Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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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
These results indicate that local structure at the nucleation site is a critical determinant for NC chaperone activity in minus-strand transfer.
[ "27", "61", "69", "73" ]
144
1,600
0
false
These results indicate that local structure at the nucleation site is a critical determinant for NC chaperone activity in minus-strand transfer.
[]
These results indicate that local structure at the nucleation site is a critical determinant for NC chaperone activity in minus-strand transfer.
true
true
true
true
true
279
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
This conclusion is consistent with other studies demonstrating the importance of local structure in NC-promoted annealing of to the primer-binding site in an HIV-1 RNA transcript (27), RT-catalyzed extension reactions with TAR RNA mutants (61), and HIV-1 recombination in vivo (69,73).
[ "27", "61", "69", "73" ]
286
1,601
1
false
This conclusion is consistent with other studies demonstrating the importance of local structure in NC-promoted annealing of to the primer-binding site in an HIV-1 RNA transcript, RT-catalyzed extension reactions with TAR RNA mutants, and HIV-1 recombination in vivo.
[ "27", "61", "69,73" ]
This conclusion is consistent with other studies demonstrating the importance of local structure in NC-promoted annealing of to the primer-binding site in an HIV-1 RNA transcript, RT-catalyzed extension reactions with TAR RNA mutants, and HIV-1 recombination in vivo.
true
true
true
true
true
279
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
Taken together with our findings, it would seem that the mechanism we have identified using a reconstituted system may also be relevant to the reverse transcription pathway utilized during the course of HIV-1 replication in infected cells.
[ "27", "61", "69", "73" ]
239
1,602
0
false
Taken together with our findings, it would seem that the mechanism we have identified using a reconstituted system may also be relevant to the reverse transcription pathway utilized during the course of HIV-1 replication in infected cells.
[]
Taken together with our findings, it would seem that the mechanism we have identified using a reconstituted system may also be relevant to the reverse transcription pathway utilized during the course of HIV-1 replication in infected cells.
true
true
true
true
true
279
2
DISCUSSION
1
56
[ "B56", "B57", "B48", "B32", "B58", "B59" ]
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
We considered the possibility that formation of a kissing loop between the complementary TAR RNA and TAR DNA apical loops might also contribute to efficient annealing and strand transfer in our system.
[ "56", "57", "48", "32", "58", "59" ]
201
1,603
0
false
We considered the possibility that formation of a kissing loop between the complementary TAR RNA and TAR DNA apical loops might also contribute to efficient annealing and strand transfer in our system.
[]
We considered the possibility that formation of a kissing loop between the complementary TAR RNA and TAR DNA apical loops might also contribute to efficient annealing and strand transfer in our system.
true
true
true
true
true
280
2
DISCUSSION
1
56
[ "B56", "B57", "B48", "B32", "B58", "B59" ]
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
Previous efforts to address this question in other TAR-based systems led to diverse results.
[ "56", "57", "48", "32", "58", "59" ]
92
1,604
0
false
Previous efforts to address this question in other TAR-based systems led to diverse results.
[]
Previous efforts to address this question in other TAR-based systems led to diverse results.
true
true
true
true
true
280
2
DISCUSSION
1
56
[ "B56", "B57", "B48", "B32", "B58", "B59" ]
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
In two studies, mutational analysis showed that nucleation via loop–loop interactions facilitates efficient NC chaperone activity in minus-strand transfer (56) and annealing (57), whereas in other work, destabilization of the central double-stranded segment of the TAR stems was reported to be the major pathway for annealing, with only a minor role for a kissing-loop complex (48).
[ "56", "57", "48", "32", "58", "59" ]
382
1,605
1
false
In two studies, mutational analysis showed that nucleation via loop–loop interactions facilitates efficient NC chaperone activity in minus-strand transfer and annealing, whereas in other work, destabilization of the central double-stranded segment of the TAR stems was reported to be the major pathway for annealing, with only a minor role for a kissing-loop complex.
[ "56", "57", "48" ]
In two studies, mutational analysis showed that nucleation via loop–loop interactions facilitates efficient NC chaperone activity in minus-strand transfer and annealing, whereas in other work, destabilization of the central double-stranded segment of the TAR stems was reported to be the major pathway for annealing, with only a minor role for a kissing-loop complex.
true
true
true
true
true
280
2
DISCUSSION
1
59
[ "B56", "B57", "B48", "B32", "B58", "B59" ]
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
Evidence has also been presented suggesting that multiple pathways may be involved in NC-dependent nucleation of annealing (32,58), although more recent studies with NC and full-length TAR favor a zipper mechanism involving the lower stems and bulges (59) (Vo,M.-N., Rouzina,I.
[ "56", "57", "48", "32", "58", "59" ]
277
1,606
1
false
Evidence has also been presented suggesting that multiple pathways may be involved in NC-dependent nucleation of annealing, although more recent studies with NC and full-length TAR favor a zipper mechanism involving the lower stems and bulges (Vo,M.-N., Rouzina,I.
[ "32,58", "59" ]
Evidence has also been presented suggesting that multiple pathways may be involved in NC-dependent nucleation of annealing, although more recent studies with NC and full-length TAR favor a zipper mechanism involving the lower stems and bulges (Vo,M.-N., Rouzina,I.
true
true
true
true
true
280
2
DISCUSSION
1
56
[ "B56", "B57", "B48", "B32", "B58", "B59" ]
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
and Musier-Forsyth,K., in preparation.)
[ "56", "57", "48", "32", "58", "59" ]
39
1,607
0
false
and Musier-Forsyth,K., in preparation.)
[]
and Musier-Forsyth,K., in preparation.)
false
true
false
true
false
280
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
Here we report that the major effect of mutating two of the three contiguous G residues (G53,G54) in the RNA 70 apical loop to A (Figure 2A) is an almost 3-fold reduction in the extent of strand transfer (Figures 4A and 5A).
[ "56", "80", "81" ]
224
1,608
0
false
Here we report that the major effect of mutating two of the three contiguous G residues (G53,G54) in the RNA 70 apical loop to A (Figure 2A) is an almost 3-fold reduction in the extent of strand transfer (Figures 4A and 5A).
[]
Here we report that the major effect of mutating two of the three contiguous G residues in the RNA 70 apical loop to A (Figure 2A) is an almost 3-fold reduction in the extent of strand transfer.
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
This is presumably due to the two mismatches that are created by the mutation, which results in a less stable product.
[ "56", "80", "81" ]
118
1,609
0
false
This is presumably due to the two mismatches that are created by the mutation, which results in a less stable product.
[]
This is presumably due to the two mismatches that are created by the mutation, which results in a less stable product.
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
A substantial effect was also observed when all three Gs were changed to A (56).
