-
1
-
-
0026315514
-
Folding of circularly permuted transfer RNAs
-
Pan T., Gutell R.R., and Uhlenbeck O.C. Folding of circularly permuted transfer RNAs. Science 254 (1991) 1361-1364
-
(1991)
Science
, vol.254
, pp. 1361-1364
-
-
Pan, T.1
Gutell, R.R.2
Uhlenbeck, O.C.3
-
2
-
-
0028088780
-
Selection of circularly permuted ribozymes from Bacillus subtilis RNase P by substrate binding
-
Pan T., and Zhong K. Selection of circularly permuted ribozymes from Bacillus subtilis RNase P by substrate binding. Biochemistry 33 (1994) 14207-14212
-
(1994)
Biochemistry
, vol.33
, pp. 14207-14212
-
-
Pan, T.1
Zhong, K.2
-
3
-
-
0345687915
-
Products transcribed from rearranged rrn genes of Escherichia coli can assemble to form functional ribosomes
-
Zaporojets D., French S., and Squires C.L. Products transcribed from rearranged rrn genes of Escherichia coli can assemble to form functional ribosomes. J. Bacteriol. 185 (2003) 6921-6927
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6921-6927
-
-
Zaporojets, D.1
French, S.2
Squires, C.L.3
-
4
-
-
16344371778
-
RNA and protein folding: common themes and variations
-
Thirumalai D., and Hyeon C. RNA and protein folding: common themes and variations. Biochemistry 44 (2005) 4957-4970
-
(2005)
Biochemistry
, vol.44
, pp. 4957-4970
-
-
Thirumalai, D.1
Hyeon, C.2
-
6
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
7
-
-
0036829967
-
Complete change of the protein folding transition state upon circular permutation
-
Lindberg M., Tangrot J., and Oliveberg M. Complete change of the protein folding transition state upon circular permutation. Nature Struct. Biol. 9 (2002) 818-822
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 818-822
-
-
Lindberg, M.1
Tangrot, J.2
Oliveberg, M.3
-
8
-
-
0041825363
-
Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks
-
Weikl T.R., and Dill K.A. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J. Mol. Biol. 332 (2003) 953-963
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 953-963
-
-
Weikl, T.R.1
Dill, K.A.2
-
9
-
-
0037432567
-
Local secondary structure content predicts folding rates for simple, two-state proteins
-
Gong H., Isom D.G., Srinivasan R., and Rose G.D. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 327 (2003) 1149-1154
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 1149-1154
-
-
Gong, H.1
Isom, D.G.2
Srinivasan, R.3
Rose, G.D.4
-
10
-
-
0042510944
-
Contact order revisited: influence of protein size on the folding rate
-
Ivankov D.N., Garbuzynskiy S.O., Alm E., Plaxco K.W., Baker D., and Finkelstein A.V. Contact order revisited: influence of protein size on the folding rate. Protein Sci. 12 (2003) 2057-2062
-
(2003)
Protein Sci.
, vol.12
, pp. 2057-2062
-
-
Ivankov, D.N.1
Garbuzynskiy, S.O.2
Alm, E.3
Plaxco, K.W.4
Baker, D.5
Finkelstein, A.V.6
-
11
-
-
0020972782
-
Theoretical studies of protein folding
-
Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12 (1983) 183-210
-
(1983)
Annu. Rev. Biophys. Bioeng.
, vol.12
, pp. 183-210
-
-
Go, N.1
-
14
-
-
0029163563
-
RNA chaperones and the RNA folding problem
-
Herschlag D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270 (1995) 20871-20874
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 20871-20874
-
-
Herschlag, D.1
-
15
-
-
0001103473
-
Kinetics of folding of protein and RNA
-
Thirumalai D., and Woodson S.A. Kinetics of folding of protein and RNA. Acc. Chem. Res. 29 (1996) 433-439
-
(1996)
Acc. Chem. Res.
