Split (1)

train · 816k rows

paragraph_index int64	sec string	p_has_citation int64	cites string	citeids list	pmid int64	cited_id string	sentences string	all_sent_cites list	sent_len int64	sentence_batch_index int64	sent_has_citation float64	qc_fail bool	cited_sentence string	cites_in_sentence list	cln_sentence string	is_cap bool	is_alpha bool	ends_wp bool	cit_qc bool	lgtm bool	__index_level_0__ int64
4	DISCUSSION	0	null	null	17,202,157	null	Inhibition of DNA methylation by AZAdC results in modest activation of CAII expression as compared to hormone-induced activation (Figure 7A).	null	141	1,500	0	false	null	null	Inhibition of DNA methylation by AZAdC results in modest activation of CAII expression as compared to hormone-induced activation (Figure 7A).	true	true	true	true	true	255
4	DISCUSSION	0	null	null	17,202,157	null	Although a significant decrease in CpG methylation is induced at the upstream part of the CpG island (Figure 6D), AZAdC treatment does not cause a positional change of the active histone marks.	null	193	1,501	0	false	null	null	Although a significant decrease in CpG methylation is induced at the upstream part of the CpG island (Figure 6D), AZAdC treatment does not cause a positional change of the active histone marks.	true	true	true	true	true	255
4	DISCUSSION	0	null	null	17,202,157	null	Instead, a moderate local increase in H3K9 acetylation and H3K4 tri-methylation is evident.	null	91	1,502	0	false	null	null	Instead, a moderate local increase in H3K9 acetylation and H3K4 tri-methylation is evident.	true	true	true	true	true	255
4	DISCUSSION	0	null	null	17,202,157	null	The increase in H3K9 acetylation could be the result of the dislodgement of MeCP2-complexed HDACs immediately upstream from the active histone marks.	null	149	1,503	0	false	null	null	The increase in H3K9 acetylation could be the result of the dislodgement of MeCP2-complexed HDACs immediately upstream from the active histone marks.	true	true	true	true	true	255
4	DISCUSSION	0	null	null	17,202,157	null	Intrusion of the active epigenetic code into the distal part of the CpG island does not occur, reinforcing the notion of the presence of a boundary or an activity that targets and maintains the active histone marks to a particular position.	null	240	1,504	0	false	null	null	Intrusion of the active epigenetic code into the distal part of the CpG island does not occur, reinforcing the notion of the presence of a boundary or an activity that targets and maintains the active histone marks to a particular position.	true	true	true	true	true	255
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	In the T2EC erythrocytic progenitor cells the CAII gene is transcribed, the active histone marks are associated with the CAII promoter, but DNA methylation is absent.	[ "12", "30" ]	166	1,505	0	false	In the T2EC erythrocytic progenitor cells the CAII gene is transcribed, the active histone marks are associated with the CAII promoter, but DNA methylation is absent.	[]	In the T2EC erythrocytic progenitor cells the CAII gene is transcribed, the active histone marks are associated with the CAII promoter, but DNA methylation is absent.	true	true	true	true	true	256
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	DNA methylation has apparently occurred later during differentiation, although it is currently unclear whether this also occurs in the animal or whether DNA methylation is due to AEV-induced transformation and/or culturing.	[ "12", "30" ]	223	1,506	0	false	DNA methylation has apparently occurred later during differentiation, although it is currently unclear whether this also occurs in the animal or whether DNA methylation is due to AEV-induced transformation and/or culturing.	[]	DNA methylation has apparently occurred later during differentiation, although it is currently unclear whether this also occurs in the animal or whether DNA methylation is due to AEV-induced transformation and/or culturing.	true	true	true	true	true	256
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	DNA methylation has been postulated to be a secondary event that occurs after initial silencing events involving other mechanisms (12).	[ "12", "30" ]	135	1,507	1	false	DNA methylation has been postulated to be a secondary event that occurs after initial silencing events involving other mechanisms.	[ "12" ]	DNA methylation has been postulated to be a secondary event that occurs after initial silencing events involving other mechanisms.	true	true	true	true	true	256
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	A possible scenario for CAII repression would involve the initial AEV-mediated delivery of a dominant negative v-ErbA that is not responsive to T3.	[ "12", "30" ]	147	1,508	0	false	A possible scenario for CAII repression would involve the initial AEV-mediated delivery of a dominant negative v-ErbA that is not responsive to T3.	[]	A possible scenario for CAII repression would involve the initial AEV-mediated delivery of a dominant negative v-ErbA that is not responsive to T3.	true	true	true	true	true	256
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	Although this subsequently repressed transcription by inhibiting PIC assembly, it did not lead to histone deacetylation at the promoter.	[ "12", "30" ]	136	1,509	0	false	Although this subsequently repressed transcription by inhibiting PIC assembly, it did not lead to histone deacetylation at the promoter.	[]	Although this subsequently repressed transcription by inhibiting PIC assembly, it did not lead to histone deacetylation at the promoter.	true	true	true	true	true	256
5	DISCUSSION	1	12	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	Subsequently, DNA methylation evoked by this repressed state could have progressed towards the CAII promoter, but halted because of the presence of a putative boundary which may involve the active histone marks in addition to other factors.	[ "12", "30" ]	240	1,510	0	false	Subsequently, DNA methylation evoked by this repressed state could have progressed towards the CAII promoter, but halted because of the presence of a putative boundary which may involve the active histone marks in addition to other factors.	[]	Subsequently, DNA methylation evoked by this repressed state could have progressed towards the CAII promoter, but halted because of the presence of a putative boundary which may involve the active histone marks in addition to other factors.	true	true	true	true	true	256
5	DISCUSSION	1	30	[ "b12", "b30" ]	17,202,157	pmid-11782440\|pmid-14716017	Such factors may include CTCF, which has been shown to protect DNA against de novo DNA methylation during imprinting (30), and the combinatorial presence of CTCF and active histone modifications hints to the possibility that they establish a chromatin state that does not permit DNA methylation to spread.	[ "12", "30" ]	305	1,511	1	false	Such factors may include CTCF, which has been shown to protect DNA against de novo DNA methylation during imprinting, and the combinatorial presence of CTCF and active histone modifications hints to the possibility that they establish a chromatin state that does not permit DNA methylation to spread.	[ "30" ]	Such factors may include CTCF, which has been shown to protect DNA against de novo DNA methylation during imprinting, and the combinatorial presence of CTCF and active histone modifications hints to the possibility that they establish a chromatin state that does not permit DNA methylation to spread.	true	true	true	true	true	256
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	We present here the first example of a bipartite CpG island code, but such codes may be a general phenomenon.	[ "31" ]	109	1,512	0	false	We present here the first example of a bipartite CpG island code, but such codes may be a general phenomenon.	[]	We present here the first example of a bipartite CpG island code, but such codes may be a general phenomenon.	true	true	true	true	true	257
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	Similar local CpG methylation patterns have been described for promoter-containing CpG islands of the mouse and human APRT, ADA and telomerase genes (31), but histone modifications have not been analyzed in these promoters.	[ "31" ]	223	1,513	1	false	Similar local CpG methylation patterns have been described for promoter-containing CpG islands of the mouse and human APRT, ADA and telomerase genes, but histone modifications have not been analyzed in these promoters.	[ "31" ]	Similar local CpG methylation patterns have been described for promoter-containing CpG islands of the mouse and human APRT, ADA and telomerase genes, but histone modifications have not been analyzed in these promoters.	true	true	true	true	true	257
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	Whether a bipartite CpG island code is linked to genes that are actively repressed like CAII remains to be elucidated.	[ "31" ]	118	1,514	0	false	Whether a bipartite CpG island code is linked to genes that are actively repressed like CAII remains to be elucidated.	[]	Whether a bipartite CpG island code is linked to genes that are actively repressed like CAII remains to be elucidated.	true	true	true	true	true	257
