had been studied before.
false
true
true
true
false
161
6
INTRODUCTION
1
31
[ "B26", "B24", "B25", "B27", "B28", "B15", "B29", "B30", "B31" ]
17,652,325
pmid-16201866|pmid-17412961|pmid-12374753|NA|NA|pmid-16314460|pmid-11006293|pmid-17349801|pmid-16495236
Moreover, we were able to enrich cross-links derived from a UV-irradiated [p14/SF3b14a-SF3b155282–424] protein complex bound to a U2 snRNA oligomer that mimics the branch-site interacting region (BSiR) of the U2 snRNA (31).
[ "26", "24", "25", "27", "28", "15", "29", "30", "31" ]
223
930
1
false
Moreover, we were able to enrich cross-links derived from a UV-irradiated protein complex bound to a U2 snRNA oligomer that mimics the branch-site interacting region (BSiR) of the U2 snRNA.
[ "p14/SF3b14a-SF3b155282–424", "31" ]
Moreover, we were able to enrich cross-links derived from a UV-irradiated protein complex bound to a U2 snRNA oligomer that mimics the branch-site interacting region (BSiR) of the U2 snRNA.
true
true
true
true
true
161
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b10", "b11", "b12", "b13", "b14", "b15", "b17", "b18", "b19" ]
17,202,171
pmid-2547163|pmid-11805826|pmid-11518523|pmid-12117803|pmid-12620108|pmid-14681455|pmid-10871269|pmid-11911893|pmid-11752321|pmid-11125102|pmid-14525934|pmid-12519996
Protein–protein interactions are fundamental to understanding biological networks and cellular processes.
[ "1", "3", "4", "10", "11", "12", "13", "14", "15", "17", "18", "19" ]
105
931
0
false
Protein–protein interactions are fundamental to understanding biological networks and cellular processes.
[]
Protein–protein interactions are fundamental to understanding biological networks and cellular processes.
true
true
true
true
true
162
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b10", "b11", "b12", "b13", "b14", "b15", "b17", "b18", "b19" ]
17,202,171
pmid-2547163|pmid-11805826|pmid-11518523|pmid-12117803|pmid-12620108|pmid-14681455|pmid-10871269|pmid-11911893|pmid-11752321|pmid-11125102|pmid-14525934|pmid-12519996
Accordingly, many experimental (1–3) and computational (4–10) techniques have been developed to probe and predict interacting protein partners.
[ "1", "3", "4", "10", "11", "12", "13", "14", "15", "17", "18", "19" ]
143
932
0
false
Accordingly, many experimental and computational techniques have been developed to probe and predict interacting protein partners.
[ "1–3", "4–10" ]
Accordingly, many experimental and computational techniques have been developed to probe and predict interacting protein partners.
true
true
true
true
true
162
0
INTRODUCTION
1
11
[ "b1", "b3", "b4", "b10", "b11", "b12", "b13", "b14", "b15", "b17", "b18", "b19" ]
17,202,171
pmid-2547163|pmid-11805826|pmid-11518523|pmid-12117803|pmid-12620108|pmid-14681455|pmid-10871269|pmid-11911893|pmid-11752321|pmid-11125102|pmid-14525934|pmid-12519996
There are several databases of protein interactions which store the information generated from high throughput experimental methods and literature curation, for example, GRID (11), the IntAct Project (12), BIND (13), MINT (14), DIP (15–17) and the HPRD (18).
[ "1", "3", "4", "10", "11", "12", "13", "14", "15", "17", "18", "19" ]
258
933
1
false
There are several databases of protein interactions which store the information generated from high throughput experimental methods and literature curation, for example, GRID, the IntAct Project, BIND, MINT, DIP and the HPRD.
[ "11", "12", "13", "14", "15–17", "18" ]
There are several databases of protein interactions which store the information generated from high throughput experimental methods and literature curation, for example, GRID, the IntAct Project, BIND, MINT, DIP and the HPRD.
true
true
true
true
true
162
0
INTRODUCTION
1
19
[ "b1", "b3", "b4", "b10", "b11", "b12", "b13", "b14", "b15", "b17", "b18", "b19" ]
17,202,171
pmid-2547163|pmid-11805826|pmid-11518523|pmid-12117803|pmid-12620108|pmid-14681455|pmid-10871269|pmid-11911893|pmid-11752321|pmid-11125102|pmid-14525934|pmid-12519996
STRING (19) also contains data derived from database and literature mining and high-throughput experimental data, but in addition contains predictions based on genomic context analysis.
[ "1", "3", "4", "10", "11", "12", "13", "14", "15", "17", "18", "19" ]
185
934
1
false
STRING also contains data derived from database and literature mining and high-throughput experimental data, but in addition contains predictions based on genomic context analysis.
[ "19" ]
STRING also contains data derived from database and literature mining and high-throughput experimental data, but in addition contains predictions based on genomic context analysis.
true
true
true
true
true
162
1
INTRODUCTION
1
20
[ "b20", "b25", "b26", "b28" ]
17,202,171
pmid-8552589|pmid-9925793|pmid-9299343|pmid-15047913
These computational and experimental techniques can yield significant information about possible interactions but they do not provide information about the structure of the interfaces at the atomic level.