[ "56", "80", "81" ]
80
1,610
1
false
A substantial effect was also observed when all three Gs were changed to A.
[ "56" ]
A substantial effect was also observed when all three Gs were changed to A.
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
Like WT RNA 70, the activity of our loop mutant is independent of NC (Figure 5A), in all likelihood because the RNA fold is unchanged by the mutation (data not shown).
[ "56", "80", "81" ]
167
1,611
0
false
Like WT RNA 70, the activity of our loop mutant is independent of NC (Figure 5A), in all likelihood because the RNA fold is unchanged by the mutation (data not shown).
[]
Like WT RNA 70, the activity of our loop mutant is independent of NC, in all likelihood because the RNA fold is unchanged by the mutation (data not shown).
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
Making the compensatory changes in DNA 50 yields only a small improvement in the extent of strand transfer, so that the overall efficiency remains lower than that achieved with the WT substrates (Figure 5A and B).
[ "56", "80", "81" ]
213
1,612
0
false
Making the compensatory changes in DNA 50 yields only a small improvement in the extent of strand transfer, so that the overall efficiency remains lower than that achieved with the WT substrates (Figure 5A and B).
[]
Making the compensatory changes in DNA 50 yields only a small improvement in the extent of strand transfer, so that the overall efficiency remains lower than that achieved with the WT substrates.
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
This finding implies that the loop–loop interaction must involve more than one G-C bp, since substitution of two A-T bp is not sufficient for optimal activity.
[ "56", "80", "81" ]
159
1,613
0
false
This finding implies that the loop–loop interaction must involve more than one G-C bp, since substitution of two A-T bp is not sufficient for optimal activity.
[]
This finding implies that the loop–loop interaction must involve more than one G-C bp, since substitution of two A-T bp is not sufficient for optimal activity.
true
true
true
true
true
281
3
DISCUSSION
1
56
[ "B56", "B80", "B81" ]
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
Conservation of Gs in the apical loop of TAR RNA may be related to NC's preference for binding to unpaired Gs (3 and references therein) and to the unusual stability of a kissing complex, even with only two G-C bp (80,81).
[ "56", "80", "81" ]
222
1,614
0
false
Conservation of Gs in the apical loop of TAR RNA may be related to NC's preference for binding to unpaired Gs (3 and references therein) and to the unusual stability of a kissing complex, even with only two G-C bp.
[ "80,81" ]
Conservation of Gs in the apical loop of TAR RNA may be related to NC's preference for binding to unpaired Gs (3 and references therein) and to the unusual stability of a kissing complex, even with only two G-C bp.
true
true
true
true
true
281
4
DISCUSSION
0
null
null
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
It is of interest that mutations in the RNA 70 local structure at the 5′ end of TAR and in the apical loops both affect the extent of strand transfer (Figures 4 and 5).
null
168
1,615
0
false
null
null
It is of interest that mutations in the RNA 70 local structure at the 5′ end of TAR and in the apical loops both affect the extent of strand transfer (Figures 4 and 5).
true
true
true
true
true
282
4
DISCUSSION
0
null
null
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
However, ‘only’ stabilizing mutations in the RNA 70 5′ stem loop have striking effects on ‘both’ the rate and extent of strand transfer and are NC dependent (Table 2A).
null
168
1,616
0
false
null
null
However, ‘only’ stabilizing mutations in the RNA 70 5′ stem loop have striking effects on ‘both’ the rate and extent of strand transfer and are NC dependent (Table 2A).
true
true
true
true
true
282
4
DISCUSSION
0
null
null
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
Thus, it appears that destabilization of the RNA 70 5′ local structure is likely to be the dominant nucleation pathway for minus-strand transfer in the RNA 70 system.
null
166
1,617
0
false
null
null
Thus, it appears that destabilization of the RNA 70 5′ local structure is likely to be the dominant nucleation pathway for minus-strand transfer in the RNA 70 system.
true
true
true
true
true
282
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
Another issue that we address concerns a comparison between annealing and strand transfer activities in the presence or absence of NC.
[ "3", "35" ]
134
1,618
0
false
Another issue that we address concerns a comparison between annealing and strand transfer activities in the presence or absence of NC.
[]
Another issue that we address concerns a comparison between annealing and strand transfer activities in the presence or absence of NC.
true
true
true
true
true
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
The RNA 70 acceptors that we tested fall into two groups, i.e.
[ "3", "35" ]
62
1,619
0
false
The RNA 70 acceptors that we tested fall into two groups, i.e.
[]
The RNA 70 acceptors that we tested fall into two groups, i.e.
true
true
true
true
true
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
having activity that is either independent (group 1) or dependent (group 2) on NC.
[ "3", "35" ]
82
1,620
0
false
having activity that is either independent (group 1) or dependent (group 2) on NC.
[]
having activity that is either independent (group 1) or dependent (group 2) on NC.
false
true
true
true
false
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
With the RNAs in the first group (WT RNA 70 and the RNA 70 loop mutant), strand transfer is unaffected by addition of NC (Figures 4A and 5A), although NC slightly stimulates the extent of annealing (Figure 6A and B).
[ "3", "35" ]
216
1,621
0
false
With the RNAs in the first group (WT RNA 70 and the RNA 70 loop mutant), strand transfer is unaffected by addition of NC (Figures 4A and 5A), although NC slightly stimulates the extent of annealing (Figure 6A and B).
[]
With the RNAs in the first group (WT RNA 70 and the RNA 70 loop mutant), strand transfer is unaffected by addition of NC (Figures 4A and 5A), although NC slightly stimulates the extent of annealing (Figure 6A and B).
true
true
true
true
true
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
The lower minus NC values for annealing compared with the corresponding values for strand transfer might reflect the fact that during strand transfer, RT-catalyzed elongation of the annealed DNA drives the equilibrium towards formation of a more thermodynamically stable product with a greater number of base pairs than the number contained in the RNA–DNA hybrid.
[ "3", "35" ]
363
1,622
0
false
The lower minus NC values for annealing compared with the corresponding values for strand transfer might reflect the fact that during strand transfer, RT-catalyzed elongation of the annealed DNA drives the equilibrium towards formation of a more thermodynamically stable product with a greater number of base pairs than the number contained in the RNA–DNA hybrid.
[]
The lower minus NC values for annealing compared with the corresponding values for strand transfer might reflect the fact that during strand transfer, RT-catalyzed elongation of the annealed DNA drives the equilibrium towards formation of a more thermodynamically stable product with a greater number of base pairs than the number contained in the RNA–DNA hybrid.
true
true
true
true
true
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
When NC is present, the rate of annealing is increased (Table 2B, lines 1 and 4) so that even in the absence of RT, the end point values for annealing and strand transfer are in close agreement.