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	Silencing by CpG methylation is believed to involve progressive spreading of DNA methylation, eventually covering entire CpG islands.	[ "31" ]	133	1,515	0	false	Silencing by CpG methylation is believed to involve progressive spreading of DNA methylation, eventually covering entire CpG islands.	[]	Silencing by CpG methylation is believed to involve progressive spreading of DNA methylation, eventually covering entire CpG islands.	true	true	true	true	true	257
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	Our data suggest that boundary elements function as crucial antagonists against such gene silencing events.	[ "31" ]	107	1,516	0	false	Our data suggest that boundary elements function as crucial antagonists against such gene silencing events.	[]	Our data suggest that boundary elements function as crucial antagonists against such gene silencing events.	true	true	true	true	true	257
6	DISCUSSION	1	31	[ "b31" ]	17,202,157	pmid-11454739	Whatever the molecular mechanism, the bipartite code within the promoter does not preclude gene activity, and as such it challenges the paradigm that methylation of promoter-containing CpG islands invariantly causes gene silencing.	[ "31" ]	231	1,517	0	false	Whatever the molecular mechanism, the bipartite code within the promoter does not preclude gene activity, and as such it challenges the paradigm that methylation of promoter-containing CpG islands invariantly causes gene silencing.	[]	Whatever the molecular mechanism, the bipartite code within the promoter does not preclude gene activity, and as such it challenges the paradigm that methylation of promoter-containing CpG islands invariantly causes gene silencing.	true	true	true	true	true	257
0	INTRODUCTION	1	1–4	[ "B1 B2 B3 B4", "B5", "B6", "B7", "B8" ]	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	The major challenges in the development of artificial ribonucleases (aRNases) are the achievement of sequence specificity of RNA cleavage and high cleavage efficiency.	[ "1–4", "5", "6", "7", "8" ]	167	1,518	0	false	The major challenges in the development of artificial ribonucleases (aRNases) are the achievement of sequence specificity of RNA cleavage and high cleavage efficiency.	[]	The major challenges in the development of artificial ribonucleases (aRNases) are the achievement of sequence specificity of RNA cleavage and high cleavage efficiency.	true	true	true	true	true	258
0	INTRODUCTION	1	1–4	[ "B1 B2 B3 B4", "B5", "B6", "B7", "B8" ]	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	Natural ribonucleases of RNase A family (1–4) exhibit pyrimidine-X specificity.	[ "1–4", "5", "6", "7", "8" ]	79	1,519	1	false	Natural ribonucleases of RNase A family exhibit pyrimidine-X specificity.	[ "1–4" ]	Natural ribonucleases of RNase A family exhibit pyrimidine-X specificity.	true	true	true	true	true	258
0	INTRODUCTION	1	6	[ "B1 B2 B3 B4", "B5", "B6", "B7", "B8" ]	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	Ribonucleases of T1 family (RNase T1 from Aspergillus oryzae (5) and RNase F1 from Fusarium moniliforme (6) exhibit guanine-X specificity, and RNase U2 from Ustilago sphaerogena (7) exhibit adenine-X specificity.	[ "1–4", "5", "6", "7", "8" ]	212	1,520	1	false	Ribonucleases of T1 family and RNase F1 from Fusarium moniliforme exhibit guanine-X specificity, and RNase U2 from Ustilago sphaerogena exhibit adenine-X specificity.	[ "RNase T1 from Aspergillus oryzae (5", "6", "7" ]	Ribonucleases of T1 family and RNase F1 from Fusarium moniliforme exhibit guanine-X specificity, and RNase U2 from Ustilago sphaerogena exhibit adenine-X specificity.	true	true	true	true	true	258
0	INTRODUCTION	1	8	[ "B1 B2 B3 B4", "B5", "B6", "B7", "B8" ]	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	Attempts have been made to alter the specificity of ribonuclease T1 by protein engineering methods (8), but this goal has not been achieved till date.	[ "1–4", "5", "6", "7", "8" ]	150	1,521	1	false	Attempts have been made to alter the specificity of ribonuclease T1 by protein engineering methods, but this goal has not been achieved till date.	[ "8" ]	Attempts have been made to alter the specificity of ribonuclease T1 by protein engineering methods, but this goal has not been achieved till date.	true	true	true	true	true	258
1	INTRODUCTION	1	9–11	[ "B9 B10 B11", "B12", "B13", "B14" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	One approach to the design of aRNases consists of mimicking active sites of natural enzymes by conjugates bearing the functional groups of amino acids that form the catalytic centre of the enzyme and catalysing the transesterification reaction [for example, imidazole (9–11), aminogroups (12), guanidinium groups (13)].	[ "9–11", "12", "13", "14" ]	319	1,522	0	false	One approach to the design of aRNases consists of mimicking active sites of natural enzymes by conjugates bearing the functional groups of amino acids that form the catalytic centre of the enzyme and catalysing the transesterification reaction.	[ "for example, imidazole (9–11), aminogroups (12), guanidinium groups (13)" ]	One approach to the design of aRNases consists of mimicking active sites of natural enzymes by conjugates bearing the functional groups of amino acids that form the catalytic centre of the enzyme and catalysing the transesterification reaction.	true	true	true	true	true	259
1	INTRODUCTION	1	14	[ "B9 B10 B11", "B12", "B13", "B14" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	aRNases designed using this approach usually display cleavage specificity similar to that of RNase A: they cleave RNA predominantly at linkages within Pyr-A motifs, which are known to be highly sensitive towards various cleaving agents (14).	[ "9–11", "12", "13", "14" ]	241	1,523	1	false	aRNases designed using this approach usually display cleavage specificity similar to that of RNase A: they cleave RNA predominantly at linkages within Pyr-A motifs, which are known to be highly sensitive towards various cleaving agents.	[ "14" ]	aRNases designed using this approach usually display cleavage specificity similar to that of RNase A: they cleave RNA predominantly at linkages within Pyr-A motifs, which are known to be highly sensitive towards various cleaving agents.	false	true	true	true	false	259
1	INTRODUCTION	1	9–11	[ "B9 B10 B11", "B12", "B13", "B14" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	These aRNases accelerate cleavage at the most sensitive sites within RNA.	[ "9–11", "12", "13", "14" ]	73	1,524	0	false	These aRNases accelerate cleavage at the most sensitive sites within RNA.	[]	These aRNases accelerate cleavage at the most sensitive sites within RNA.	true	true	true	true	true	259
2	INTRODUCTION	0	null	null	17,389,642	pmid-16615805	The sequence specificity of natural RNases is determined by the substrate recognition centre in which the specific interaction of amino acids with RNA provides for the specific binding and placement of a particular heterocyclic base, thus resulting in the optimal conformation of internucleotide phosphodiester bonds, which are subjected to cleavage.	null	350	1,525	0	false	null	null	The sequence specificity of natural RNases is determined by the substrate recognition centre in which the specific interaction of amino acids with RNA provides for the specific binding and placement of a particular heterocyclic base, thus resulting in the optimal conformation of internucleotide phosphodiester bonds, which are subjected to cleavage.	true	true	true	true	true	260
2	INTRODUCTION	0	null	null	17,389,642	pmid-16615805	Accurate mimicking of ribonuclease active centres is a difficult task because of their complex spatial structure providing for multipoint contacts within the enzyme–substrate complex, and specific and dynamic nature of the centres that undergo conformational changes.	null	267	1,526	0	false	null	null	Accurate mimicking of ribonuclease active centres is a difficult task because of their complex spatial structure providing for multipoint contacts within the enzyme–substrate complex, and specific and dynamic nature of the centres that undergo conformational changes.	true	true	true	true	true	260
3	INTRODUCTION	1	15	[ "B15", "B13", "B16 B17 B18 B19 B20 B21" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	Attempts were made to stabilize the RNA heterocyclic bases optimally for cleavage conformations via stacking interactions with aromatic amino acids [for example, phenylalanine (15)], which were introduced into the structure of conjugates mimicking RNase active centres.	[ "15", "13", "16–21" ]	269	1,527	0	false	Attempts were made to stabilize the RNA heterocyclic bases optimally for cleavage conformations via stacking interactions with aromatic amino acids, which were introduced into the structure of conjugates mimicking RNase active centres.	[ "for example, phenylalanine (15)" ]	Attempts were made to stabilize the RNA heterocyclic bases optimally for cleavage conformations via stacking interactions with aromatic amino acids, which were introduced into the structure of conjugates mimicking RNase active centres.	true	true	true	true	true	261
3	INTRODUCTION	1	15	[ "B15", "B13", "B16 B17 B18 B19 B20 B21" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	However, these conjugates did not exhibit any cleavage specificity other than Pyr-A.	[ "15", "13", "16–21" ]	84	1,528	0	false	However, these conjugates did not exhibit any cleavage specificity other than Pyr-A.	[]	However, these conjugates did not exhibit any cleavage specificity other than Pyr-A.	true	true	true	true	true	261