[ "20", "25", "26", "28" ]
204
935
0
false
These computational and experimental techniques can yield significant information about possible interactions but they do not provide information about the structure of the interfaces at the atomic level.
[]
These computational and experimental techniques can yield significant information about possible interactions but they do not provide information about the structure of the interfaces at the atomic level.
true
true
true
true
true
163
1
INTRODUCTION
1
20
[ "b20", "b25", "b26", "b28" ]
17,202,171
pmid-8552589|pmid-9925793|pmid-9299343|pmid-15047913
High-resolution X-ray and NMR structures can provide an atomic level of detail and have therefore been utilised for both investigation and prediction of protein–protein interactions.
[ "20", "25", "26", "28" ]
182
936
0
false
High-resolution X-ray and NMR structures can provide an atomic level of detail and have therefore been utilised for both investigation and prediction of protein–protein interactions.
[]
High-resolution X-ray and NMR structures can provide an atomic level of detail and have therefore been utilised for both investigation and prediction of protein–protein interactions.
true
true
true
true
true
163
1
INTRODUCTION
1
20
[ "b20", "b25", "b26", "b28" ]
17,202,171
pmid-8552589|pmid-9925793|pmid-9299343|pmid-15047913
Analyses of interaction sites from 3-D structures have identified a number of properties that distinguish interaction sites from other areas of protein surfaces, including: residue conservation across species; a tendency to be polar, uncharged and hydrophobic; a planar protruding shape and a higher solvent accessible area (20–25).
[ "20", "25", "26", "28" ]
332
937
0
false
Analyses of interaction sites from 3-D structures have identified a number of properties that distinguish interaction sites from other areas of protein surfaces, including: residue conservation across species; a tendency to be polar, uncharged and hydrophobic; a planar protruding shape and a higher solvent accessible area.
[ "20–25" ]
Analyses of interaction sites from 3-D structures have identified a number of properties that distinguish interaction sites from other areas of protein surfaces, including: residue conservation across species; a tendency to be polar, uncharged and hydrophobic; a planar protruding shape and a higher solvent accessible area.
true
true
true
true
true
163
1
INTRODUCTION
1
20
[ "b20", "b25", "b26", "b28" ]
17,202,171
pmid-8552589|pmid-9925793|pmid-9299343|pmid-15047913
These properties have been exploited to predict interaction surfaces on protein structures (26–28).
[ "20", "25", "26", "28" ]
99
938
0
false
These properties have been exploited to predict interaction surfaces on protein structures.
[ "26–28" ]
These properties have been exploited to predict interaction surfaces on protein structures.
true
true
true
true
true
163
2
INTRODUCTION
1
29
[ "b29", "b30", "b31", "b32", "b33" ]
17,202,171
pmid-11972061|pmid-12499311|pmid-12360525|pmid-15855251|pmid-16204844
Predictions of protein–protein interactions using structural data have been based on the hypothesis that if two proteins are seen to interact in a known 3-D structure, their homologues will interact in a similar fashion (29,30).
[ "29", "30", "31", "32", "33" ]
228
939
0
false
Predictions of protein–protein interactions using structural data have been based on the hypothesis that if two proteins are seen to interact in a known 3-D structure, their homologues will interact in a similar fashion.
[ "29,30" ]
Predictions of protein–protein interactions using structural data have been based on the hypothesis that if two proteins are seen to interact in a known 3-D structure, their homologues will interact in a similar fashion.
true
true
true
true
true
164
2
INTRODUCTION
1
31
[ "b29", "b30", "b31", "b32", "b33" ]
17,202,171
pmid-11972061|pmid-12499311|pmid-12360525|pmid-15855251|pmid-16204844
A multimeric threading method has been used to extend this approach to distantly related homologous and analogous pairs (31).
[ "29", "30", "31", "32", "33" ]
125
940
1
false
A multimeric threading method has been used to extend this approach to distantly related homologous and analogous pairs.
[ "31" ]
A multimeric threading method has been used to extend this approach to distantly related homologous and analogous pairs.
true
true
true
true
true
164
2
INTRODUCTION
1
32
[ "b29", "b30", "b31", "b32", "b33" ]
17,202,171
pmid-11972061|pmid-12499311|pmid-12360525|pmid-15855251|pmid-16204844
Structural data for interfaces has also been used to create templates that capture the essential features of interactions sites and which are employed to screen protein structures for the presence of interaction sites (32).
[ "29", "30", "31", "32", "33" ]
223
941
1
false
Structural data for interfaces has also been used to create templates that capture the essential features of interactions sites and which are employed to screen protein structures for the presence of interaction sites.
[ "32" ]
Structural data for interfaces has also been used to create templates that capture the essential features of interactions sites and which are employed to screen protein structures for the presence of interaction sites.
true
true
true
true
true
164
2
INTRODUCTION
1
29
[ "b29", "b30", "b31", "b32", "b33" ]
17,202,171
pmid-11972061|pmid-12499311|pmid-12360525|pmid-15855251|pmid-16204844
Methods of protein–protein interaction prediction have been extensively reviewed by Szilagyi et al.
[ "29", "30", "31", "32", "33" ]
99
942
0
false
Methods of protein–protein interaction prediction have been extensively reviewed by Szilagyi et al.