[ "3", "35" ]
194
1,623
0
false
When NC is present, the rate of annealing is increased (Table 2B, lines 1 and 4) so that even in the absence of RT, the end point values for annealing and strand transfer are in close agreement.
[]
When NC is present, the rate of annealing is increased (Table 2B, lines 1 and 4) so that even in the absence of RT, the end point values for annealing and strand transfer are in close agreement.
true
true
true
true
true
283
5
DISCUSSION
1
3
[ "B3", "B35" ]
17,553,835
pmid-15271979|pmid-16164976|pmid-10233940
The RT effect observed here is reminiscent of a somewhat similar scenario that occurs during plus-strand transfer (3): annealing of the complementary primer-binding site sequences in (+) SSDNA and minus-strand acceptor DNA is ultimately favored over hybrid formation between the 3′ terminus of tRNA3Lys and (+) SSDNA, since RT extends each strand of the DNA duplex to yield the more stable double-stranded DNA transfer product (35).
[ "3", "35" ]
432
1,624
1
false
The RT effect observed here is reminiscent of a somewhat similar scenario that occurs during plus-strand transfer : annealing of the complementary primer-binding site sequences in (+) SSDNA and minus-strand acceptor DNA is ultimately favored over hybrid formation between the 3′ terminus of tRNA3Lys and (+) SSDNA, since RT extends each strand of the DNA duplex to yield the more stable double-stranded DNA transfer product.
[ "3", "35" ]
The RT effect observed here is reminiscent of a somewhat similar scenario that occurs during plus-strand transfer : annealing of the complementary primer-binding site sequences in (+) SSDNA and minus-strand acceptor DNA is ultimately favored over hybrid formation between the 3′ terminus of tRNA3Lys and (+) SSDNA, since RT extends each strand of the DNA duplex to yield the more stable double-stranded DNA transfer product.
true
true
true
true
true
283
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
RNA 70 acceptors with stabilizing changes in the 5′ local stem-loop structure, e.g.
[ "17", "20" ]
83
1,625
0
false
RNA 70 acceptors with stabilizing changes in the 5′ local stem-loop structure, e.g.
[]
RNA 70 acceptors with stabilizing changes in the 5′ local stem-loop structure, e.g.
true
true
true
true
true
284
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
RNA 70U28C and RNA 70U28,30C (group 2), show a clear dependence on NC for efficient annealing and strand transfer (Figures 4 and 6) and a striking reduction in the rates of these reactions relative to the rates for WT RNA 70 (Table 2).
[ "17", "20" ]
235
1,626
0
false
RNA 70U28C and RNA 70U28,30C (group 2), show a clear dependence on NC for efficient annealing and strand transfer (Figures 4 and 6) and a striking reduction in the rates of these reactions relative to the rates for WT RNA 70 (Table 2).
[]
RNA 70U28C and RNA 70U28,30C (group 2), show a clear dependence on NC for efficient annealing and strand transfer (Figures 4 and 6) and a striking reduction in the rates of these reactions relative to the rates for WT RNA 70 (Table 2).
true
true
true
true
true
284
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
In the absence of NC, the annealing and strand transfer activities of both the single and double mutants are quite low.
[ "17", "20" ]
119
1,627
0
false
In the absence of NC, the annealing and strand transfer activities of both the single and double mutants are quite low.
[]
In the absence of NC, the annealing and strand transfer activities of both the single and double mutants are quite low.
true
true
true
true
true
284
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
However, in reactions with NC, the annealing activities of both mutants are greatly increased and reach a value of almost 60% at the highest NC concentration (Figure 6C and D), whereas the comparable values for strand transfer are significantly lower (Figure 4B and D).
[ "17", "20" ]
269
1,628
0
false
However, in reactions with NC, the annealing activities of both mutants are greatly increased and reach a value of almost 60% at the highest NC concentration (Figure 6C and D), whereas the comparable values for strand transfer are significantly lower (Figure 4B and D).
[]
However, in reactions with NC, the annealing activities of both mutants are greatly increased and reach a value of almost 60% at the highest NC concentration (Figure 6C and D), whereas the comparable values for strand transfer are significantly lower (Figure 4B and D).
true
true
true
true
true
284
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
These results indicate that optimal experimental conditions for annealing and strand transfer may differ when activity is dependent on NC's chaperone function.
[ "17", "20" ]
159
1,629
0
false
These results indicate that optimal experimental conditions for annealing and strand transfer may differ when activity is dependent on NC's chaperone function.
[]
These results indicate that optimal experimental conditions for annealing and strand transfer may differ when activity is dependent on NC's chaperone function.
true
true
true
true
true
284
6
DISCUSSION
1
17
[ "B17", "B20" ]
17,553,835
pmid-16394022|pmid-10982342|pmid-11932404
We have reported similar findings in studies with NC mutants having changes in the CCHC motif (17,20).
[ "17", "20" ]
102
1,630
0
false
We have reported similar findings in studies with NC mutants having changes in the CCHC motif.
[ "17,20" ]
We have reported similar findings in studies with NC mutants having changes in the CCHC motif.
true
true
true
true
true
284
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
To investigate this discrepancy between the efficiency of annealing and strand transfer with structured RNA acceptors, we tested annealing under strand transfer conditions.
[ "32" ]
172
1,631
0
false
To investigate this discrepancy between the efficiency of annealing and strand transfer with structured RNA acceptors, we tested annealing under strand transfer conditions.
[]
To investigate this discrepancy between the efficiency of annealing and strand transfer with structured RNA acceptors, we tested annealing under strand transfer conditions.
true
true
true
true
true
285
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
We found that of the components present specifically in strand transfer reactions, it is only Mg2+ that inhibits NC chaperone activity during annealing and in a dose-dependent manner (Figure 7C).
[ "32" ]
195
1,632
0
false
We found that of the components present specifically in strand transfer reactions, it is only Mg2+ that inhibits NC chaperone activity during annealing and in a dose-dependent manner (Figure 7C).
[]
We found that of the components present specifically in strand transfer reactions, it is only Mg2+ that inhibits NC chaperone activity during annealing and in a dose-dependent manner (Figure 7C).
true
true
true
true
true
285
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
This would explain why a potential stabilizing effect of Mg2+ on the nucleic acid substrates does not lead to greater stimulation of strand transfer by NC, as might be expected.
[ "32" ]
177
1,633
0
false
This would explain why a potential stabilizing effect of Mg2+ on the nucleic acid substrates does not lead to greater stimulation of strand transfer by NC, as might be expected.
[]
This would explain why a potential stabilizing effect of Mg2+ on the nucleic acid substrates does not lead to greater stimulation of strand transfer by NC, as might be expected.
true
true
true
true
true
285
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
In fact, since Mg2+ is present in vast excess over NC in our reactions, the data strongly suggest that Mg2+ successfully competes with NC for non-specific binding to the phosphodiester backbone of the nucleic acid substrates and partially displaces NC.