3	INTRODUCTION	1	13	[ "B15", "B13", "B16 B17 B18 B19 B20 B21" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	aRNases displaying other specificity were developed by introducing guanidinium groups and arginine residues into the structure of aRNases: some G–X cleavage activity was reported for conjugates of anthraquinone and imidodiacetate bearing carboxylic and ammonium ions (13) and conjugates of oligodeoxyribonucleotides and peptide (LR)4-G-amide (16–21).	[ "15", "13", "16–21" ]	350	1,529	1	false	aRNases displaying other specificity were developed by introducing guanidinium groups and arginine residues into the structure of aRNases: some G–X cleavage activity was reported for conjugates of anthraquinone and imidodiacetate bearing carboxylic and ammonium ions and conjugates of oligodeoxyribonucleotides and peptide (LR)4-G-amide.	[ "13", "16–21" ]	aRNases displaying other specificity were developed by introducing guanidinium groups and arginine residues into the structure of aRNases: some G–X cleavage activity was reported for conjugates of anthraquinone and imidodiacetate bearing carboxylic and ammonium ions and conjugates of oligodeoxyribonucleotides and peptide (LR)4-G-amide.	false	true	true	true	false	261
4	INTRODUCTION	1	16	[ "B16", "B19", "B16", "B19", "B17", "B20" ]	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	Recently, the conjugates of peptide (LR)4-G-NH2 attached to 5′-terminal phosphate of antisense oligonucleotides were obtained (16,19).	[ "16", "19", "16", "19", "17", "20" ]	134	1,530	0	false	Recently, the conjugates of peptide (LR)4-G-NH2 attached to 5′-terminal phosphate of antisense oligonucleotides were obtained.	[ "16,19" ]	Recently, the conjugates of peptide (LR)4-G-NH2 attached to 5′-terminal phosphate of antisense oligonucleotides were obtained.	true	true	true	true	true	262
4	INTRODUCTION	1	16	[ "B16", "B19", "B16", "B19", "B17", "B20" ]	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	These conjugates were found to cleave RNA both in the vicinity of oligonucleotide complementary sequence and in a random manner at Pyr-A and G–X linkages (16,19).	[ "16", "19", "16", "19", "17", "20" ]	162	1,531	0	false	These conjugates were found to cleave RNA both in the vicinity of oligonucleotide complementary sequence and in a random manner at Pyr-A and G–X linkages.	[ "16,19" ]	These conjugates were found to cleave RNA both in the vicinity of oligonucleotide complementary sequence and in a random manner at Pyr-A and G–X linkages.	true	true	true	true	true	262
4	INTRODUCTION	1	16	[ "B16", "B19", "B16", "B19", "B17", "B20" ]	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	We found that the oligonucleotide in the conjugates plays an unusual role: it promotes formation of an ‘active’ peptide conformation because the peptide itself exhibits no ribonuclease activity (17,20).	[ "16", "19", "16", "19", "17", "20" ]	202	1,532	0	false	We found that the oligonucleotide in the conjugates plays an unusual role: it promotes formation of an ‘active’ peptide conformation because the peptide itself exhibits no ribonuclease activity.	[ "17,20" ]	We found that the oligonucleotide in the conjugates plays an unusual role: it promotes formation of an ‘active’ peptide conformation because the peptide itself exhibits no ribonuclease activity.	true	true	true	true	true	262
4	INTRODUCTION	1	16	[ "B16", "B19", "B16", "B19", "B17", "B20" ]	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	All designed oligonucleotide–peptide conjugates displayed either G–X > Pyr-A or G–X < Pyr-A activity, but both activities were observed simultaneously.	[ "16", "19", "16", "19", "17", "20" ]	151	1,533	0	false	All designed oligonucleotide–peptide conjugates displayed either G–X > Pyr-A or G–X < Pyr-A activity, but both activities were observed simultaneously.	[]	All designed oligonucleotide–peptide conjugates displayed either G–X > Pyr-A or G–X < Pyr-A activity, but both activities were observed simultaneously.	true	true	true	true	true	262
4	INTRODUCTION	1	16	[ "B16", "B19", "B16", "B19", "B17", "B20" ]	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	The main task of this work was to design the conjugate(s) exhibiting G–X cleavage activity similar only to RNase T1.	[ "16", "19", "16", "19", "17", "20" ]	116	1,534	0	false	The main task of this work was to design the conjugate(s) exhibiting G–X cleavage activity similar only to RNase T1.	[]	The main task of this work was to design the conjugate(s) exhibiting G–X cleavage activity similar only to RNase T1.	true	true	true	true	true	262
5	INTRODUCTION	0	null	null	17,389,642	NA\|pmid-15250719\|NA	In this article, we solve this problem and describe the first single-stranded guanine-specific aRNase—conjugate of nonadeoxyribonucleotide GGATCTCTT and peptide (RL)4-G-amide connected by the linker of three deoxyribose residues (pep-9), which display only G–X cleavage activity under various conditions.	null	304	1,535	0	false	null	null	In this article, we solve this problem and describe the first single-stranded guanine-specific aRNase—conjugate of nonadeoxyribonucleotide GGATCTCTT and peptide (RL)4-G-amide connected by the linker of three deoxyribose residues (pep-9), which display only G–X cleavage activity under various conditions.	true	true	true	true	true	263
5	INTRODUCTION	0	null	null	17,389,642	NA\|pmid-15250719\|NA	Rate enhancement of RNA cleavage at G–X linkages catalysed by pep-9 is 108, as compared to non-catalysed reactions; pep-9 cleaves G–X linkages only 105-fold less rapidly than RNase T1 (kcat_RNase T1/kcat_pep-9 = 105).	null	217	1,536	0	false	null	null	Rate enhancement of RNA cleavage at G–X linkages catalysed by pep-9 is 108, as compared to non-catalysed reactions; pep-9 cleaves G–X linkages only 105-fold less rapidly than RNase T1 (kcat_RNase T1/kcat_pep-9 = 105).	true	true	true	true	true	263
0	DISCUSSION	0	null	null	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	The data obtained show that oligonucleotide–peptide conjugate pep-9 is the first aRNase exhibiting RNase T1-like cleavage activity under a wide range of conditions.	null	164	1,537	0	false	null	null	The data obtained show that oligonucleotide–peptide conjugate pep-9 is the first aRNase exhibiting RNase T1-like cleavage activity under a wide range of conditions.	true	true	true	true	true	264
0	DISCUSSION	0	null	null	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	The low molecular weight catalyst (pep-9) discovered is 105-fold less active as compared to RNase T1, but it accelerates cleavage at G–X linkages in RNA 107–108-fold as compared to spontaneous hydrolysis.	null	204	1,538	0	false	null	null	The low molecular weight catalyst (pep-9) discovered is 105-fold less active as compared to RNase T1, but it accelerates cleavage at G–X linkages in RNA 107–108-fold as compared to spontaneous hydrolysis.	true	true	true	true	true	264
0	DISCUSSION	0	null	null	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	The unique specificity found is a surprising fact per se and requires explanations on which factors (oligonucleotide or/and peptide sequence, conjugate structure, etc.)	null	168	1,539	0	false	null	null	The unique specificity found is a surprising fact per se and requires explanations on which factors (oligonucleotide or/and peptide sequence, conjugate structure, etc.)	true	true	false	true	false	264
0	DISCUSSION	0	null	null	17,389,642	pmid-4508150\|pmid-2866795\|pmid-1373237\|pmid-1985896\|NA\|pmid-8386773\|pmid-5416897\|pmid-9931000	provide for this specificity.	null	29	1,540	0	false	null	null	provide for this specificity.	false	true	true	true	false	264
1	DISCUSSION	1	17	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	The conjugate pep-9 functionally mimics RNase T1.	[ "17", "30" ]	49	1,541	0	false	The conjugate pep-9 functionally mimics RNase T1.	[]	The conjugate pep-9 functionally mimics RNase T1.	true	true	true	true	true	265
1	DISCUSSION	1	17	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	The conjugate pep-9 is a single-stranded guanine-specific ribonuclease exhibiting multiple reaction turnover and yielding cleavage products similar to the products of RNase T1 (17).	[ "17", "30" ]	181	1,542	1	false	The conjugate pep-9 is a single-stranded guanine-specific ribonuclease exhibiting multiple reaction turnover and yielding cleavage products similar to the products of RNase T1.	[ "17" ]	The conjugate pep-9 is a single-stranded guanine-specific ribonuclease exhibiting multiple reaction turnover and yielding cleavage products similar to the products of RNase T1.	true	true	true	true	true	265
1	DISCUSSION	1	30	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	Cleavage of RNA by the conjugate as well as by RNase T1 displays only moderate temperature dependence (30).	[ "17", "30" ]	107	1,543	1	false	Cleavage of RNA by the conjugate as well as by RNase T1 displays only moderate temperature dependence.	[ "30" ]	Cleavage of RNA by the conjugate as well as by RNase T1 displays only moderate temperature dependence.	true	true	true	true	true	265