[]
Methods of protein–protein interaction prediction have been extensively reviewed by Szilagyi et al.
true
true
true
true
true
164
3
INTRODUCTION
1
34
[ "b34", "b35", "b36", "b37", "b38" ]
17,202,171
pmid-15608228|pmid-15657096|pmid-16381874|pmid-15749693|pmid-15991339
The advantages of structural data have motivated the creation of several databases of protein-protein interactions and interfaces including 3did (database of 3-D interacting domains) (34), PIBASE (structurally defined protein interfaces) (35), SCOPPI (a structural classification of protein–protein interfaces) (36), PSIBase (Protein Structural Interactome map) (37) and PRISM (PRotein Interactions by Structural Matching) (38).
[ "34", "35", "36", "37", "38" ]
428
943
1
false
The advantages of structural data have motivated the creation of several databases of protein-protein interactions and interfaces including 3did (database of 3-D interacting domains), PIBASE (structurally defined protein interfaces), SCOPPI (a structural classification of protein–protein interfaces), PSIBase (Protein Structural Interactome map) and PRISM (PRotein Interactions by Structural Matching).
[ "34", "35", "36", "37", "38" ]
The advantages of structural data have motivated the creation of several databases of protein-protein interactions and interfaces including 3did, PIBASE (structurally defined protein interfaces), SCOPPI (a structural classification of protein–protein interfaces), PSIBase (Protein Structural Interactome map) and PRISM (PRotein Interactions by Structural Matching).
true
true
true
true
true
165
4
INTRODUCTION
0
null
null
17,202,171
null
In this paper, a system is presented which provides a foundation for analysis and prediction of structural data with an emphasis on domain–domain interactions.
null
159
944
0
false
null
null
In this paper, a system is presented which provides a foundation for analysis and prediction of structural data with an emphasis on domain–domain interactions.
true
true
true
true
true
166
4
INTRODUCTION
0
null
null
17,202,171
null
This system consists of SNAPPI-DB, a database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Application Programming Interface (API).
null
179
945
0
false
null
null
This system consists of SNAPPI-DB, a database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Application Programming Interface (API).
true
true
true
true
true
166
4
INTRODUCTION
0
null
null
17,202,171
null
SNAPPI-DB, a high performance, object oriented database provides consistent, enhanced quality structural data, enriched with additional data such as multiple domain classifications, quaternary structures and domain-domain interactions.
null
235
946
0
false
null
null
SNAPPI-DB, a high performance, object oriented database provides consistent, enhanced quality structural data, enriched with additional data such as multiple domain classifications, quaternary structures and domain-domain interactions.
true
true
true
true
true
166
4
INTRODUCTION
0
null
null
17,202,171
null
The API facilitates rapid development, is extensible, allows easy access to the data and circumvents the need to write complex SQL queries.
null
139
947
0
false
null
null
The API facilitates rapid development, is extensible, allows easy access to the data and circumvents the need to write complex SQL queries.
true
true
true
true
true
166
5
INTRODUCTION
0
null
null
17,202,171
null
The contents and creation of SNAPPI-DB are discussed, followed by an overview of the API.
null
89
948
0
false
null
null
The contents and creation of SNAPPI-DB are discussed, followed by an overview of the API.
true
true
true
true
true
167
5
INTRODUCTION
0
null
null
17,202,171
null
The system is then compared to other databases of protein–protein interactions observed in structural data.
null
107
949
0
false
null
null
The system is then compared to other databases of protein–protein interactions observed in structural data.
true
true
true
true
true
167
5
INTRODUCTION
0
null
null
17,202,171
null
Finally, the unique features of the system and its applications are discussed.
null
78
950
0
false
null
null
Finally, the unique features of the system and its applications are discussed.
true
true
true
true
true
167
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,287,295
NA|pmid-9882324|pmid-10660678|pmid-10966112|pmid-11233983
Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV) are members of the family Dicistroviridae (1).
[ "1", "2–4", "5" ]
118
951
1
false
Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV) are members of the family Dicistroviridae.
[ "1" ]
Plautia stali intestine virus (PSIV) and Cricket paralysis virus (CrPV) are members of the family Dicistroviridae.
true
true
true
true
true
168
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,287,295
NA|pmid-9882324|pmid-10660678|pmid-10966112|pmid-11233983
Known dicistroviruses contain a structurally conserved intergenic region-internal ribosome entry site (IGR-IRES) for translation of the capsid protein.
[ "1", "2–4", "5" ]
151
952
0
false
Known dicistroviruses contain a structurally conserved intergenic region-internal ribosome entry site (IGR-IRES) for translation of the capsid protein.
[]
Known dicistroviruses contain a structurally conserved intergenic region-internal ribosome entry site (IGR-IRES) for translation of the capsid protein.
true
true
true
true
true
168
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4", "B5" ]
17,287,295
NA|pmid-9882324|pmid-10660678|pmid-10966112|pmid-11233983
Translation initiation mediated by the IRES of dicistroviruses does not require base-pair interaction between an AUG initiation codon and initiator Met-tRNA (2–4).
[ "1", "2–4", "5" ]
163
953
1
false
Translation initiation mediated by the IRES of dicistroviruses does not require base-pair interaction between an AUG initiation codon and initiator Met-tRNA.