, vol.29
, pp. 433-439
-
-
Thirumalai, D.1
Woodson, S.A.2
-
17
-
-
0027467740
-
Circularly permuted DNA, RNA and proteins-a review
-
Pan T., and Uhlenbeck O.C. Circularly permuted DNA, RNA and proteins-a review. Gene 125 (1993) 111-114
-
(1993)
Gene
, vol.125
, pp. 111-114
-
-
Pan, T.1
Uhlenbeck, O.C.2
-
18
-
-
0029422261
-
Circular permutation of polypeptide chains: implications for protein folding and stability
-
Heinemann U., and Hahn M. Circular permutation of polypeptide chains: implications for protein folding and stability. Prog. Biophys. Mol. Biol. 64 (1995) 121-143
-
(1995)
Prog. Biophys. Mol. Biol.
, vol.64
, pp. 121-143
-
-
Heinemann, U.1
Hahn, M.2
-
19
-
-
0029859408
-
Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase
-
Graf R., and Schachman H.K. Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase. Proc. Natl Acad. Sci. USA 93 (1996) 11591-11596
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 11591-11596
-
-
Graf, R.1
Schachman, H.K.2
-
20
-
-
0037466322
-
Perturbed folding kinetics of circularly permuted RNAs with altered topology
-
Heilman-Miller S.L., and Woodson S.A. Perturbed folding kinetics of circularly permuted RNAs with altered topology. J. Mol. Biol. 328 (2003) 385-394
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 385-394
-
-
Heilman-Miller, S.L.1
Woodson, S.A.2
-
21
-
-
0032549780
-
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
-
Sclavi B., Sullivan M., Chance M.R., Brenowitz M., and Woodson S.A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279 (1998) 1940-1943
-
(1998)
Science
, vol.279
, pp. 1940-1943
-
-
Sclavi, B.1
Sullivan, M.2
Chance, M.R.3
Brenowitz, M.4
Woodson, S.A.5
-
22
-
-
33646089899
-
Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule
-
Laederach A., Shcherbakova I., Liang M.P., Brenowitz M., and Altman R.B. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J. Mol. Biol. 358 (2006) 1179-1190
-
(2006)
J. Mol. Biol.
, vol.358
, pp. 1179-1190
-
-
Laederach, A.1
Shcherbakova, I.2
Liang, M.P.3
Brenowitz, M.4
Altman, R.B.5
-
23
-
-
0032563297
-
Folding intermediates of a self-splicing RNA: mispairing of the catalytic core
-
Pan J., and Woodson S.A. Folding intermediates of a self-splicing RNA: mispairing of the catalytic core. J. Mol. Biol. 280 (1998) 597-609
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 597-609
-
-
Pan, J.1
Woodson, S.A.2
-
24
-
-
0021354772
-
A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA
-
Zaug A.J., Kent J.R., and Cech T.R. A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA. Science 224 (1984) 574-578
-
(1984)
Science
, vol.224
, pp. 574-578
-
-
Zaug, A.J.1
Kent, J.R.2
Cech, T.R.3
-
25
-
-
0022422372
-
Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure
-
Been M.D., and Cech T.R. Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure. Nucl. Acids Res. 13 (1985) 8389-8408
-
(1985)
Nucl. Acids Res.
, vol.13
, pp. 8389-8408
-
-
Been, M.D.1
Cech, T.R.2
-
26
-
-
0025134897
-
Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns
-
Michel F., Ellington A.D., Couture S., and Szostak J. W. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347 (1990) 578-580
-
(1990)
Nature
, vol.347
, pp. 578-580
-
-
Michel, F.1
Ellington, A.D.2
Couture, S.3
Szostak, J. W.4
-
27
-
-
0038475911
-
Effect of transcription on folding of the Tetrahymena ribozyme
-
Heilman-Miller S.L., and Woodson S.A. Effect of transcription on folding of the Tetrahymena ribozyme. RNA 9 (2003) 722-733
-
(2003)
RNA
, vol.9
, pp. 722-733
-
-
Heilman-Miller, S.L.1
Woodson, S.A.2
-
28
-
-
0026729278
-
RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme
-
Pyle A.M., Murphy F.L., and Cech T.R. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature 358 (1992) 123-128
-
(1992)
Nature
, vol.358
, pp. 123-128
-
-
Pyle, A.M.1
Murphy, F.L.2
Cech, T.R.3
-
29
-
-
0031731420
-
A minor groove RNA triple helix within the catalytic core of a group I intron
-
Szewczak A.A., Ortoleva-Donnelly L., Ryder S.P., Moncoeur E., and Strobel S.A. A minor groove RNA triple helix within the catalytic core of a group I intron. Nature Struct. Biol. 5 (1998) 1037-1042
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 1037-1042