1	DISCUSSION	1	17	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	This fact as well as the saturation curve of the concentration profile of pep-9 are evidences for the cleavage reaction proceeding within the complex RNA/pep-9.	[ "17", "30" ]	160	1,544	0	false	This fact as well as the saturation curve of the concentration profile of pep-9 are evidences for the cleavage reaction proceeding within the complex RNA/pep-9.	[]	This fact as well as the saturation curve of the concentration profile of pep-9 are evidences for the cleavage reaction proceeding within the complex RNA/pep-9.	true	true	true	true	true	265
1	DISCUSSION	1	17	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	The affinity of the conjugate to RNA is provided by the peptide moiety and oligonucleotide, which is not complementary to RNA substrate, is not involved in binding with RNA.	[ "17", "30" ]	173	1,545	0	false	The affinity of the conjugate to RNA is provided by the peptide moiety and oligonucleotide, which is not complementary to RNA substrate, is not involved in binding with RNA.	[]	The affinity of the conjugate to RNA is provided by the peptide moiety and oligonucleotide, which is not complementary to RNA substrate, is not involved in binding with RNA.	true	true	true	true	true	265
1	DISCUSSION	1	17	[ "B17", "B30" ]	17,389,642	pmid-9528657\|NA\|pmid-8604321\|NA\|NA\|pmid-3331337\|pmid-15047859\|NA	This allows us to postulate pep-9 as an artificial enzyme with aptamer-like peculiarities.	[ "17", "30" ]	90	1,546	0	false	This allows us to postulate pep-9 as an artificial enzyme with aptamer-like peculiarities.	[]	This allows us to postulate pep-9 as an artificial enzyme with aptamer-like peculiarities.	true	true	true	true	true	265
2	DISCUSSION	1	18	[ "B18" ]	17,389,642	pmid-16615805	Analysis of structure–function relationships in the conjugate pep-9 clearly shows that any alterations of oligonucleotide sequence and length in pep-9 and deletion of the linker group result in the loss of ribonuclease activity and the appearance of Pyr-A cleavage specificity; thus, the sequence of nonadeoxyribonucleotide GGATCTCTT is obligatory for the conjugate to exhibit G–X specificity.	[ "18" ]	393	1,547	0	false	Analysis of structure–function relationships in the conjugate pep-9 clearly shows that any alterations of oligonucleotide sequence and length in pep-9 and deletion of the linker group result in the loss of ribonuclease activity and the appearance of Pyr-A cleavage specificity; thus, the sequence of nonadeoxyribonucleotide GGATCTCTT is obligatory for the conjugate to exhibit G–X specificity.	[]	Analysis of structure–function relationships in the conjugate pep-9 clearly shows that any alterations of oligonucleotide sequence and length in pep-9 and deletion of the linker group result in the loss of ribonuclease activity and the appearance of Pyr-A cleavage specificity; thus, the sequence of nonadeoxyribonucleotide GGATCTCTT is obligatory for the conjugate to exhibit G–X specificity.	true	true	true	true	true	266
2	DISCUSSION	1	18	[ "B18" ]	17,389,642	pmid-16615805	The importance of the linker group between oligonucleotide and peptide parts of the conjugate correlate with the data published in (18).	[ "18" ]	136	1,548	1	false	The importance of the linker group between oligonucleotide and peptide parts of the conjugate correlate with the data published in.	[ "18" ]	The importance of the linker group between oligonucleotide and peptide parts of the conjugate correlate with the data published in.	true	true	true	true	true	266
2	DISCUSSION	1	18	[ "B18" ]	17,389,642	pmid-16615805	It was found that two or three nucleotides adjacent to the peptide serve as a linker, providing a turn of oligonucleotide around the peptide and facilitating intramolecular oligonucleotide and peptide interactions.	[ "18" ]	214	1,549	0	false	It was found that two or three nucleotides adjacent to the peptide serve as a linker, providing a turn of oligonucleotide around the peptide and facilitating intramolecular oligonucleotide and peptide interactions.	[]	It was found that two or three nucleotides adjacent to the peptide serve as a linker, providing a turn of oligonucleotide around the peptide and facilitating intramolecular oligonucleotide and peptide interactions.	true	true	true	true	true	266
3	DISCUSSION	1	31	[ "B31", "B31", "B32" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	It is known that arginine is a multiple-donor amino acid that can form a number of specific hydrogen bonds with nucleotides (31).	[ "31", "31", "32" ]	129	1,550	1	false	It is known that arginine is a multiple-donor amino acid that can form a number of specific hydrogen bonds with nucleotides.	[ "31" ]	It is known that arginine is a multiple-donor amino acid that can form a number of specific hydrogen bonds with nucleotides.	true	true	true	true	true	267
3	DISCUSSION	1	31	[ "B31", "B31", "B32" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	The ability of arginine to form hydrogen bonds with DNA/RNA nucleobases within DNA(RNA)–protein complexes decreases in order G > T >	[ "31", "31", "32" ]	132	1,551	0	false	The ability of arginine to form hydrogen bonds with DNA/RNA nucleobases within DNA(RNA)–protein complexes decreases in order G > T >	[]	The ability of arginine to form hydrogen bonds with DNA/RNA nucleobases within DNA(RNA)–protein complexes decreases in order G > T >	true	true	false	true	false	267
3	DISCUSSION	1	31	[ "B31", "B31", "B32" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	A > C (31,32).	[ "31", "31", "32" ]	14	1,552	0	false	A > C.	[ "31,32" ]	A > C.	true	true	true	true	true	267
3	DISCUSSION	1	31	[ "B31", "B31", "B32" ]	17,389,642	pmid-1379732\|NA\|NA\|pmid-15047859\|pmid-16615805\|NA\|pmid-12462971\|NA\|pmid-11433033\|pmid-11433033\|pmid-12654263	These properties can be important not only for the interaction of the peptide (LR)4-G with guanine residues in RNA, but also for the specific intramolecular binding of arginine with guanine residues presented in the conjugate.	[ "31", "31", "32" ]	226	1,553	0	false	These properties can be important not only for the interaction of the peptide (LR)4-G with guanine residues in RNA, but also for the specific intramolecular binding of arginine with guanine residues presented in the conjugate.	[]	These properties can be important not only for the interaction of the peptide (LR)4-G with guanine residues in RNA, but also for the specific intramolecular binding of arginine with guanine residues presented in the conjugate.	true	true	true	true	true	267
4	DISCUSSION	0	null	null	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	Thus, the obtained data let us to suppose existence of some active conformation of the conjugate, which is formed as the result of a set of intermolecular contacts between the oligonucleotide and the peptide parts.	null	214	1,554	0	false	null	null	Thus, the obtained data let us to suppose existence of some active conformation of the conjugate, which is formed as the result of a set of intermolecular contacts between the oligonucleotide and the peptide parts.	true	true	true	true	true	268
4	DISCUSSION	0	null	null	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	Electrostatic contacts play an important role in G–X activity of pep-9, either by stabilization of an ‘active’ conjugate conformation and/or by stabilization of RNA (G–X motif)/pep-9 reactive complex.	null	200	1,555	0	false	null	null	Electrostatic contacts play an important role in G–X activity of pep-9, either by stabilization of an ‘active’ conjugate conformation and/or by stabilization of RNA (G–X motif)/pep-9 reactive complex.	true	true	true	true	true	268
4	DISCUSSION	0	null	null	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	This is suggested by the high activity of pep-9 in the absence of mono- and divalent cations and inhibition of its activity in their presence.	null	142	1,556	0	false	null	null	This is suggested by the high activity of pep-9 in the absence of mono- and divalent cations and inhibition of its activity in their presence.	true	true	true	true	true	268
4	DISCUSSION	0	null	null	17,389,642	NA\|NA\|NA\|NA\|pmid-15047859\|pmid-12462971	High ribonuclease activity of pep-9 under the salt-free conditions is an apparent result of the removal of electrostatic shielding of RNA, which facilitates RNA–pep-9 interaction.	null	179	1,557	0	false	null	null	High ribonuclease activity of pep-9 under the salt-free conditions is an apparent result of the removal of electrostatic shielding of RNA, which facilitates RNA–pep-9 interaction.	true	true	true	true	true	268
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	The main question is: how does pep-9 cleave G–X linkages?	[ "33", "34", "35" ]	57	1,558	0	false	The main question is: how does pep-9 cleave G–X linkages?	[]	The main question is: how does pep-9 cleave G–X linkages?	true	true	true	true	true	269
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	pH profile did not shed light on the possible mechanism of RNA cleavage by pep-9.	[ "33", "34", "35" ]	81	1,559	0	false	pH profile did not shed light on the possible mechanism of RNA cleavage by pep-9.	[]	pH profile did not shed light on the possible mechanism of RNA cleavage by pep-9.	false	true	true	true	false	269