[ "32" ]
252
1,634
0
false
In fact, since Mg2+ is present in vast excess over NC in our reactions, the data strongly suggest that Mg2+ successfully competes with NC for non-specific binding to the phosphodiester backbone of the nucleic acid substrates and partially displaces NC.
[]
In fact, since Mg2+ is present in vast excess over NC in our reactions, the data strongly suggest that Mg2+ successfully competes with NC for non-specific binding to the phosphodiester backbone of the nucleic acid substrates and partially displaces NC.
true
true
true
true
true
285
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
Not surprisingly, since Mg2+ does not have nucleic acid chaperone activity, we observe that formation of the annealed RNA–DNA hybrid becomes very inefficient in the presence of high Mg2+ concentrations.
[ "32" ]
202
1,635
0
false
Not surprisingly, since Mg2+ does not have nucleic acid chaperone activity, we observe that formation of the annealed RNA–DNA hybrid becomes very inefficient in the presence of high Mg2+ concentrations.
[]
Not surprisingly, since Mg2+ does not have nucleic acid chaperone activity, we observe that formation of the annealed RNA–DNA hybrid becomes very inefficient in the presence of high Mg2+ concentrations.
true
true
true
true
true
285
7
DISCUSSION
1
32
[ "B32" ]
17,553,835
pmid-16962137
This conclusion is consistent with a similar observation made by Musier-Forsyth and colleagues (32) (Vo,M.-N., Rouzina, I. and Musier-Forsyth,K., in preparation).
[ "32" ]
162
1,636
1
false
This conclusion is consistent with a similar observation made by Musier-Forsyth and colleagues (Vo,M.-N., Rouzina, I. and Musier-Forsyth,K., in preparation).
[ "32" ]
This conclusion is consistent with a similar observation made by Musier-Forsyth and colleagues (Vo,M.-N., Rouzina, I. and Musier-Forsyth,K., in preparation).
true
true
true
true
true
285
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
The Mg2+ concentration in virions and in infected cells is not known.
[ "10", "13", "14", "82" ]
69
1,637
0
false
The Mg2+ concentration in virions and in infected cells is not known.
[]
The Mg2+ concentration in virions and in infected cells is not known.
true
true
true
true
true
286
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
However, in some instances the concentration in uninfected cells has been reported to be much lower (∼0.2–0.25 mM) than the amounts typically used in reverse transcription reactions in vitro (6–8 mM) (75 and references therein).
[ "10", "13", "14", "82" ]
228
1,638
0
false
However, in some instances the concentration in uninfected cells has been reported to be much lower (∼0.2–0.25 mM) than the amounts typically used in reverse transcription reactions in vitro (6–8 mM) (75 and references therein).
[]
However, in some instances the concentration in uninfected cells has been reported to be much lower than the amounts typically used in reverse transcription reactions in vitro (6–8 mM) (75 and references therein).
true
true
true
true
true
286
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
If the intracellular Mg2+ concentration in infected cells is also low, it would suggest that RT-catalyzed extension can proceed at a lower Mg2+ concentration in vivo than in vitro and that, under such conditions, Mg2+ should not interfere with the efficiency of NC-dependent annealing during HIV-1 infection.
[ "10", "13", "14", "82" ]
308
1,639
0
false
If the intracellular Mg2+ concentration in infected cells is also low, it would suggest that RT-catalyzed extension can proceed at a lower Mg2+ concentration in vivo than in vitro and that, under such conditions, Mg2+ should not interfere with the efficiency of NC-dependent annealing during HIV-1 infection.
[]
If the intracellular Mg2+ concentration in infected cells is also low, it would suggest that RT-catalyzed extension can proceed at a lower Mg2+ concentration in vivo than in vitro and that, under such conditions, Mg2+ should not interfere with the efficiency of NC-dependent annealing during HIV-1 infection.
true
true
true
true
true
286
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
Interestingly, in reactions containing 0.25 mM Mg2+ and NC, we find only an ∼8% reduction in annealing (Figure 7C).
[ "10", "13", "14", "82" ]
115
1,640
0
false
Interestingly, in reactions containing 0.25 mM Mg2+ and NC, we find only an ∼8% reduction in annealing (Figure 7C).
[]
Interestingly, in reactions containing 0.25 mM Mg2+ and NC, we find only an ∼8% reduction in annealing (Figure 7C).
true
true
true
true
true
286
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
In reactions with WT RNA 70 and the loop mutant, which have a fairly minor requirement for NC, annealing is stimulated by Mg2+ to a small, but constant extent, over a wide range of Mg2+ concentrations (Figure 7A and B).
[ "10", "13", "14", "82" ]
219
1,641
0
false
In reactions with WT RNA 70 and the loop mutant, which have a fairly minor requirement for NC, annealing is stimulated by Mg2+ to a small, but constant extent, over a wide range of Mg2+ concentrations (Figure 7A and B).
[]
In reactions with WT RNA 70 and the loop mutant, which have a fairly minor requirement for NC, annealing is stimulated by Mg2+ to a small, but constant extent, over a wide range of Mg2+ concentrations (Figure 7A and B).
true
true
true
true
true
286
8
DISCUSSION
1
10
[ "B10", "B13", "B14", "B82" ]
17,553,835
pmid-16434700|pmid-9057495|pmid-9465785|pmid-8443601
In this case, when the ionic strength is increased, the increase in positive charge leads to greater attraction between the nucleic acid strands and results in more efficient annealing, in accord with studies on the aggregation properties of NC (10,13,14,82).
[ "10", "13", "14", "82" ]
259
1,642
0
false
In this case, when the ionic strength is increased, the increase in positive charge leads to greater attraction between the nucleic acid strands and results in more efficient annealing, in accord with studies on the aggregation properties of NC.