-
-
Szewczak, A.A.1
Ortoleva-Donnelly, L.2
Ryder, S.P.3
Moncoeur, E.4
Strobel, S.A.5
-
30
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
Adams P.L., Stahley M.R., Gill M.L., Kosek A.B., Wang J., and Strobel S.A. Crystal structure of a group I intron splicing intermediate. RNA 10 (2004) 1867-1887
-
(2004)
RNA
, vol.10
, pp. 1867-1887
-
-
Adams, P.L.1
Stahley, M.R.2
Gill, M.L.3
Kosek, A.B.4
Wang, J.5
Strobel, S.A.6
-
31
-
-
0025963132
-
Visualizing the higher order folding of a catalytic RNA molecule
-
Celander D.W., and Cech T.R. Visualizing the higher order folding of a catalytic RNA molecule. Science 251 (1991) 401-407
-
(1991)
Science
, vol.251
, pp. 401-407
-
-
Celander, D.W.1
Cech, T.R.2
-
32
-
-
0024359787
-
Defining the inside and outside of a catalytic RNA molecule
-
Latham J.A., and Cech T.R. Defining the inside and outside of a catalytic RNA molecule. Science 245 (1989) 276-282
-
(1989)
Science
, vol.245
, pp. 276-282
-
-
Latham, J.A.1
Cech, T.R.2
-
33
-
-
0031566962
-
Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein- DNA interactions and RNA folding
-
Sclavi B., Woodson S., Sullivan M., Chance M.R., and Brenowitz M. Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein- DNA interactions and RNA folding. J. Mol. Biol. 266 (1997) 144-159
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 144-159
-
-
Sclavi, B.1
Woodson, S.2
Sullivan, M.3
Chance, M.R.4
Brenowitz, M.5
-
34
-
-
0033644180
-
Time-resolved synchrotron X-ray footprinting and its application to RNA folding
-
Ralston C.Y., Sclavi B., Sullivan M., Deras M.L., Woodson S.A., Chance M.R., and Brenowitz M. Time-resolved synchrotron X-ray footprinting and its application to RNA folding. Methods Enzymol. 317 (2000) 353-368
-
(2000)
Methods Enzymol.
, vol.317
, pp. 353-368
-
-
Ralston, C.Y.1
Sclavi, B.2
Sullivan, M.3
Deras, M.L.4
Woodson, S.A.5
Chance, M.R.6
Brenowitz, M.7
-
35
-
-
0034641668
-
Folding mechanism of the Tetrahymena ribozyme P4-P6 domain
-
Deras M.L., Brenowitz M., Ralston C.Y., Chance M. R., and Woodson S.A. Folding mechanism of the Tetrahymena ribozyme P4-P6 domain. Biochemistry 39 (2000) 10975-10985
-
(2000)
Biochemistry
, vol.39
, pp. 10975-10985
-
-
Deras, M.L.1
Brenowitz, M.2
Ralston, C.Y.3
Chance, M. R.4
Woodson, S.A.5
-
36
-
-
0035946973
-
Counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion dependence of folding kinetics
-
Heilman-Miller S.L., Pan J., Thirumalai D., and Woodson S.A. Counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion dependence of folding kinetics. J. Mol. Biol. 309 (2001) 57-68
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 57-68
-
-
Heilman-Miller, S.L.1
Pan, J.2
Thirumalai, D.3
Woodson, S.A.4
-
37
-
-
4444370899
-
Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme
-
Shcherbakova I., Gupta S., Chance M.R., and Brenowitz M. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J. Mol. Biol. 342 (2004) 1431-1442
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 1431-1442
-
-
Shcherbakova, I.1
Gupta, S.2
Chance, M.R.3
Brenowitz, M.4
-
38
-
-
0021991295
-
Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase
-
Inoue T., and Cech T.R. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. Proc. Natl Acad. Sci. USA 82 (1985) 648-652
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 648-652
-
-
Inoue, T.1
Cech, T.R.2
-
39
-
-
0025091663
-
Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate
-
Jaeger J.A., Zuker M., and Turner D.H. Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate. Biochemistry 29 (1990) 10147-10158
-
(1990)
Biochemistry
, vol.29
, pp. 10147-10158
-
-
Jaeger, J.A.1
Zuker, M.2
Turner, D.H.3
-
40
-
-
0032578472
-
RNA folding causes secondary structure rearrangement
-
Wu M., and Tinoco Jr. I. RNA folding causes secondary structure rearrangement. Proc. Natl Acad. Sci. USA 95 (1998) 11555-11560
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 11555-11560
-
-
Wu, M.1
Tinoco Jr., I.2
-
41
-
-
0030452773
-
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme
-
Lehnert V., Jaeger L., Michel F., and Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3 (1996) 993-1009
-
(1996)
Chem. Biol.