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	Strong decrease of activity could not be attributed to the pKa values of amino acids and heterocyclic bases because, in this range of pH, charges of arginine and glycine amide remain constant (pKa are 12.48 and ∼9.7 for guanidinium group and for Gly-amide, respectively) (33), and pKa values of heterocyclic bases (G, C, A and T) lies in the range 9.4–11.2, depending on sequence (34) and microenvironments (35).	[ "33", "34", "35" ]	412	1,560	1	false	Strong decrease of activity could not be attributed to the pKa values of amino acids and heterocyclic bases because, in this range of pH, charges of arginine and glycine amide remain constant (pKa are 12.48 and ∼9.7 for guanidinium group and for Gly-amide, respectively), and pKa values of heterocyclic bases (G, C, A and T) lies in the range 9.4–11.2, depending on sequence and microenvironments.	[ "33", "34", "35" ]	Strong decrease of activity could not be attributed to the pKa values of amino acids and heterocyclic bases because, in this range of pH, charges of arginine and glycine amide remain constant (pKa are 12.48 and ∼9.7 for guanidinium group and for Gly-amide, respectively), and pKa values of heterocyclic bases (G, C, A and T) lies in the range 9.4–11.2, depending on sequence and microenvironments.	true	true	true	true	true	269
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	The data presented allow us to assume that multipoint contacts formed between pep-9 and guanine residue disrupt its stacking with adjacent nucleobases in RNA chain and change conformation to close to the ‘in-line’ one.	[ "33", "34", "35" ]	218	1,561	0	false	The data presented allow us to assume that multipoint contacts formed between pep-9 and guanine residue disrupt its stacking with adjacent nucleobases in RNA chain and change conformation to close to the ‘in-line’ one.	[]	The data presented allow us to assume that multipoint contacts formed between pep-9 and guanine residue disrupt its stacking with adjacent nucleobases in RNA chain and change conformation to close to the ‘in-line’ one.	true	true	true	true	true	269
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	Thus, by a set of hydrogen bonds formed with guanine residue, pep-9 causes conformational changes to ribose phosphate of the guanine residue, followed by self-cleavage of the phosphodiester bond.	[ "33", "34", "35" ]	195	1,562	0	false	Thus, by a set of hydrogen bonds formed with guanine residue, pep-9 causes conformational changes to ribose phosphate of the guanine residue, followed by self-cleavage of the phosphodiester bond.	[]	Thus, by a set of hydrogen bonds formed with guanine residue, pep-9 causes conformational changes to ribose phosphate of the guanine residue, followed by self-cleavage of the phosphodiester bond.	true	true	true	true	true	269
5	DISCUSSION	1	33	[ "B33", "B34", "B35" ]	17,389,642	NA\|pmid-15250719\|NA	It worth noting that this type of interaction was never described for guanine nucleotides to date, while this reaction is typical for uridine and cytosine nucleotides.	[ "33", "34", "35" ]	167	1,563	0	false	It worth noting that this type of interaction was never described for guanine nucleotides to date, while this reaction is typical for uridine and cytosine nucleotides.	[]	It worth noting that this type of interaction was never described for guanine nucleotides to date, while this reaction is typical for uridine and cytosine nucleotides.	true	true	true	true	true	269
6	DISCUSSION	0	null	null	17,389,642	null	Thus, we developed aRNase displaying G–X cleavage specificity with a unique structure: a chimeric biopolymer built of nonadeoxyribonucleotide and peptide connected by a linker of three deoxyribose residues.	null	206	1,564	0	false	null	null	Thus, we developed aRNase displaying G–X cleavage specificity with a unique structure: a chimeric biopolymer built of nonadeoxyribonucleotide and peptide connected by a linker of three deoxyribose residues.	true	true	true	true	true	270
6	DISCUSSION	0	null	null	17,389,642	null	Identification of such a unique catalytic structure capable of specific cleaving at G–X linkages is an evidence for the existence of catalysts with aptamer-like peculiarities displaying other specificities.	null	206	1,565	0	false	null	null	Identification of such a unique catalytic structure capable of specific cleaving at G–X linkages is an evidence for the existence of catalysts with aptamer-like peculiarities displaying other specificities.	true	true	true	true	true	270
6	DISCUSSION	0	null	null	17,389,642	null	The study of interactions that provide for the activity of this structure can lead to the elucidation of the principles of recognition topology that can be used to design other molecules with unique properties.	null	210	1,566	0	false	null	null	The study of interactions that provide for the activity of this structure can lead to the elucidation of the principles of recognition topology that can be used to design other molecules with unique properties.	true	true	true	true	true	270
0	INTRODUCTION	1	1–3	[ "B1 B2 B3", "B3", "B4 B5 B6 B7 B8 B9 B10", "B11", "B12", "B3", "B13 B14 B15 B16", "B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31 B32" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a small, basic, nucleic-acid-binding protein having two zinc fingers connected by a short, basic amino acid linker.	[ "1–3", "3", "4–10", "11", "12", "3", "13–16", "16–32" ]	188	1,567	0	false	Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a small, basic, nucleic-acid-binding protein having two zinc fingers connected by a short, basic amino acid linker.	[]	Human immunodeficiency virus type 1 nucleocapsid protein (NC) is a small, basic, nucleic-acid-binding protein having two zinc fingers connected by a short, basic amino acid linker.	true	true	true	true	true	271
0	INTRODUCTION	1	1–3	[ "B1 B2 B3", "B3", "B4 B5 B6 B7 B8 B9 B10", "B11", "B12", "B3", "B13 B14 B15 B16", "B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31 B32" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	Each finger contains the invariant CCHC metal-ion-binding motif (1–3).	[ "1–3", "3", "4–10", "11", "12", "3", "13–16", "16–32" ]	70	1,568	1	false	Each finger contains the invariant CCHC metal-ion-binding motif.	[ "1–3" ]	Each finger contains the invariant CCHC metal-ion-binding motif.	true	true	true	true	true	271
0	INTRODUCTION	1	3	[ "B1 B2 B3", "B3", "B4 B5 B6 B7 B8 B9 B10", "B11", "B12", "B3", "B13 B14 B15 B16", "B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31 B32" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	NC binds non-specifically to the phosphodiester backbone of nucleic acids (3), but also exhibits sequence-specific binding at sites with runs of Gs or T/UGs (4–10).	[ "1–3", "3", "4–10", "11", "12", "3", "13–16", "16–32" ]	164	1,569	1	false	NC binds non-specifically to the phosphodiester backbone of nucleic acids, but also exhibits sequence-specific binding at sites with runs of Gs or T/UGs.	[ "3", "4–10" ]	NC binds non-specifically to the phosphodiester backbone of nucleic acids, but also exhibits sequence-specific binding at sites with runs of Gs or T/UGs.	true	true	true	true	true	271
0	INTRODUCTION	1	11	[ "B1 B2 B3", "B3", "B4 B5 B6 B7 B8 B9 B10", "B11", "B12", "B3", "B13 B14 B15 B16", "B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31 B32" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	In addition, NC is a nucleic acid chaperone and is able to catalyze nucleic acid conformational rearrangements that lead to formation of the most thermodynamically stable structures (11) (reviewed in 1–3,12).	[ "1–3", "3", "4–10", "11", "12", "3", "13–16", "16–32" ]	208	1,570	1	false	In addition, NC is a nucleic acid chaperone and is able to catalyze nucleic acid conformational rearrangements that lead to formation of the most thermodynamically stable structures.	[ "11", "reviewed in 1–3,12" ]	In addition, NC is a nucleic acid chaperone and is able to catalyze nucleic acid conformational rearrangements that lead to formation of the most thermodynamically stable structures.	true	true	true	true	true	271
0	INTRODUCTION	1	3	[ "B1 B2 B3", "B3", "B4 B5 B6 B7 B8 B9 B10", "B11", "B12", "B3", "B13 B14 B15 B16", "B16 B17 B18 B19 B20 B21 B22 B23 B24 B25 B26 B27 B28 B29 B30 B31 B32" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	The chaperone function has two independent activities (3): aggregation of nucleic acids, localized primarily to the N-terminal basic residues (13–16); and weak destabilization of duplex molecules, associated with the zinc fingers (16–32).	[ "1–3", "3", "4–10", "11", "12", "3", "13–16", "16–32" ]	238	1,571	1	false	The chaperone function has two independent activities : aggregation of nucleic acids, localized primarily to the N-terminal basic residues ; and weak destabilization of duplex molecules, associated with the zinc fingers.	[ "3", "13–16", "16–32" ]	The chaperone function has two independent activities : aggregation of nucleic acids, localized primarily to the N-terminal basic residues ; and weak destabilization of duplex molecules, associated with the zinc fingers.	true	true	true	true	true	271
1	INTRODUCTION	1	2	[ "B2", "B3", "B33", "B9", "B34 B35 B36 B37 B38", "B3", "B39" ]	17,553,835	pmid-9757830\|pmid-16164976\|pmid-12206453\|pmid-10924101\|pmid-9933645\|pmid-10233940\|pmid-11786014\|pmid-15327946\|pmid-16314282\|pmid-16164976\|NA\|pmid-15033363\|pmid-15542863\|pmid-15218022\|pmid-16291743	The nucleic acid chaperone activity of NC is required for efficient and highly specific DNA synthesis.	[ "2", "3", "33", "9", "34–38", "3", "39" ]	102	1,572	0	false	The nucleic acid chaperone activity of NC is required for efficient and highly specific DNA synthesis.	[]	The nucleic acid chaperone activity of NC is required for efficient and highly specific DNA synthesis.	true	true	true	true	true	272