[ "10,13,14,82" ]
In this case, when the ionic strength is increased, the increase in positive charge leads to greater attraction between the nucleic acid strands and results in more efficient annealing, in accord with studies on the aggregation properties of NC.
true
true
true
true
true
286
9
DISCUSSION
0
null
null
17,553,835
null
In conclusion, we have demonstrated that the local structure in acceptor RNA at the nucleation site is a critical determinant for nucleation of annealing that occurs during HIV-1 minus-strand transfer.
null
201
1,643
0
false
null
null
In conclusion, we have demonstrated that the local structure in acceptor RNA at the nucleation site is a critical determinant for nucleation of annealing that occurs during HIV-1 minus-strand transfer.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
Moreover, destabilization of a short secondary structure at the 5′ end of the TAR sequence in RNA 70 appears to be the dominant nucleation pathway.
null
147
1,644
0
false
null
null
Moreover, destabilization of a short secondary structure at the 5′ end of the TAR sequence in RNA 70 appears to be the dominant nucleation pathway.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
Our data also point to different consequences for annealing versus strand transfer when in vitro reactions are strongly or weakly dependent on NC.
null
146
1,645
0
false
null
null
Our data also point to different consequences for annealing versus strand transfer when in vitro reactions are strongly or weakly dependent on NC.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
Where NC has little or no effect, annealing and strand transfer occur with similar efficiencies.
null
96
1,646
0
false
null
null
Where NC has little or no effect, annealing and strand transfer occur with similar efficiencies.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
However, when NC-catalyzed destabilization of acceptor structure is required, annealing appears to be more efficient than strand transfer.
null
138
1,647
0
false
null
null
However, when NC-catalyzed destabilization of acceptor structure is required, annealing appears to be more efficient than strand transfer.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
We attribute this result to the presence of a high Mg2+ concentration in reconstituted strand transfer reactions, which leads to a competition between Mg2+ and NC for binding to the negatively charged phosphate groups in the nucleic acid strands.
null
246
1,648
0
false
null
null
We attribute this result to the presence of a high Mg2+ concentration in reconstituted strand transfer reactions, which leads to a competition between Mg2+ and NC for binding to the negatively charged phosphate groups in the nucleic acid strands.
true
true
true
true
true
287
9
DISCUSSION
0
null
null
17,553,835
null
Taken together, these findings contribute significantly to a greater understanding of the mechanism of NC nucleic acid chaperone activity during minus-strand transfer.
null
167
1,649
0
false
null
null
Taken together, these findings contribute significantly to a greater understanding of the mechanism of NC nucleic acid chaperone activity during minus-strand transfer.
true
true
true
true
true
287
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b7", "b5", "b8", "b9" ]
17,041,234
pmid-2574119|pmid-6146362|pmid-8863825|pmid-12904281|pmid-8657572|pmid-10869552|pmid-9737971
The transmembrane P-glycoprotein (P-gp), encoded by the MDR1 gene, acts as an energy-dependent drug-efflux pump and is involved in cellular drug excretion (1).
[ "1", "2", "3", "7", "5", "8", "9" ]
159
1,650
1
false
The transmembrane P-glycoprotein (P-gp), encoded by the MDR1 gene, acts as an energy-dependent drug-efflux pump and is involved in cellular drug excretion.
[ "1" ]
The transmembrane P-glycoprotein (P-gp), encoded by the MDR1 gene, acts as an energy-dependent drug-efflux pump and is involved in cellular drug excretion.
true
true
true
true
true
288
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b7", "b5", "b8", "b9" ]
17,041,234
pmid-2574119|pmid-6146362|pmid-8863825|pmid-12904281|pmid-8657572|pmid-10869552|pmid-9737971
The over-expression of P-gp is directly linked to multidrug resistance (2), a major problem in cancer therapeutics.
[ "1", "2", "3", "7", "5", "8", "9" ]
115
1,651
1
false
The over-expression of P-gp is directly linked to multidrug resistance, a major problem in cancer therapeutics.
[ "2" ]
The over-expression of P-gp is directly linked to multidrug resistance, a major problem in cancer therapeutics.
true
true
true
true
true
288
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b7", "b5", "b8", "b9" ]
17,041,234
pmid-2574119|pmid-6146362|pmid-8863825|pmid-12904281|pmid-8657572|pmid-10869552|pmid-9737971
Antisense oligonucleotides directed against the PGY1/MDR1 human mRNA inhibit the expression of P-gp (3–7).
[ "1", "2", "3", "7", "5", "8", "9" ]
106
1,652
0
false
Antisense oligonucleotides directed against the PGY1/MDR1 human mRNA inhibit the expression of P-gp.
[ "3–7" ]
Antisense oligonucleotides directed against the PGY1/MDR1 human mRNA inhibit the expression of P-gp.
true
true
true
true
true
288
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b7", "b5", "b8", "b9" ]
17,041,234
pmid-2574119|pmid-6146362|pmid-8863825|pmid-12904281|pmid-8657572|pmid-10869552|pmid-9737971
The most efficient antisense oligomers are all complementary to GGGAUG RNA sequences containing the AUG initiation site and belonging to a hairpin hexaloop (5–8).
[ "1", "2", "3", "7", "5", "8", "9" ]
162
1,653
0
false
The most efficient antisense oligomers are all complementary to GGGAUG RNA sequences containing the AUG initiation site and belonging to a hairpin hexaloop.
[ "5–8" ]
The most efficient antisense oligomers are all complementary to GGGAUG RNA sequences containing the AUG initiation site and belonging to a hairpin hexaloop.
true
true
true
true
true
288
0
INTRODUCTION
1
9
[ "b1", "b2", "b3", "b7", "b5", "b8", "b9" ]
17,041,234
pmid-2574119|pmid-6146362|pmid-8863825|pmid-12904281|pmid-8657572|pmid-10869552|pmid-9737971
The GGGA motif seems to be the preferential target for mRNA inhibition, as it is recognized by 48% of the most potent antisense oligonucleotides reported in the literature (9).
[ "1", "2", "3", "7", "5", "8", "9" ]
176
1,654
1
false
The GGGA motif seems to be the preferential target for mRNA inhibition, as it is recognized by 48% of the most potent antisense oligonucleotides reported in the literature.
[ "9" ]
The GGGA motif seems to be the preferential target for mRNA inhibition, as it is recognized by 48% of the most potent antisense oligonucleotides reported in the literature.
true
true
true
true
true
288
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
The main purpose of the present study is to determine the structure of the antisense target RNA hairpin in order to highlight the properties that allow efficient hybridization.
[ "10", "11", "12", "14", "15", "16" ]
176
1,655
0
false
The main purpose of the present study is to determine the structure of the antisense target RNA hairpin in order to highlight the properties that allow efficient hybridization.
[]
The main purpose of the present study is to determine the structure of the antisense target RNA hairpin in order to highlight the properties that allow efficient hybridization.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
Also, this hairpin presents some features that are of general interest from a purely structural point of view.
[ "10", "11", "12", "14", "15", "16" ]
110
1,656
0
false
Also, this hairpin presents some features that are of general interest from a purely structural point of view.
[]
Also, this hairpin presents some features that are of general interest from a purely structural point of view.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
The stem–loop of interest is constituted by a 6 bp stem comprising a G•U mismatch and the G-rich hexaloop 5′r(GGGAUG)3′.
[ "10", "11", "12", "14", "15", "16" ]
120
1,657
0
false
The stem–loop of interest is constituted by a 6 bp stem comprising a G•U mismatch and the G-rich hexaloop 5′r(GGGAUG)3′.