[ "2–4" ]
Translation initiation mediated by the IRES of dicistroviruses does not require base-pair interaction between an AUG initiation codon and initiator Met-tRNA.
true
true
true
true
true
168
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4", "B5" ]
17,287,295
NA|pmid-9882324|pmid-10660678|pmid-10966112|pmid-11233983
The IRES elements of dicistroviruses share a common secondary structure domain arrangement, constructed by three pseudoknots (PK I, PK II, PK III).
[ "1", "2–4", "5" ]
147
954
0
false
The IRES elements of dicistroviruses share a common secondary structure domain arrangement, constructed by three pseudoknots (PK I, PK II, PK III).
[]
The IRES elements of dicistroviruses share a common secondary structure domain arrangement, constructed by three pseudoknots (PK I, PK II, PK III).
true
true
true
true
true
168
0
INTRODUCTION
1
5
[ "B1", "B2 B3 B4", "B5" ]
17,287,295
NA|pmid-9882324|pmid-10660678|pmid-10966112|pmid-11233983
Because of this similarity in IRES secondary structure, it has been thought that IRES elements function via the same mechanism (5).
[ "1", "2–4", "5" ]
131
955
1
false
Because of this similarity in IRES secondary structure, it has been thought that IRES elements function via the same mechanism.
[ "5" ]
Because of this similarity in IRES secondary structure, it has been thought that IRES elements function via the same mechanism.
true
true
true
true
true
168
1
INTRODUCTION
1
6
[ "B6", "B4", "B7", "B8", "B7", "B9", "B10", "B11" ]
17,287,295
pmid-11416183|pmid-10966112|pmid-12470947|pmid-12533507|pmid-12470947|pmid-12711689|pmid-15332113|pmid-14581537
Usually, assembly of the eukaryotic 80S ribosome on normal mRNA is completed under the control of eIFs (6).
[ "6", "4", "7", "8", "7", "9", "10", "11" ]
107
956
1
false
Usually, assembly of the eukaryotic 80S ribosome on normal mRNA is completed under the control of eIFs.
[ "6" ]
Usually, assembly of the eukaryotic 80S ribosome on normal mRNA is completed under the control of eIFs.
true
true
true
true
true
169
1
INTRODUCTION
1
6
[ "B6", "B4", "B7", "B8", "B7", "B9", "B10", "B11" ]
17,287,295
pmid-11416183|pmid-10966112|pmid-12470947|pmid-12533507|pmid-12470947|pmid-12711689|pmid-15332113|pmid-14581537
In contrast, ribosomal assembly occurs directly on the dicistroviral IGR-IRES in the absence of eIFs (4,7,8).
[ "6", "4", "7", "8", "7", "9", "10", "11" ]
109
957
0
false
In contrast, ribosomal assembly occurs directly on the dicistroviral IGR-IRES in the absence of eIFs.
[ "4,7,8" ]
In contrast, ribosomal assembly occurs directly on the dicistroviral IGR-IRES in the absence of eIFs.
true
true
true
true
true
169
1
INTRODUCTION
1
10
[ "B6", "B4", "B7", "B8", "B7", "B9", "B10", "B11" ]
17,287,295
pmid-11416183|pmid-10966112|pmid-12470947|pmid-12533507|pmid-12470947|pmid-12711689|pmid-15332113|pmid-14581537
The nucleotides in the IRES that interact with 40S ribosomes have been attributed to the 5′ region of the IRES by chemical and enzymatic footprint analyses (7,9), whereas the 3′ region of the IRES, which consists of PK I that is responsible for determining the reading frame of the mRNA, has been shown to be exposed to the interface side at very close to the P site of the 40S ribosome (10).
[ "6", "4", "7", "8", "7", "9", "10", "11" ]
392
958
1
false
The nucleotides in the IRES that interact with 40S ribosomes have been attributed to the 5′ region of the IRES by chemical and enzymatic footprint analyses, whereas the 3′ region of the IRES, which consists of PK I that is responsible for determining the reading frame of the mRNA, has been shown to be exposed to the interface side at very close to the P site of the 40S ribosome.
[ "7,9", "10" ]
The nucleotides in the IRES that interact with 40S ribosomes have been attributed to the 5′ region of the IRES by chemical and enzymatic footprint analyses, whereas the 3′ region of the IRES, which consists of PK I that is responsible for determining the reading frame of the mRNA, has been shown to be exposed to the interface side at very close to the P site of the 40S ribosome.
true
true
true
true
true
169
1
INTRODUCTION
1
11
[ "B6", "B4", "B7", "B8", "B7", "B9", "B10", "B11" ]
17,287,295
pmid-11416183|pmid-10966112|pmid-12470947|pmid-12533507|pmid-12470947|pmid-12711689|pmid-15332113|pmid-14581537
Although the IGR-IRES of dicistroviruses is recognized by ribosomes from various eukaryotes, such as insects, yeast, human and wheat, ribosomes from E. coli cannot recognize the IGR-IRES (Yamamoto and Uchiumi, unpublished data) and the S30 extract of E. coli cannot conduct IGR-IRES-mediated translation (11).