1	INTRODUCTION	1	2	[ "B2", "B3", "B33", "B9", "B34 B35 B36 B37 B38", "B3", "B39" ]	17,553,835	pmid-9757830\|pmid-16164976\|pmid-12206453\|pmid-10924101\|pmid-9933645\|pmid-10233940\|pmid-11786014\|pmid-15327946\|pmid-16314282\|pmid-16164976\|NA\|pmid-15033363\|pmid-15542863\|pmid-15218022\|pmid-16291743	Indeed, NC plays an important role in almost every step in reverse transcription including the minus-strand (2,3,33) and plus-strand (9,34–38) transfer events that are mandatory for synthesis of full-length minus- and plus-strand DNAs and formation of the long-terminal repeats present at the ends of proviral DNA.	[ "2", "3", "33", "9", "34–38", "3", "39" ]	314	1,573	0	false	Indeed, NC plays an important role in almost every step in reverse transcription including the minus-strand and plus-strand transfer events that are mandatory for synthesis of full-length minus- and plus-strand DNAs and formation of the long-terminal repeats present at the ends of proviral DNA.	[ "2,3,33", "9,34–38" ]	Indeed, NC plays an important role in almost every step in reverse transcription including the minus-strand and plus-strand transfer events that are mandatory for synthesis of full-length minus- and plus-strand DNAs and formation of the long-terminal repeats present at the ends of proviral DNA.	true	true	true	true	true	272
1	INTRODUCTION	1	2	[ "B2", "B3", "B33", "B9", "B34 B35 B36 B37 B38", "B3", "B39" ]	17,553,835	pmid-9757830\|pmid-16164976\|pmid-12206453\|pmid-10924101\|pmid-9933645\|pmid-10233940\|pmid-11786014\|pmid-15327946\|pmid-16314282\|pmid-16164976\|NA\|pmid-15033363\|pmid-15542863\|pmid-15218022\|pmid-16291743	In minus-strand transfer, the initial DNA product of reverse transcription, known as (−) strong-stop DNA [(−) SSDNA], is translocated to the 3′ end of the viral genome (acceptor RNA) in a reaction mediated by base pairing of the complementary repeat (R) regions at the 3′ ends of the DNA and RNA molecules (3,39).	[ "2", "3", "33", "9", "34–38", "3", "39" ]	313	1,574	0	false	In minus-strand transfer, the initial DNA product of reverse transcription, known as (−) strong-stop DNA [(−) SSDNA], is translocated to the 3′ end of the viral genome (acceptor RNA) in a reaction mediated by base pairing of the complementary repeat (R) regions at the 3′ ends of the DNA and RNA molecules.	[ "3,39" ]	In minus-strand transfer, the initial DNA product of reverse transcription, known as (−) strong-stop DNA [(−) SSDNA], is translocated to the 3′ end of the viral genome (acceptor RNA) in a reaction mediated by base pairing of the complementary repeat (R) regions at the 3′ ends of the DNA and RNA molecules.	true	true	true	true	true	272
2	INTRODUCTION	1	16	[ "B16", "B19", "B23 B24 B25 B26", "B40 B41 B42", "B17", "B20", "B32", "B41", "B43 B44 B45 B46 B47 B48", "B3" ]	17,553,835	pmid-15854648\|pmid-11922672\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-9188585\|pmid-12473448\|pmid-16471833\|pmid-10982342\|pmid-11932404\|pmid-16962137\|pmid-12473448\|pmid-7989315\|pmid-7543198\|pmid-9760259\|pmid-9658119\|pmid-12846564\|pmid-16406407\|pmid-16164976\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16962137\|pmid-16100256\|pmid-17372205	For HIV-1, R consists of 97 nucleotides (nt).	[ "16", "19", "23–26", "40–42", "17", "20", "32", "41", "43–48", "3" ]	45	1,575	0	false	For HIV-1, R consists of 97 nucleotides (nt).	[]	For HIV-1, R consists of 97 nucleotides (nt).	true	true	true	true	true	273
2	INTRODUCTION	1	16	[ "B16", "B19", "B23 B24 B25 B26", "B40 B41 B42", "B17", "B20", "B32", "B41", "B43 B44 B45 B46 B47 B48", "B3" ]	17,553,835	pmid-15854648\|pmid-11922672\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-9188585\|pmid-12473448\|pmid-16471833\|pmid-10982342\|pmid-11932404\|pmid-16962137\|pmid-12473448\|pmid-7989315\|pmid-7543198\|pmid-9760259\|pmid-9658119\|pmid-12846564\|pmid-16406407\|pmid-16164976\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16962137\|pmid-16100256\|pmid-17372205	The first 59 nt in acceptor RNA and (−) SSDNA form highly stable, complementary stem-loop structures, which are referred to as transactivation response elements (TAR) RNA and TAR DNA, respectively.	[ "16", "19", "23–26", "40–42", "17", "20", "32", "41", "43–48", "3" ]	197	1,576	0	false	The first 59 nt in acceptor RNA and (−) SSDNA form highly stable, complementary stem-loop structures, which are referred to as transactivation response elements (TAR) RNA and TAR DNA, respectively.	[]	The first 59 nt in acceptor RNA and (−) SSDNA form highly stable, complementary stem-loop structures, which are referred to as transactivation response elements (TAR) RNA and TAR DNA, respectively.	true	true	true	true	true	273
2	INTRODUCTION	1	16	[ "B16", "B19", "B23 B24 B25 B26", "B40 B41 B42", "B17", "B20", "B32", "B41", "B43 B44 B45 B46 B47 B48", "B3" ]	17,553,835	pmid-15854648\|pmid-11922672\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-9188585\|pmid-12473448\|pmid-16471833\|pmid-10982342\|pmid-11932404\|pmid-16962137\|pmid-12473448\|pmid-7989315\|pmid-7543198\|pmid-9760259\|pmid-9658119\|pmid-12846564\|pmid-16406407\|pmid-16164976\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16962137\|pmid-16100256\|pmid-17372205	NC stimulates HIV-1 minus-strand transfer (3 and references therein) by transiently destabilizing the TAR structures (16,19,23–26,40–42).	[ "16", "19", "23–26", "40–42", "17", "20", "32", "41", "43–48", "3" ]	137	1,577	0	false	NC stimulates HIV-1 minus-strand transfer by transiently destabilizing the TAR structures.	[ "3 and references therein", "16,19,23–26,40–42" ]	NC stimulates HIV-1 minus-strand transfer by transiently destabilizing the TAR structures.	true	true	true	true	true	273
2	INTRODUCTION	1	3	[ "B16", "B19", "B23 B24 B25 B26", "B40 B41 B42", "B17", "B20", "B32", "B41", "B43 B44 B45 B46 B47 B48", "B3" ]	17,553,835	pmid-15854648\|pmid-11922672\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-9188585\|pmid-12473448\|pmid-16471833\|pmid-10982342\|pmid-11932404\|pmid-16962137\|pmid-12473448\|pmid-7989315\|pmid-7543198\|pmid-9760259\|pmid-9658119\|pmid-12846564\|pmid-16406407\|pmid-16164976\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16962137\|pmid-16100256\|pmid-17372205	Destabilization of these structures promotes annealing of TAR RNA to TAR DNA (17,20,32,41,43–48) and inhibits a competing self-priming reaction at the 3′ end of (−) SSDNA (3).	[ "16", "19", "23–26", "40–42", "17", "20", "32", "41", "43–48", "3" ]	175	1,578	1	false	Destabilization of these structures promotes annealing of TAR RNA to TAR DNA and inhibits a competing self-priming reaction at the 3′ end of (−) SSDNA.	[ "17,20,32,41,43–48", "3" ]	Destabilization of these structures promotes annealing of TAR RNA to TAR DNA and inhibits a competing self-priming reaction at the 3′ end of (−) SSDNA.	true	true	true	true	true	273
3	INTRODUCTION	1	49–51	[ "B49 B50 B51", "B52 B53 B54 B55", "B56", "B57", "B48", "B58", "B32", "B59" ]	17,553,835	pmid-15152202\|pmid-15345057\|pmid-16064056\|pmid-8078946\|pmid-10212256\|pmid-10954609\|pmid-10756194\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16100256\|pmid-16962137\|pmid-17372205\|pmid-11497429\|pmid-10931958\|pmid-17043221	Loop–loop interactions have been shown to be critical for dimerization and packaging of retroviral RNA (49–51) as well as for the formation of kissing complexes containing TAR RNA (52–55).	[ "49–51", "52–55", "56", "57", "48", "58", "32", "59" ]	188	1,579	1	false	Loop–loop interactions have been shown to be critical for dimerization and packaging of retroviral RNA as well as for the formation of kissing complexes containing TAR RNA.	[ "49–51", "52–55" ]	Loop–loop interactions have been shown to be critical for dimerization and packaging of retroviral RNA as well as for the formation of kissing complexes containing TAR RNA.	true	true	true	true	true	274
3	INTRODUCTION	1	49–51	[ "B49 B50 B51", "B52 B53 B54 B55", "B56", "B57", "B48", "B58", "B32", "B59" ]	17,553,835	pmid-15152202\|pmid-15345057\|pmid-16064056\|pmid-8078946\|pmid-10212256\|pmid-10954609\|pmid-10756194\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16100256\|pmid-16962137\|pmid-17372205\|pmid-11497429\|pmid-10931958\|pmid-17043221	Indeed, nucleation of the NC-catalyzed annealing step in minus-strand transfer was proposed to occur through interaction between the apical loops of TAR RNA and TAR DNA (56,57).	[ "49–51", "52–55", "56", "57", "48", "58", "32", "59" ]	177	1,580	0	false	Indeed, nucleation of the NC-catalyzed annealing step in minus-strand transfer was proposed to occur through interaction between the apical loops of TAR RNA and TAR DNA.	[ "56,57" ]	Indeed, nucleation of the NC-catalyzed annealing step in minus-strand transfer was proposed to occur through interaction between the apical loops of TAR RNA and TAR DNA.	true	true	true	true	true	274