[]
The stem–loop of interest is constituted by a 6 bp stem comprising a G•U mismatch and the G-rich hexaloop 5′r(GGGAUG)3′.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
G•U pairs are highly conserved in functional RNA and have been shown to play essential roles in a wide range of processes (10).
[ "10", "11", "12", "14", "15", "16" ]
127
1,658
1
false
G•U pairs are highly conserved in functional RNA and have been shown to play essential roles in a wide range of processes.
[ "10" ]
G•U pairs are highly conserved in functional RNA and have been shown to play essential roles in a wide range of processes.
true
true
true
true
true
289
1
INTRODUCTION
1
11
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
The geometrical and conformational properties of G•U wobble pairs have been described (11), but essentially on the basis of crystal structures.
[ "10", "11", "12", "14", "15", "16" ]
143
1,659
1
false
The geometrical and conformational properties of G•U wobble pairs have been described, but essentially on the basis of crystal structures.
[ "11" ]
The geometrical and conformational properties of G•U wobble pairs have been described, but essentially on the basis of crystal structures.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
Three solution studies of a single G•U wobble pair embedded within RNA helices have given detailed structural information about this mismatch (12–14).
[ "10", "11", "12", "14", "15", "16" ]
150
1,660
0
false
Three solution studies of a single G•U wobble pair embedded within RNA helices have given detailed structural information about this mismatch.
[ "12–14" ]
Three solution studies of a single G•U wobble pair embedded within RNA helices have given detailed structural information about this mismatch.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
The complete structural investigation undertaken in the present study should help to evaluate the common characteristics of this type of mismatch.
[ "10", "11", "12", "14", "15", "16" ]
146
1,661
0
false
The complete structural investigation undertaken in the present study should help to evaluate the common characteristics of this type of mismatch.
[]
The complete structural investigation undertaken in the present study should help to evaluate the common characteristics of this type of mismatch.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
Concerning the loop region, in contrast to the well-studied purine-rich tetraloops, little is known about the solution properties of purine-rich hexaloops.
[ "10", "11", "12", "14", "15", "16" ]
155
1,662
0
false
Concerning the loop region, in contrast to the well-studied purine-rich tetraloops, little is known about the solution properties of purine-rich hexaloops.
[]
Concerning the loop region, in contrast to the well-studied purine-rich tetraloops, little is known about the solution properties of purine-rich hexaloops.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
Perusal of the recent website SCOR (), revealed that among the known hexaloop solution structures only two contain five purines, i.e.
[ "10", "11", "12", "14", "15", "16" ]
133
1,663
0
false
Perusal of the recent website SCOR (), revealed that among the known hexaloop solution structures only two contain five purines, i.e.
[]
Perusal of the recent website SCOR (), revealed that among the known hexaloop solution structures only two contain five purines, i.e.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
UGAAAG [1R2P; (15)] and GUAAAA [1BVJ; (16)].
[ "10", "11", "12", "14", "15", "16" ]
44
1,664
0
false
UGAAAG and GUAAAA.
[ "1R2P; (15)", "1BVJ; (16)" ]
UGAAAG and GUAAAA.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
These loops include A-rich parts on their 3′ sides and, therefore, we anticipated that their structures would differ strongly from the GGGAUG one in which a G-rich region is located at the 5′ side.
[ "10", "11", "12", "14", "15", "16" ]
197
1,665
0
false
These loops include A-rich parts on their 3′ sides and, therefore, we anticipated that their structures would differ strongly from the GGGAUG one in which a G-rich region is located at the 5′ side.
[]
These loops include A-rich parts on their 3′ sides and, therefore, we anticipated that their structures would differ strongly from the GGGAUG one in which a G-rich region is located at the 5′ side.
true
true
true
true
true
289
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b14", "b15", "b16" ]
17,041,234
pmid-11256617|pmid-10668794|pmid-1371071|pmid-9153306|pmid-14745440|pmid-9846871
Thus, determining the structure of GGGAUG loop should provide additional insight into the folds encountered in purine-rich loops.
[ "10", "11", "12", "14", "15", "16" ]
129
1,666
0
false
Thus, determining the structure of GGGAUG loop should provide additional insight into the folds encountered in purine-rich loops.
[]
Thus, determining the structure of GGGAUG loop should provide additional insight into the folds encountered in purine-rich loops.
true
true
true
true
true
289
2
INTRODUCTION
0
null
null
17,041,234
null
In the present work, study of the solution conformation of the GGGAUG loop closed by a stem containing a G•U pair was undertaken by NMR and molecular modeling.
null
159
1,667
0
false
null
null
In the present work, study of the solution conformation of the GGGAUG loop closed by a stem containing a G•U pair was undertaken by NMR and molecular modeling.
true
true
true
true
true
290
2
INTRODUCTION
0
null
null
17,041,234
null
Long trajectories of molecular dynamics in explicit solvent should further the investigation of the hairpin flexibility.
null
120
1,668
0
false
null
null
Long trajectories of molecular dynamics in explicit solvent should further the investigation of the hairpin flexibility.
true
true
true
true
true
290
2
INTRODUCTION
0
null
null
17,041,234
null
We find that the whole hairpin is highly ordered thanks to numerous standard and non-standard interactions in both the stem and the loop.
null
137
1,669
0
false
null
null
We find that the whole hairpin is highly ordered thanks to numerous standard and non-standard interactions in both the stem and the loop.
true
true
true
true
true
290
2
INTRODUCTION
0
null
null
17,041,234
null
Finally, the hexaloop adopts a new fold in which the GGGA intrinsic properties account for the hairpin ability to form duplex with oligonucleotides.
null
148
1,670
0
false
null
null
Finally, the hexaloop adopts a new fold in which the GGGA intrinsic properties account for the hairpin ability to form duplex with oligonucleotides.
true
true
true
true
true
290
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
Protein biosynthesis in plastids relies on prokaryotic-type 70S ribosomes.
[ "1", "3", "4", "5", "7" ]
74
1,671
0
false
Protein biosynthesis in plastids relies on prokaryotic-type 70S ribosomes.
[]
Protein biosynthesis in plastids relies on prokaryotic-type 70S ribosomes.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
The RNA components of these ribosomes are exclusively encoded by the plastid genome (plastome) whereas only part of the ribosomal proteins is encoded in the plastome.
[ "1", "3", "4", "5", "7" ]
166
1,672
0
false
The RNA components of these ribosomes are exclusively encoded by the plastid genome (plastome) whereas only part of the ribosomal proteins is encoded in the plastome.