[ "6", "4", "7", "8", "7", "9", "10", "11" ]
309
959
1
false
Although the IGR-IRES of dicistroviruses is recognized by ribosomes from various eukaryotes, such as insects, yeast, human and wheat, ribosomes from E. coli cannot recognize the IGR-IRES (Yamamoto and Uchiumi, unpublished data) and the S30 extract of E. coli cannot conduct IGR-IRES-mediated translation.
[ "11" ]
Although the IGR-IRES of dicistroviruses is recognized by ribosomes from various eukaryotes, such as insects, yeast, human and wheat, ribosomes from E. coli cannot recognize the IGR-IRES (Yamamoto and Uchiumi, unpublished data) and the S30 extract of E. coli cannot conduct IGR-IRES-mediated translation.
true
true
true
true
true
169
2
INTRODUCTION
1
12
[ "B12" ]
17,287,295
pmid-15315759
A cryo-electron microscopy study has reconstituted an image of the IGR-IRES of CrPV docking on the human ribosome (12).
[ "12" ]
119
960
1
false
A cryo-electron microscopy study has reconstituted an image of the IGR-IRES of CrPV docking on the human ribosome.
[ "12" ]
A cryo-electron microscopy study has reconstituted an image of the IGR-IRES of CrPV docking on the human ribosome.
true
true
true
true
true
170
2
INTRODUCTION
1
12
[ "B12" ]
17,287,295
pmid-15315759
At ∼20 Å resolution, the model reveals several structural elements of the ribosome that contact the IGR-IRES, such as helices 18, 30 and 34.
[ "12" ]
140
961
0
false
At ∼20 Å resolution, the model reveals several structural elements of the ribosome that contact the IGR-IRES, such as helices 18, 30 and 34.
[]
At ∼20 Å resolution, the model reveals several structural elements of the ribosome that contact the IGR-IRES, such as helices 18, 30 and 34.
true
true
true
true
true
170
2
INTRODUCTION
1
12
[ "B12" ]
17,287,295
pmid-15315759
However, biochemical evidence showing one-to-one correspondence between nucleotides in the IRES and structural elements of the ribosome remains lacking.
[ "12" ]
152
962
0
false
However, biochemical evidence showing one-to-one correspondence between nucleotides in the IRES and structural elements of the ribosome remains lacking.
[]
However, biochemical evidence showing one-to-one correspondence between nucleotides in the IRES and structural elements of the ribosome remains lacking.
true
true
true
true
true
170
3
INTRODUCTION
0
null
null
17,287,295
null
Here, to identify sites on the 40S ribosomal subunit that interact with the IGR-IRES of PSIV, chemical modification and crosslinking analyses against the 18S rRNA and 40S ribosomal proteins were carried out.
null
207
963
0
false
null
null
Here, to identify sites on the 40S ribosomal subunit that interact with the IGR-IRES of PSIV, chemical modification and crosslinking analyses against the 18S rRNA and 40S ribosomal proteins were carried out.
true
true
true
true
true
171
3
INTRODUCTION
0
null
null
17,287,295
null
The crosslinking results suggest that the IGR-IRES interacts mainly with ribosomal proteins, rather than the 18S rRNA.
null
118
964
0
false
null
null
The crosslinking results suggest that the IGR-IRES interacts mainly with ribosomal proteins, rather than the 18S rRNA.
true
true
true
true
true
171
3
INTRODUCTION
0
null
null
17,287,295
null
In addition, the ribosomal protein S25 (rpS25), which was crosslinked to the conserved domain 2 region in the IRES, does not have a prokaryotic counterpart, explaining why IGR-IRES-mediated translation does not occur with bacterial ribosomes.
null
242
965
0
false
null
null
In addition, the ribosomal protein S25 (rpS25), which was crosslinked to the conserved domain 2 region in the IRES, does not have a prokaryotic counterpart, explaining why IGR-IRES-mediated translation does not occur with bacterial ribosomes.
true
true
true
true
true
171
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
Gene expression often requires the interplay of two distant genetic regions and thus sharp bending of DNA is an essential component of gene functioning.
[ "1", "2", "3", "4", "5" ]
152
966
0
false
Gene expression often requires the interplay of two distant genetic regions and thus sharp bending of DNA is an essential component of gene functioning.
[]
Gene expression often requires the interplay of two distant genetic regions and thus sharp bending of DNA is an essential component of gene functioning.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
Conventional thinking holds that bending of short DNA strands below the persistent length, Np ≈ 150 bp, is facilitated by DNA binding proteins, such as integration host factor (IHF) and a histone-like protein (HU) (1).
[ "1", "2", "3", "4", "5" ]
218
967
1
false
Conventional thinking holds that bending of short DNA strands below the persistent length, Np ≈ 150 bp, is facilitated by DNA binding proteins, such as integration host factor (IHF) and a histone-like protein (HU).
[ "1" ]
Conventional thinking holds that bending of short DNA strands below the persistent length, Np ≈ 150 bp, is facilitated by DNA binding proteins, such as integration host factor (IHF) and a histone-like protein (HU).
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
DNA cyclization experiments provide a convenient method for evaluating this hypothesis (2,3).
[ "1", "2", "3", "4", "5" ]
93
968
0
false
DNA cyclization experiments provide a convenient method for evaluating this hypothesis.