, vol.3
, pp. 993-1009
-
-
Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
-
42
-
-
0030873521
-
Isoalloxazine derivatives promote photocleavage of natural RNAs at G•U base-pairs embedded within helices
-
Burgstaller P., Hermann T., Huber C., Westhof E., and Famulok M. Isoalloxazine derivatives promote photocleavage of natural RNAs at G•U base-pairs embedded within helices. Nucl. Acids Res. 25 (1997) 4018-4027
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 4018-4027
-
-
Burgstaller, P.1
Hermann, T.2
Huber, C.3
Westhof, E.4
Famulok, M.5
-
43
-
-
0028239266
-
Two major tertiary folding transitions of the Tetrahymena catalytic RNA
-
Laggerbauer B., Murphy F.L., and Cech T.R. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13 (1994) 2669-2676
-
(1994)
EMBO J.
, vol.13
, pp. 2669-2676
-
-
Laggerbauer, B.1
Murphy, F.L.2
Cech, T.R.3
-
44
-
-
0029864990
-
The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme
-
Zarrinkar P.P., and Williamson J.R. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme. Nucl. Acids Res. 24 (1996) 854-858
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 854-858
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
-
46
-
-
0030032613
-
Effects of circular permutation on the cis-cleavage reaction of a hepatitis delta virus ribozyme: application to trans-acting ribozyme design
-
Lai Y.C., Lee J.Y., Liu H.J., Lin J.Y., and Wu H. N. Effects of circular permutation on the cis-cleavage reaction of a hepatitis delta virus ribozyme: application to trans-acting ribozyme design. Biochemistry 35 (1996) 124-131
-
(1996)
Biochemistry
, vol.35
, pp. 124-131
-
-
Lai, Y.C.1
Lee, J.Y.2
Liu, H.J.3
Lin, J.Y.4
Wu, H. N.5
-
47
-
-
0034043484
-
Recent insights on RNA folding mechanisms from catalytic RNA
-
Woodson S.A. Recent insights on RNA folding mechanisms from catalytic RNA. Cell Mol. Life Sci. 57 (2000) 796-808
-
(2000)
Cell Mol. Life Sci.
, vol.57
, pp. 796-808
-
-
Woodson, S.A.1
-
48
-
-
23744470902
-
Single-molecule RNA folding
-
Bokinsky G., and Zhuang X. Single-molecule RNA folding. Acc. Chem. Res. 38 (2005) 566-573
-
(2005)
Acc. Chem. Res.