[]
The RNA components of these ribosomes are exclusively encoded by the plastid genome (plastome) whereas only part of the ribosomal proteins is encoded in the plastome.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
The chloroplast genomes of higher plants harbor a conserved set of 21 ribosomal protein genes [reviewed e.g.
[ "1", "3", "4", "5", "7" ]
108
1,673
0
false
The chloroplast genomes of higher plants harbor a conserved set of 21 ribosomal protein genes [reviewed e.g.
[]
The chloroplast genomes of higher plants harbor a conserved set of 21 ribosomal protein genes [reviewed e.g.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
in (1–3)] which, with only few exceptions, are also found in the plastomes of all other plastid-containing taxa.
[ "1", "3", "4", "5", "7" ]
112
1,674
0
false
in ] which, with only few exceptions, are also found in the plastomes of all other plastid-containing taxa.
[ "1–3" ]
in ] which, with only few exceptions, are also found in the plastomes of all other plastid-containing taxa.
false
true
true
true
false
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
A notable exception is the gene for the ribosomal protein 18 of the 30S subunit of the plastid ribosome (S18) which was recently found to be absent from plastid genomes of several non-green unicellular organisms, including the colorless alga Euglena longa
[ "1", "3", "4", "5", "7" ]
255
1,675
0
false
A notable exception is the gene for the ribosomal protein 18 of the 30S subunit of the plastid ribosome which was recently found to be absent from plastid genomes of several non-green unicellular organisms, including the colorless alga Euglena longa
[ "S18" ]
A notable exception is the gene for the ribosomal protein 18 of the 30S subunit of the plastid ribosome which was recently found to be absent from plastid genomes of several non-green unicellular organisms, including the colorless alga Euglena longa
true
true
false
true
false
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
[= Astasia longa; Ref.
[ "1", "3", "4", "5", "7" ]
22
1,676
0
false
[= Astasia longa; Ref.
[]
[= Astasia longa; Ref.
false
false
true
true
false
291
0
INTRODUCTION
1
4
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
(4); database accession no.
[ "1", "3", "4", "5", "7" ]
27
1,677
1
false
; database accession no.
[ "4" ]
; database accession no.
false
false
true
true
false
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
AJ294725] and the parasitic protozoans Eimeria tenella (database accession no.
[ "1", "3", "4", "5", "7" ]
78
1,678
0
false
AJ294725] and the parasitic protozoans Eimeria tenella (database accession no.
[]
AJ294725] and the parasitic protozoans Eimeria tenella (database accession no.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
NC_004823), Theileria parva (database accession no.
[ "1", "3", "4", "5", "7" ]
51
1,679
0
false
NC_004823), Theileria parva (database accession no.
[]
NC_004823), Theileria parva (database accession no.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
NC_007758) and Toxoplasma gondii [database accession no.
[ "1", "3", "4", "5", "7" ]
56
1,680
0
false
NC_007758) and Toxoplasma gondii [database accession no.
[]
NC_007758) and Toxoplasma gondii [database accession no.
true
true
true
true
true
291
0
INTRODUCTION
1
1
[ "b1", "b3", "b4", "b5", "b7" ]
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
Refs (5–7)].
[ "1", "3", "4", "5", "7" ]
12
1,681
0
false
Refs ].
[ "5–7" ]
Refs ].
true
true
true
true
true
291
1
INTRODUCTION
1
8
[ "b8", "b9" ]
16,945,948
pmid-16212603|pmid-9445368
Absence of rps18 from the plastid genomes of non-green organisms as diverse as E.longa and Toxoplasma gondii raises the possibility that the ribosomal protein S18 is not required for translation in non-photosynthetic plastids.
[ "8", "9" ]
226
1,682
0
false
Absence of rps18 from the plastid genomes of non-green organisms as diverse as E.longa and Toxoplasma gondii raises the possibility that the ribosomal protein S18 is not required for translation in non-photosynthetic plastids.
[]
Absence of rps18 from the plastid genomes of non-green organisms as diverse as E.longa and Toxoplasma gondii raises the possibility that the ribosomal protein S18 is not required for translation in non-photosynthetic plastids.
true
true
true
true
true
292
1
INTRODUCTION
1
8
[ "b8", "b9" ]
16,945,948
pmid-16212603|pmid-9445368
This could be a reasonable assumption, because photosynthesis is the main function of plastids and most plastid genes are either directly or indirectly involved in supporting photosynthesis.
[ "8", "9" ]
190
1,683
0
false
This could be a reasonable assumption, because photosynthesis is the main function of plastids and most plastid genes are either directly or indirectly involved in supporting photosynthesis.
[]
This could be a reasonable assumption, because photosynthesis is the main function of plastids and most plastid genes are either directly or indirectly involved in supporting photosynthesis.
true
true
true
true
true
292
1
INTRODUCTION
1
8
[ "b8", "b9" ]
16,945,948
pmid-16212603|pmid-9445368
Thus, the absence of photosynthesis results in a much lower demand for plastid protein biosynthesis and ribosomes without S18 could provide sufficient basal translational activity to support the very few extraphotosynthetic functions of the chloroplast [such as, fatty acid biosynthesis for which a plastid-encoded acetyl-CoA carboxylase subunit is required; Ref.
[ "8", "9" ]
363
1,684
0
false
Thus, the absence of photosynthesis results in a much lower demand for plastid protein biosynthesis and ribosomes without S18 could provide sufficient basal translational activity to support the very few extraphotosynthetic functions of the chloroplast [such as, fatty acid biosynthesis for which a plastid-encoded acetyl-CoA carboxylase subunit is required; Ref.
[]
Thus, the absence of photosynthesis results in a much lower demand for plastid protein biosynthesis and ribosomes without S18 could provide sufficient basal translational activity to support the very few extraphotosynthetic functions of the chloroplast [such as, fatty acid biosynthesis for which a plastid-encoded acetyl-CoA carboxylase subunit is required; Ref.
true
true
true
true
true
292
1
INTRODUCTION
1
9
[ "b8", "b9" ]
16,945,948
pmid-16212603|pmid-9445368
In addition, S18 does not bind directly to the RNA component of the small ribosomal subunit, the 16S rRNA, and thus assembles only relatively late into the 30S subunit (9) which would also be compatible with a non-essential role of the S18 protein.
[ "8", "9" ]
248
1,685
1
false
In addition, S18 does not bind directly to the RNA component of the small ribosomal subunit, the 16S rRNA, and thus assembles only relatively late into the 30S subunit which would also be compatible with a non-essential role of the S18 protein.
[ "9" ]
In addition, S18 does not bind directly to the RNA component of the small ribosomal subunit, the 16S rRNA, and thus assembles only relatively late into the 30S subunit which would also be compatible with a non-essential role of the S18 protein.
true
true
true
true
true
292
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
To address the requirement for S18 in plastid translation directly, we constructed knockout alleles and introduced them into the tobacco plastid genome by genetic transformation.