[ "2,3" ]
DNA cyclization experiments provide a convenient method for evaluating this hypothesis.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
In a typical cyclization experiment, DNA fragments are designed with two complementary sticky ends.
[ "1", "2", "3", "4", "5" ]
99
969
0
false
In a typical cyclization experiment, DNA fragments are designed with two complementary sticky ends.
[]
In a typical cyclization experiment, DNA fragments are designed with two complementary sticky ends.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
A cyclization reaction is then performed by adding DNA ligase, e.g.
[ "1", "2", "3", "4", "5" ]
67
970
0
false
A cyclization reaction is then performed by adding DNA ligase, e.g.
[]
A cyclization reaction is then performed by adding DNA ligase, e.g.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
T4 DNA ligase, to the DNA solution.
[ "1", "2", "3", "4", "5" ]
35
971
0
false
T4 DNA ligase, to the DNA solution.
[]
T4 DNA ligase, to the DNA solution.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
The efficiency of the cyclization reaction (J), i.e.
[ "1", "2", "3", "4", "5" ]
52
972
0
false
The efficiency of the cyclization reaction (J), i.e.
[]
The efficiency of the cyclization reaction (J), i.e.
true
true
true
true
true
172
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
the relative yield of cyclized versus linear DNA product, is related to the bending rigidity of the DNA analyte.
[ "1", "2", "3", "4", "5" ]
112
973
0
false
the relative yield of cyclized versus linear DNA product, is related to the bending rigidity of the DNA analyte.
[]
the relative yield of cyclized versus linear DNA product, is related to the bending rigidity of the DNA analyte.
false
true
true
true
false
172
0
INTRODUCTION
1
4
[ "b1", "b2", "b3", "b4", "b5" ]
16,954,151
pmid-15102446|pmid-1518450|pmid-6272277|pmid-12524271|NA
By analyzing the J factor using Zhang–Crothers (4) or Shimada–Yamakawa (5) theory, it is in fact possible to extract the intrinsic rigidity of short DNA fragments.
[ "1", "2", "3", "4", "5" ]
163
974
1
false
By analyzing the J factor using Zhang–Crothers or Shimada–Yamakawa theory, it is in fact possible to extract the intrinsic rigidity of short DNA fragments.
[ "4", "5" ]
By analyzing the J factor using Zhang–Crothers or Shimada–Yamakawa theory, it is in fact possible to extract the intrinsic rigidity of short DNA fragments.
true
true
true
true
true
172
1
INTRODUCTION
0
null
null
16,954,151
null
Fundamental understanding of how a short DNA fragment forms a complete cycle during the cyclization assay is then an important first step for developing a more complete understanding of how DNA is packaged and transcribed in cells.
null
231
975
0
false
null
null
Fundamental understanding of how a short DNA fragment forms a complete cycle during the cyclization assay is then an important first step for developing a more complete understanding of how DNA is packaged and transcribed in cells.
true
true
true
true
true
173
1
INTRODUCTION
0
null
null
16,954,151
null
This information should also make it possible to determine how DNA achieves the required enhancement in flexibility to form sharp bends at minimum energetic cost.
null
162
976
0
false
null
null
This information should also make it possible to determine how DNA achieves the required enhancement in flexibility to form sharp bends at minimum energetic cost.
true
true
true
true
true
173
2
INTRODUCTION
1
6
[ "b6", "b7", "b8", "b9" ]
16,954,151
pmid-15125838|pmid-15718281|NA|NA
Recent cyclization experiments by Widom's group using short DNA fragments below the persistence length indicate that even these fragments spontaneously form sharp bends (6,7).
[ "6", "7", "8", "9" ]
175
977
0
false
Recent cyclization experiments by Widom's group using short DNA fragments below the persistence length indicate that even these fragments spontaneously form sharp bends.
[ "6,7" ]
Recent cyclization experiments by Widom's group using short DNA fragments below the persistence length indicate that even these fragments spontaneously form sharp bends.
true
true
true
true
true
174
2
INTRODUCTION
1
6
[ "b6", "b7", "b8", "b9" ]
16,954,151
pmid-15125838|pmid-15718281|NA|NA
This finding simultaneously challenges conventional thinking about the role of DNA bending catalysts and questions the suitability of classical theories based on worm-like chain (WLC) models for interpreting bending stiffness of double-stranded DNA (dsDNA) (8,9).
[ "6", "7", "8", "9" ]
263
978
0
false
This finding simultaneously challenges conventional thinking about the role of DNA bending catalysts and questions the suitability of classical theories based on worm-like chain (WLC) models for interpreting bending stiffness of double-stranded DNA (dsDNA).
[ "8,9" ]
This finding simultaneously challenges conventional thinking about the role of DNA bending catalysts and questions the suitability of classical theories based on worm-like chain (WLC) models for interpreting bending stiffness of double-stranded DNA (dsDNA).
true
true
true
true
true
174
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
It has long been suspected that local, spontaneous opening-up of the dsDNA duplex can dramatically enhance DNA flexibility, perhaps explaining its ability to form sharp bends.
[ "8", "10", "9", "10", "10", "6", "11" ]
175
979
0
false
It has long been suspected that local, spontaneous opening-up of the dsDNA duplex can dramatically enhance DNA flexibility, perhaps explaining its ability to form sharp bends.