3	INTRODUCTION	1	48	[ "B49 B50 B51", "B52 B53 B54 B55", "B56", "B57", "B48", "B58", "B32", "B59" ]	17,553,835	pmid-15152202\|pmid-15345057\|pmid-16064056\|pmid-8078946\|pmid-10212256\|pmid-10954609\|pmid-10756194\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16100256\|pmid-16962137\|pmid-17372205\|pmid-11497429\|pmid-10931958\|pmid-17043221	However, an alternative proposal suggested that nucleation proceeds through destabilization of the 3′ and 5′ stem termini (48).	[ "49–51", "52–55", "56", "57", "48", "58", "32", "59" ]	127	1,581	1	false	However, an alternative proposal suggested that nucleation proceeds through destabilization of the 3′ and 5′ stem termini.	[ "48" ]	However, an alternative proposal suggested that nucleation proceeds through destabilization of the 3′ and 5′ stem termini.	true	true	true	true	true	274
3	INTRODUCTION	1	58	[ "B49 B50 B51", "B52 B53 B54 B55", "B56", "B57", "B48", "B58", "B32", "B59" ]	17,553,835	pmid-15152202\|pmid-15345057\|pmid-16064056\|pmid-8078946\|pmid-10212256\|pmid-10954609\|pmid-10756194\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16100256\|pmid-16962137\|pmid-17372205\|pmid-11497429\|pmid-10931958\|pmid-17043221	Based on single-molecule FRET experiments (58) and a detailed kinetic study of NC-promoted annealing of mini-TAR constructs (32), it was also proposed that multiple pathways might be involved.	[ "49–51", "52–55", "56", "57", "48", "58", "32", "59" ]	192	1,582	1	false	Based on single-molecule FRET experiments and a detailed kinetic study of NC-promoted annealing of mini-TAR constructs, it was also proposed that multiple pathways might be involved.	[ "58", "32" ]	Based on single-molecule FRET experiments and a detailed kinetic study of NC-promoted annealing of mini-TAR constructs, it was also proposed that multiple pathways might be involved.	true	true	true	true	true	274
3	INTRODUCTION	1	59	[ "B49 B50 B51", "B52 B53 B54 B55", "B56", "B57", "B48", "B58", "B32", "B59" ]	17,553,835	pmid-15152202\|pmid-15345057\|pmid-16064056\|pmid-8078946\|pmid-10212256\|pmid-10954609\|pmid-10756194\|pmid-11497429\|pmid-15854644\|pmid-16406407\|pmid-16100256\|pmid-16962137\|pmid-17372205\|pmid-11497429\|pmid-10931958\|pmid-17043221	More recent studies with full-length TAR suggest that a zipper mechanism involving the lower stems and bulges is the major nucleation pathway for TAR annealing in the presence of NC (59) (Vo, M.-N., Rouzina, I. and Musier-Forsyth, K., in preparation).	[ "49–51", "52–55", "56", "57", "48", "58", "32", "59" ]	251	1,583	1	false	More recent studies with full-length TAR suggest that a zipper mechanism involving the lower stems and bulges is the major nucleation pathway for TAR annealing in the presence of NC (Vo, M.-N., Rouzina, I. and Musier-Forsyth, K., in preparation).	[ "59" ]	More recent studies with full-length TAR suggest that a zipper mechanism involving the lower stems and bulges is the major nucleation pathway for TAR annealing in the presence of NC (Vo, M.-N., Rouzina, I. and Musier-Forsyth, K., in preparation).	true	true	true	true	true	274
4	INTRODUCTION	1	24–26	[ "B24 B25 B26", "B59 B60 B61", "B28", "B32", "B62 B63 B64 B65 B66 B67 B68 B69 B70 B71 B72 B73 B74", "B19", "B28", "B28" ]	17,553,835	pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-17372205\|pmid-10982320\|pmid-15542863\|pmid-15271979\|pmid-16962137\|pmid-7666433\|pmid-12097560\|pmid-12595541\|pmid-12783894\|pmid-12595540\|pmid-12801926\|pmid-15342633\|pmid-15218022\|pmid-16092503\|pmid-16216274\|pmid-15751967\|pmid-16291743\|pmid-16782713\|pmid-11922672\|pmid-15271979\|pmid-15271979	The structure and thermostability of the nucleic acid intermediates are major determinants for NC-facilitated minus-strand transfer.	[ "24–26", "59–61", "28", "32", "62–74", "19", "28", "28" ]	132	1,584	0	false	The structure and thermostability of the nucleic acid intermediates are major determinants for NC-facilitated minus-strand transfer.	[]	The structure and thermostability of the nucleic acid intermediates are major determinants for NC-facilitated minus-strand transfer.	true	true	true	true	true	275
4	INTRODUCTION	1	24–26	[ "B24 B25 B26", "B59 B60 B61", "B28", "B32", "B62 B63 B64 B65 B66 B67 B68 B69 B70 B71 B72 B73 B74", "B19", "B28", "B28" ]	17,553,835	pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-17372205\|pmid-10982320\|pmid-15542863\|pmid-15271979\|pmid-16962137\|pmid-7666433\|pmid-12097560\|pmid-12595541\|pmid-12783894\|pmid-12595540\|pmid-12801926\|pmid-15342633\|pmid-15218022\|pmid-16092503\|pmid-16216274\|pmid-15751967\|pmid-16291743\|pmid-16782713\|pmid-11922672\|pmid-15271979\|pmid-15271979	A number of studies have emphasized the importance of maintaining the bulges in the TAR DNA structure of (−) SSDNA (24–26,59–61) as well as the critical role of acceptor RNA structure (28,32,62–74).	[ "24–26", "59–61", "28", "32", "62–74", "19", "28", "28" ]	198	1,585	0	false	A number of studies have emphasized the importance of maintaining the bulges in the TAR DNA structure of (−) SSDNA as well as the critical role of acceptor RNA structure.	[ "24–26,59–61", "28,32,62–74" ]	A number of studies have emphasized the importance of maintaining the bulges in the TAR DNA structure of (−) SSDNA as well as the critical role of acceptor RNA structure.	true	true	true	true	true	275
4	INTRODUCTION	1	24–26	[ "B24 B25 B26", "B59 B60 B61", "B28", "B32", "B62 B63 B64 B65 B66 B67 B68 B69 B70 B71 B72 B73 B74", "B19", "B28", "B28" ]	17,553,835	pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-17372205\|pmid-10982320\|pmid-15542863\|pmid-15271979\|pmid-16962137\|pmid-7666433\|pmid-12097560\|pmid-12595541\|pmid-12783894\|pmid-12595540\|pmid-12801926\|pmid-15342633\|pmid-15218022\|pmid-16092503\|pmid-16216274\|pmid-15751967\|pmid-16291743\|pmid-16782713\|pmid-11922672\|pmid-15271979\|pmid-15271979	Interestingly, minus-strand transfer is more sensitive to the thermostability of acceptor RNA than to the stability and structure of (−) SSDNA (19,28).	[ "24–26", "59–61", "28", "32", "62–74", "19", "28", "28" ]	151	1,586	0	false	Interestingly, minus-strand transfer is more sensitive to the thermostability of acceptor RNA than to the stability and structure of (−) SSDNA.	[ "19,28" ]	Interestingly, minus-strand transfer is more sensitive to the thermostability of acceptor RNA than to the stability and structure of (−) SSDNA.	true	true	true	true	true	275
4	INTRODUCTION	1	28	[ "B24 B25 B26", "B59 B60 B61", "B28", "B32", "B62 B63 B64 B65 B66 B67 B68 B69 B70 B71 B72 B73 B74", "B19", "B28", "B28" ]	17,553,835	pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-17372205\|pmid-10982320\|pmid-15542863\|pmid-15271979\|pmid-16962137\|pmid-7666433\|pmid-12097560\|pmid-12595541\|pmid-12783894\|pmid-12595540\|pmid-12801926\|pmid-15342633\|pmid-15218022\|pmid-16092503\|pmid-16216274\|pmid-15751967\|pmid-16291743\|pmid-16782713\|pmid-11922672\|pmid-15271979\|pmid-15271979	These findings are consistent with NC's weak destabilizing activity (see above) and led to the conclusion that efficient minus-strand transfer requires a delicate thermodynamic balance between the structures of (−) SSDNA and acceptor RNA and the stability of the annealed RNA–DNA hybrid (28).	[ "24–26", "59–61", "28", "32", "62–74", "19", "28", "28" ]	292	1,587	1	false	These findings are consistent with NC's weak destabilizing activity (see above) and led to the conclusion that efficient minus-strand transfer requires a delicate thermodynamic balance between the structures of (−) SSDNA and acceptor RNA and the stability of the annealed RNA–DNA hybrid.	[ "28" ]	These findings are consistent with NC's weak destabilizing activity (see above) and led to the conclusion that efficient minus-strand transfer requires a delicate thermodynamic balance between the structures of (−) SSDNA and acceptor RNA and the stability of the annealed RNA–DNA hybrid.	true	true	true	true	true	275
5	INTRODUCTION	1	28	[ "B28" ]	17,553,835	pmid-15271979\|pmid-16164976\|pmid-10233940	In the present study, we have elucidated the paradoxical activity of two acceptor RNAs (RNA 70 and RNA 50) in minus-strand transfer: Despite the fact that RNA 70 has a higher predicted overall free energy of folding (ΔG) than RNA 50, more transfer product is synthesized with the RNA 70 acceptor than with RNA 50 in assays with the same (−) SSDNA (28).	[ "28" ]	352	1,588	1	false	In the present study, we have elucidated the paradoxical activity of two acceptor RNAs (RNA 70 and RNA 50) in minus-strand transfer: Despite the fact that RNA 70 has a higher predicted overall free energy of folding (ΔG) than RNA 50, more transfer product is synthesized with the RNA 70 acceptor than with RNA 50 in assays with the same (−) SSDNA.	[ "28" ]	In the present study, we have elucidated the paradoxical activity of two acceptor RNAs (RNA 70 and RNA 50) in minus-strand transfer: Despite the fact that RNA 70 has a higher predicted overall free energy of folding (ΔG) than RNA 50, more transfer product is synthesized with the RNA 70 acceptor than with RNA 50 in assays with the same (−) SSDNA.	true	true	true	true	true	276
5	INTRODUCTION	1	28	[ "B28" ]	17,553,835	pmid-15271979\|pmid-16164976\|pmid-10233940	Based on extensive mutational analysis, we demonstrate for the first time that the local structure of acceptor RNA at potential nucleation sites, rather than overall thermodynamic stability, is a crucial determinant for NC chaperone activity during the minus-strand transfer step of reverse transcription.	[ "28" ]	305	1,589	0	false	Based on extensive mutational analysis, we demonstrate for the first time that the local structure of acceptor RNA at potential nucleation sites, rather than overall thermodynamic stability, is a crucial determinant for NC chaperone activity during the minus-strand transfer step of reverse transcription.	[]	Based on extensive mutational analysis, we demonstrate for the first time that the local structure of acceptor RNA at potential nucleation sites, rather than overall thermodynamic stability, is a crucial determinant for NC chaperone activity during the minus-strand transfer step of reverse transcription.	true	true	true	true	true	276