[ "10", "11", "12", "13" ]
178
1,686
0
false
To address the requirement for S18 in plastid translation directly, we constructed knockout alleles and introduced them into the tobacco plastid genome by genetic transformation.
[]
To address the requirement for S18 in plastid translation directly, we constructed knockout alleles and introduced them into the tobacco plastid genome by genetic transformation.
true
true
true
true
true
293
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
A second purpose of the present study was to test directly the requirement for plastid translation by generating a possibly translation-deficient rps18 knockout mutant.
[ "10", "11", "12", "13" ]
168
1,687
0
false
A second purpose of the present study was to test directly the requirement for plastid translation by generating a possibly translation-deficient rps18 knockout mutant.
[]
A second purpose of the present study was to test directly the requirement for plastid translation by generating a possibly translation-deficient rps18 knockout mutant.
true
true
true
true
true
293
2
INTRODUCTION
1
12
[ "b10", "b11", "b12", "b13" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
Earlier studies in barley (10,11) and Brassica (12) have provided evidence for plastid translation being dispensable under heterotrophic growth conditions (i.e.
[ "10", "11", "12", "13" ]
160
1,688
1
false
Earlier studies in barley and Brassica have provided evidence for plastid translation being dispensable under heterotrophic growth conditions (i.e.
[ "10,11", "12" ]
Earlier studies in barley and Brassica have provided evidence for plastid translation being dispensable under heterotrophic growth conditions (i.e.
true
true
true
true
true
293
2
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b13" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
in the presence of sucrose).
[ "10", "11", "12", "13" ]
28
1,689
0
false
in the presence of sucrose).
[]
in the presence of sucrose).
false
true
true
true
false
293
2
INTRODUCTION
1
13
[ "b10", "b11", "b12", "b13" ]
16,945,948
pmid-7994178|pmid-8440246|pmid-9721684|pmid-14660796|pmid-8127916|pmid-10545095|pmid-11251102
In contrast, recent transgenic experiments have suggested that plastid translation is essential in tobacco: Recombination-induced elimination of a spectinomycin resistance gene led to arrested cell division in the presence of the antibiotic which in turn resulted in severe defects in leaf and floral development (13).
[ "10", "11", "12", "13" ]
318
1,690
1
false
In contrast, recent transgenic experiments have suggested that plastid translation is essential in tobacco: Recombination-induced elimination of a spectinomycin resistance gene led to arrested cell division in the presence of the antibiotic which in turn resulted in severe defects in leaf and floral development.
[ "13" ]
In contrast, recent transgenic experiments have suggested that plastid translation is essential in tobacco: Recombination-induced elimination of a spectinomycin resistance gene led to arrested cell division in the presence of the antibiotic which in turn resulted in severe defects in leaf and floral development.
true
true
true
true
true
293
0
DISCUSSION
0
null
null
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
In this work, we have shown that the plastid genome-encoded gene for the plastid ribosomal protein S18 is essential.
null
116
1,691
0
false
null
null
In this work, we have shown that the plastid genome-encoded gene for the plastid ribosomal protein S18 is essential.
true
true
true
true
true
294
0
DISCUSSION
0
null
null
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
Knockout of the corresponding chloroplast gene results in stable heteroplasmy under antibiotic selection (balancing selection).
null
127
1,692
0
false
null
null
Knockout of the corresponding chloroplast gene results in stable heteroplasmy under antibiotic selection (balancing selection).
true
true
true
true
true
294
0
DISCUSSION
0
null
null
16,945,948
NA|pmid-7854253|pmid-7859309|pmid-8757284|pmid-12051904
In contrast, release of the selective pressure for the transplastome by growth in the absence of the antibiotic results in rapid loss of the rps18 knockout allele by random plastome segregation.
null
194
1,693
0
false
null
null
In contrast, release of the selective pressure for the transplastome by growth in the absence of the antibiotic results in rapid loss of the rps18 knockout allele by random plastome segregation.
true
true
true
true
true
294
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
Genome segregation into homoplasmy produces two distinct phenotypes: White sectors in otherwise normally shaped leaves are seen in cotyledons and in spectinomycin re-exposure experiments (Figures 5C, D and 7A).
null
210
1,694
0
false
null
null
Genome segregation into homoplasmy produces two distinct phenotypes: White sectors in otherwise normally shaped leaves are seen in cotyledons and in spectinomycin re-exposure experiments (Figures 5C, D and 7A).
true
true
true
true
true
295
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
In contrast, the true leaves are green but lack parts of their leaf blades (Figures 6 and 7A).
null
94
1,695
0
false
null
null
In contrast, the true leaves are green but lack parts of their leaf blades (Figures 6 and 7A).
true
true
true
true
true
295
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
The appearance of misshapen true leaves is independent of treatment with spectinomycin in that it occurs upon continuous growth in either the presence or the absence of the antibiotic (Figures 6 and 7A and data not shown).
null
222
1,696
0
false
null
null
The appearance of misshapen true leaves is independent of treatment with spectinomycin in that it occurs upon continuous growth in either the presence or the absence of the antibiotic (Figures 6 and 7A and data not shown).
true
true
true
true
true
295
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
The white sectors seen in the cotyledons of variegated rps18 knockout seedlings (Figure 5C and D) are not seen in true leaves that develop continuously either in the presence or absence of spectinomycin.
null
203
1,697
0
false
null
null
The white sectors seen in the cotyledons of variegated rps18 knockout seedlings (Figure 5C and D) are not seen in true leaves that develop continuously either in the presence or absence of spectinomycin.
true
true
true
true
true
295
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
This is explained with the development of the cotyledons taking place already during embryogenesis and seed development (i.e.
null
125
1,698
0
false
null
null
This is explained with the development of the cotyledons taking place already during embryogenesis and seed development (i.e.
true
true
true
true
true
295
1
DISCUSSION
0
null
null
16,945,948
pmid-16212603|pmid-9445368
in the absence of antibiotic exposure) and suggests that white sectors in the cotyledons are not equivalent to missing sectors in true leaves: While the white sectors in the cotyledons (and in our spectinomycin re-exposure experiments) are homoplasmic for the wild-type genome, the missing sectors in the misshapen true leaves result from segregation into homoplasmy for the transplastome.
null
389
1,699
0
false
null
null
in the absence of antibiotic exposure) and suggests that white sectors in the cotyledons are not equivalent to missing sectors in true leaves: While the white sectors in the cotyledons (and in our spectinomycin re-exposure experiments) are homoplasmic for the wild-type genome, the missing sectors in the misshapen true leaves result from segregation into homoplasmy for the transplastome.
false
true
true
true
false
295