[]
It has long been suspected that local, spontaneous opening-up of the dsDNA duplex can dramatically enhance DNA flexibility, perhaps explaining its ability to form sharp bends.
true
true
true
true
true
175
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
Treating DNA as a kinkable elastic chain, simple models have been proposed to describe this effect (8–10).
[ "8", "10", "9", "10", "10", "6", "11" ]
106
980
0
false
Treating DNA as a kinkable elastic chain, simple models have been proposed to describe this effect.
[ "8–10" ]
Treating DNA as a kinkable elastic chain, simple models have been proposed to describe this effect.
true
true
true
true
true
175
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
Single or multiple bubble(s) on DNA backbone is/are capable of creating local kinks, and thus effectively reduce(s) its bending stiffness.
[ "8", "10", "9", "10", "10", "6", "11" ]
138
981
0
false
Single or multiple bubble(s) on DNA backbone is/are capable of creating local kinks, and thus effectively reduce(s) its bending stiffness.
[]
Single or multiple bubble(s) on DNA backbone is/are capable of creating local kinks, and thus effectively reduce(s) its bending stiffness.
true
true
true
true
true
175
3
INTRODUCTION
1
10
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
Studies using these models conclude that two melting bubbles are essential (9,10), and indeed likely (10), for interpreting Widom's cyclization experimental data (6).
[ "8", "10", "9", "10", "10", "6", "11" ]
166
982
1
false
Studies using these models conclude that two melting bubbles are essential, and indeed likely, for interpreting Widom's cyclization experimental data.
[ "9,10", "10", "6" ]
Studies using these models conclude that two melting bubbles are essential, and indeed likely, for interpreting Widom's cyclization experimental data.
true
true
true
true
true
175
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
A recent study by Du et al.
[ "8", "10", "9", "10", "10", "6", "11" ]
27
983
0
false
A recent study by Du et al.
[]
A recent study by Du et al.
true
true
true
true
true
175
3
INTRODUCTION
1
11
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
(11), however, challenges the enhanced DNA flexibility observed in Widom's experiment.
[ "8", "10", "9", "10", "10", "6", "11" ]
86
984
1
false
, however, challenges the enhanced DNA flexibility observed in Widom's experiment.
[ "11" ]
, however, challenges the enhanced DNA flexibility observed in Widom's experiment.
false
false
true
true
false
175
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
These authors attribute the exceptionally high cyclization efficiency to higher than normal ligase concentration, which they contend invalidates the kinetic assumptions used to relate J to the bending stiffness of DNA.
[ "8", "10", "9", "10", "10", "6", "11" ]
218
985
0
false
These authors attribute the exceptionally high cyclization efficiency to higher than normal ligase concentration, which they contend invalidates the kinetic assumptions used to relate J to the bending stiffness of DNA.
[]
These authors attribute the exceptionally high cyclization efficiency to higher than normal ligase concentration, which they contend invalidates the kinetic assumptions used to relate J to the bending stiffness of DNA.
true
true
true
true
true
175
3
INTRODUCTION
1
8
[ "b8", "b10", "b9", "b10", "b10", "b6", "b11" ]
16,954,151
NA|pmid-16089763|NA|pmid-16089763|pmid-16089763|pmid-15125838|pmid-15809441
This ongoing debate underscores the need for other types of experiments that complement cyclization measurements to elucidate the mechanism(s) by which DNA is bent in cells.
[ "8", "10", "9", "10", "10", "6", "11" ]
173
986
0
false
This ongoing debate underscores the need for other types of experiments that complement cyclization measurements to elucidate the mechanism(s) by which DNA is bent in cells.
[]
This ongoing debate underscores the need for other types of experiments that complement cyclization measurements to elucidate the mechanism(s) by which DNA is bent in cells.
true
true
true
true
true
175
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
The spontaneous base pair flip-out rate for DNA has been determined experimentally to be ∼10−3 s−1 (12).
[ "12", "11", "11", "13" ]
104
987
1
false
The spontaneous base pair flip-out rate for DNA has been determined experimentally to be ∼10−3 s−1.
[ "12" ]
The spontaneous base pair flip-out rate for DNA has been determined experimentally to be ∼10−3 s−1.
true
true
true
true
true
176
4
INTRODUCTION
1
11
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
The rate of cyclization of 199 bp DNA fragments under normal experimental conditions (11), ranges from 10−3 to 10−2 s−1 with increasing ligase concentration.
[ "12", "11", "11", "13" ]
157
988
1
false
The rate of cyclization of 199 bp DNA fragments under normal experimental conditions, ranges from 10−3 to 10−2 s−1 with increasing ligase concentration.
[ "11" ]
The rate of cyclization of 199 bp DNA fragments under normal experimental conditions, ranges from 10−3 to 10−2 s−1 with increasing ligase concentration.
true
true
true
true
true
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
This means that cyclization of fragments containing flip-out bases will generally make a small to insignificant contribution to J.
[ "12", "11", "11", "13" ]
130
989
0
false
This means that cyclization of fragments containing flip-out bases will generally make a small to insignificant contribution to J.
[]
This means that cyclization of fragments containing flip-out bases will generally make a small to insignificant contribution to J.
true
true
true
true
true
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
On the other hand, the cyclization rate of the short DNA fragments used by Widom et al., i.e.