6	INTRODUCTION	1	75	[ "B75" ]	17,553,835	pmid-16394022\|pmid-10982342\|pmid-11932404	We also show that in our reconstituted system, NC-mediated annealing is more efficient than strand transfer (i.e.	[ "75" ]	113	1,590	0	false	We also show that in our reconstituted system, NC-mediated annealing is more efficient than strand transfer (i.e.	[]	We also show that in our reconstituted system, NC-mediated annealing is more efficient than strand transfer (i.e.	true	true	true	true	true	277
6	INTRODUCTION	1	75	[ "B75" ]	17,553,835	pmid-16394022\|pmid-10982342\|pmid-11932404	annealing plus reverse transcriptase (RT)-catalyzed elongation of minus-strand DNA).	[ "75" ]	84	1,591	0	false	annealing plus reverse transcriptase (RT)-catalyzed elongation of minus-strand DNA).	[]	annealing plus reverse transcriptase (RT)-catalyzed elongation of minus-strand DNA).	false	true	true	true	false	277
6	INTRODUCTION	1	75	[ "B75" ]	17,553,835	pmid-16394022\|pmid-10982342\|pmid-11932404	Since RT activity (but not annealing) requires Mg2+ (75), it seemed likely that the lower values for strand transfer might be due to the presence of a high concentration of Mg2+ in strand transfer reactions.	[ "75" ]	207	1,592	1	false	Since RT activity (but not annealing) requires Mg2+, it seemed likely that the lower values for strand transfer might be due to the presence of a high concentration of Mg2+ in strand transfer reactions.	[ "75" ]	Since RT activity (but not annealing) requires Mg2+, it seemed likely that the lower values for strand transfer might be due to the presence of a high concentration of Mg2+ in strand transfer reactions.	true	true	true	true	true	277
6	INTRODUCTION	1	75	[ "B75" ]	17,553,835	pmid-16394022\|pmid-10982342\|pmid-11932404	In fact, experiments presented below strongly suggest that Mg2+ competes with NC for binding to the negatively charged phosphodiester backbone in (−) SSDNA and acceptor RNA.	[ "75" ]	173	1,593	0	false	In fact, experiments presented below strongly suggest that Mg2+ competes with NC for binding to the negatively charged phosphodiester backbone in (−) SSDNA and acceptor RNA.	[]	In fact, experiments presented below strongly suggest that Mg2+ competes with NC for binding to the negatively charged phosphodiester backbone in (−) SSDNA and acceptor RNA.	true	true	true	true	true	277
6	INTRODUCTION	1	75	[ "B75" ]	17,553,835	pmid-16394022\|pmid-10982342\|pmid-11932404	Finally, we present data indicating that for our system, destabilization of a secondary structure formed by the 5′ TAR RNA sequence and to a lesser extent, loop–loop interactions between TAR RNA and TAR DNA contribute to efficient minus-strand transfer.	[ "75" ]	253	1,594	0	false	Finally, we present data indicating that for our system, destabilization of a secondary structure formed by the 5′ TAR RNA sequence and to a lesser extent, loop–loop interactions between TAR RNA and TAR DNA contribute to efficient minus-strand transfer.	[]	Finally, we present data indicating that for our system, destabilization of a secondary structure formed by the 5′ TAR RNA sequence and to a lesser extent, loop–loop interactions between TAR RNA and TAR DNA contribute to efficient minus-strand transfer.	true	true	true	true	true	277
0	DISCUSSION	1	28	[ "B28", "B28" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	The goal of the present study was to provide new insights into the mechanism of HIV-1 NC nucleic acid chaperone activity in the minus-strand transfer step of reverse transcription.	[ "28", "28" ]	180	1,595	0	false	The goal of the present study was to provide new insights into the mechanism of HIV-1 NC nucleic acid chaperone activity in the minus-strand transfer step of reverse transcription.	[]	The goal of the present study was to provide new insights into the mechanism of HIV-1 NC nucleic acid chaperone activity in the minus-strand transfer step of reverse transcription.	true	true	true	true	true	278
0	DISCUSSION	1	28	[ "B28", "B28" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	Our approach was to use a reconstituted system with model substrates described in an earlier report (28), since their structures are not overly complex and are therefore especially suitable for mutagenic analysis (Figure 2).	[ "28", "28" ]	224	1,596	1	false	Our approach was to use a reconstituted system with model substrates described in an earlier report, since their structures are not overly complex and are therefore especially suitable for mutagenic analysis (Figure 2).	[ "28" ]	Our approach was to use a reconstituted system with model substrates described in an earlier report, since their structures are not overly complex and are therefore especially suitable for mutagenic analysis.	true	true	true	true	true	278
0	DISCUSSION	1	28	[ "B28", "B28" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	We initially focused on the question of whether efficient strand transfer is determined by the overall thermodynamic stability and structure of acceptor RNA or more directly, by local structure at the nucleation site.	[ "28", "28" ]	217	1,597	0	false	We initially focused on the question of whether efficient strand transfer is determined by the overall thermodynamic stability and structure of acceptor RNA or more directly, by local structure at the nucleation site.	[]	We initially focused on the question of whether efficient strand transfer is determined by the overall thermodynamic stability and structure of acceptor RNA or more directly, by local structure at the nucleation site.	true	true	true	true	true	278
0	DISCUSSION	1	28	[ "B28", "B28" ]	17,553,835	pmid-7500330\|pmid-9757830\|pmid-16164976\|pmid-16164976\|pmid-8443588\|pmid-9430589\|pmid-9499042\|pmid-9769215\|pmid-10606514\|pmid-10924101\|pmid-16434700\|pmid-8057466\|pmid-7545662\|pmid-16164976\|pmid-9057495\|pmid-9465785\|pmid-12954779\|pmid-15854648\|pmid-15854648\|pmid-10982342\|pmid-11344257\|pmid-11922672\|pmid-11932404\|pmid-12054820\|pmid-12084921\|pmid-12581633\|pmid-12684000\|pmid-15099739\|pmid-15454467\|pmid-15033363\|pmid-15271979\|pmid-16077025\|pmid-16997322\|pmid-17029416\|pmid-16962137\|pmid-15271979\|pmid-15271979	In assays with RNA 70 and RNA 50, we found that the higher strand transfer activity exhibited by RNA 70 is correlated with the local stem-loop structure at the 5′ end of the TAR sequence, which contains 11 bases complementary to an 11-nt single-stranded region in DNA 50 (Figure 2), and not with RNA 70's predicted overall thermodynamic stability, which is actually considerably higher than that of RNA 50 (Figure 2A) (28).	[ "28", "28" ]	423	1,598	1	false	In assays with RNA 70 and RNA 50, we found that the higher strand transfer activity exhibited by RNA 70 is correlated with the local stem-loop structure at the 5′ end of the TAR sequence, which contains 11 bases complementary to an 11-nt single-stranded region in DNA 50 (Figure 2), and not with RNA 70's predicted overall thermodynamic stability, which is actually considerably higher than that of RNA 50 (Figure 2A).	[ "28" ]	In assays with RNA 70 and RNA 50, we found that the higher strand transfer activity exhibited by RNA 70 is correlated with the local stem-loop structure at the 5′ end of the TAR sequence, which contains 11 bases complementary to an 11-nt single-stranded region in DNA 50, and not with RNA 70's predicted overall thermodynamic stability, which is actually considerably higher than that of RNA 50.	true	true	true	true	true	278
1	DISCUSSION	1	27	[ "B27", "B61", "B69", "B73" ]	17,553,835	pmid-9757830\|pmid-16164976\|pmid-12206453\|pmid-10924101\|pmid-9933645\|pmid-10233940\|pmid-11786014\|pmid-15327946\|pmid-16314282\|pmid-16164976\|NA\|pmid-15033363\|pmid-15542863\|pmid-15218022\|pmid-16291743	In further support of our ideas, the data clearly demonstrated that stabilizing mutations in the relevant local structure dramatically reduce the rate and extent of strand transfer and increase dependence on NC (Figures 3 and 4), whereas destabilizing mutations lead to a marked increase in strand transfer efficiency and loss of the NC requirement (Figure 3).	[ "27", "61", "69", "73" ]	360	1,599	0	false	In further support of our ideas, the data clearly demonstrated that stabilizing mutations in the relevant local structure dramatically reduce the rate and extent of strand transfer and increase dependence on NC (Figures 3 and 4), whereas destabilizing mutations lead to a marked increase in strand transfer efficiency and loss of the NC requirement (Figure 3).	[]	In further support of our ideas, the data clearly demonstrated that stabilizing mutations in the relevant local structure dramatically reduce the rate and extent of strand transfer and increase dependence on NC (Figures 3 and 4), whereas destabilizing mutations lead to a marked increase in strand transfer efficiency and loss of the NC requirement (Figure 3).	true	true	true	true	true	279

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