[ "12", "11", "11", "13" ]
93
990
0
false
On the other hand, the cyclization rate of the short DNA fragments used by Widom et al., i.e.
[]
On the other hand, the cyclization rate of the short DNA fragments used by Widom et al., i.e.
true
true
true
true
true
176
4
INTRODUCTION
1
11
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
<106 bp, is in the range of 10−5 to 10−6 s−1 and even lower (11).
[ "12", "11", "11", "13" ]
65
991
1
false
<106 bp, is in the range of 10−5 to 10−6 s−1 and even lower.
[ "11" ]
<106 bp, is in the range of 10−5 to 10−6 s−1 and even lower.
false
false
true
true
false
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
This means that as DNA fragment length is gradually reduced below the persistence length, fragments containing one or more transiently flipped-out bases become more probable during the lifetime of the cyclization assay.
[ "12", "11", "11", "13" ]
219
992
0
false
This means that as DNA fragment length is gradually reduced below the persistence length, fragments containing one or more transiently flipped-out bases become more probable during the lifetime of the cyclization assay.
[]
This means that as DNA fragment length is gradually reduced below the persistence length, fragments containing one or more transiently flipped-out bases become more probable during the lifetime of the cyclization assay.
true
true
true
true
true
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
Furthermore, if these flip-out bases significantly enhance the cyclization rate, the population of fragments whose cyclization is assisted by base flip-out can become very large.
[ "12", "11", "11", "13" ]
178
993
0
false
Furthermore, if these flip-out bases significantly enhance the cyclization rate, the population of fragments whose cyclization is assisted by base flip-out can become very large.
[]
Furthermore, if these flip-out bases significantly enhance the cyclization rate, the population of fragments whose cyclization is assisted by base flip-out can become very large.
true
true
true
true
true
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
For short DNA fragments well below Np, this effect should become dominant, since the cyclization rate of DNA without base flip-out approaches zero.
[ "12", "11", "11", "13" ]
147
994
0
false
For short DNA fragments well below Np, this effect should become dominant, since the cyclization rate of DNA without base flip-out approaches zero.
[]
For short DNA fragments well below Np, this effect should become dominant, since the cyclization rate of DNA without base flip-out approaches zero.
true
true
true
true
true
176
4
INTRODUCTION
1
13
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
Indeed conventional cyclization measurements have already shown that internal base pair mismatches in DNA can significantly enhance the cyclization efficiency (13).
[ "12", "11", "11", "13" ]
164
995
1
false
Indeed conventional cyclization measurements have already shown that internal base pair mismatches in DNA can significantly enhance the cyclization efficiency.
[ "13" ]
Indeed conventional cyclization measurements have already shown that internal base pair mismatches in DNA can significantly enhance the cyclization efficiency.
true
true
true
true
true
176
4
INTRODUCTION
1
12
[ "b12", "b11", "b11", "b13" ]
16,954,151
pmid-12440903|pmid-15809441|pmid-15809441|pmid-8139661
Precise information about how the kink(s) form and about how their location(s) impact cyclization efficiency of DNA therefore seems required to use any theoretical model to quantitatively explain cyclization data for short DNA.
[ "12", "11", "11", "13" ]
227
996
0
false
Precise information about how the kink(s) form and about how their location(s) impact cyclization efficiency of DNA therefore seems required to use any theoretical model to quantitatively explain cyclization data for short DNA.
[]
Precise information about how the kink(s) form and about how their location(s) impact cyclization efficiency of DNA therefore seems required to use any theoretical model to quantitatively explain cyclization data for short DNA.
true
true
true
true
true
176
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
As a first step towards understanding the effect of flip-out bases on bending of short DNA, we investigate bending properties of idealized analytes containing one or more permanent base pair mismatch(s) or melting bubbles.
[ "14" ]
222
997
0
false
As a first step towards understanding the effect of flip-out bases on bending of short DNA, we investigate bending properties of idealized analytes containing one or more permanent base pair mismatch(s) or melting bubbles.
[]
As a first step towards understanding the effect of flip-out bases on bending of short DNA, we investigate bending properties of idealized analytes containing one or more permanent base pair mismatch(s) or melting bubbles.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
Because the lifetime of base unpairing events in these analytes is effectively infinite, these systems best model short DNA fragments with ‘trapped’ base flip-out by the ligase-mediated cyclization reaction.
[ "14" ]
207
998
0
false
Because the lifetime of base unpairing events in these analytes is effectively infinite, these systems best model short DNA fragments with ‘trapped’ base flip-out by the ligase-mediated cyclization reaction.
[]
Because the lifetime of base unpairing events in these analytes is effectively infinite, these systems best model short DNA fragments with ‘trapped’ base flip-out by the ligase-mediated cyclization reaction.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
Their bending properties therefore provide insight into a potential alternative reaction pathway for cyclization reactions involving short dsDNA fragments.
[ "14" ]
155
999
0
false
Their bending properties therefore provide insight into a potential alternative reaction pathway for cyclization reactions involving short dsDNA fragments.
[]
Their bending properties therefore provide insight into a potential alternative reaction pathway for cyclization reactions involving short dsDNA fragments.
true
true
true
true
true
177