, vol.38
, pp. 566-573
-
-
Bokinsky, G.1
Zhuang, X.2
-
49
-
-
0027991626
-
Kinetic intermediates in RNA folding
-
Zarrinkar P.P., and Williamson J.R. Kinetic intermediates in RNA folding. Science 265 (1994) 918-924
-
(1994)
Science
, vol.265
, pp. 918-924
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
-
50
-
-
0034041087
-
Maximizing RNA folding rates: a balancing act
-
Thirumalai D., and Woodson S.A. Maximizing RNA folding rates: a balancing act. RNA 6 (2000) 790-794
-
(2000)
RNA
, vol.6
, pp. 790-794
-
-
Thirumalai, D.1
Woodson, S.A.2
-
52
-
-
0034674420
-
A single-molecule study of RNA catalysis and folding
-
Zhuang X., Bartley L.E., Babcock H.P., Russell R., Ha T., Herschlag D., and Chu S. A single-molecule study of RNA catalysis and folding. Science 288 (2000) 2048-2051
-
(2000)
Science
, vol.288
, pp. 2048-2051
-
-
Zhuang, X.1
Bartley, L.E.2
Babcock, H.P.3
Russell, R.4
Ha, T.5
Herschlag, D.6
Chu, S.7
-
53
-
-
0029874598
-
The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
-
Zarrinkar P.P., and Williamson J.R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nature Struct. Biol. 3 (1996) 432-438
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 432-438
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
-
54
-
-
0029258956
-
Self-assembly of a group I intron active site from its component tertiary structural domains
-
Doudna J.A., and Cech T.R. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1 (1995) 36-45
-
(1995)
RNA
, vol.1
, pp. 36-45
-
-
Doudna, J.A.1
Cech, T.R.2
-
55
-
-
0034633940
-
Multiple folding pathways for the P4-P6 RNA domain
-
Silverman S.K., Deras M.L., Woodson S.A., Scaringe S.A., and Cech T.R. Multiple folding pathways for the P4-P6 RNA domain. Biochemistry 39 (2000) 12465-12475
-
(2000)
Biochemistry
, vol.39
, pp. 12465-12475
-
-
Silverman, S.K.1
Deras, M.L.2
Woodson, S.A.3
Scaringe, S.A.4
Cech, T.R.5
-
56
-
-
0034635353
-
Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA
-
Pan J., Deras M.L., and Woodson S.A. Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA. J. Mol. Biol. 296 (2000) 133-144
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 133-144
-
-
Pan, J.1
Deras, M.L.2
Woodson, S.A.3
-
57
-
-
0037039464
-
Exploring the folding landscape of a structured RNA
-
Russell R., Zhuang X., Babcock H.P., Millett I.S., Doniach S., Chu S., and Herschlag D. Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA 99 (2002) 155-160
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 155-160
-
-
Russell, R.1
Zhuang, X.2
Babcock, H.P.3
Millett, I.S.4
Doniach, S.5
Chu, S.6
Herschlag, D.7
-
58
-
-
0031984645
-
Complementary sets of noncanonical base-pairs mediate RNA helix packing in the group I intron active site
-
Strobel S.A., Ortoleva-Donnelly L., Ryder S.P., Cate J.H., and Moncoeur E. Complementary sets of noncanonical base-pairs mediate RNA helix packing in the group I intron active site. Nature Struct. Biol. 5 (1998) 60-66
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 60-66
-
-
Strobel, S.A.1
Ortoleva-Donnelly, L.2
Ryder, S.P.3
Cate, J.H.4
Moncoeur, E.5
-
59
-
-
0347364655
-
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
-
Xayaphoummine A., Bucher T., Thalmann F., and Isambert H. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl Acad. Sci. USA 100 (2003) 15310-15315
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 15310-15315
-
-
Xayaphoummine, A.1
Bucher, T.2
Thalmann, F.3
Isambert, H.4
-
60
-
-
23144463133
-
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
-
Xayaphoummine A., Bucher T., and Isambert H. Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucl. Acids Res. 33 (2005) W605-W610
-
(2005)
Nucl. Acids Res.
, vol.33
-
-
Xayaphoummine, A.1
Bucher, T.2
Isambert, H.3
-
62
-
-
0015497428
-
Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli)
-
Cole P.E., and Crothers D.M. Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry 11 (1972) 4368-4374
-
(1972)
Biochemistry
, vol.11
, pp. 4368-4374
-
-
Cole, P.E.1
Crothers, D.M.2
-
63
-
-
0015914592
-
Free energy of imperfect nucleic acid helices. II. Small hairpin loops
-
Gralla J., and Crothers D.M. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol. 73 (1973) 497-511
-
(1973)
J. Mol. Biol.
, vol.73
, pp. 497-511
-
-
Gralla, J.1
Crothers, D.M.2
-
64
-
-
0024295554
-
Characterization of RNA hairpin loop stability
-
Groebe D.R., and Uhlenbeck O.C. Characterization of RNA hairpin loop stability. Nucl. Acids Res. 16 (1988) 11725-11735
-
(1988)
Nucl. Acids Res.
, vol.16
, pp. 11725-11735
-
-
Groebe, D.R.1
Uhlenbeck, O.C.2
-
65
-
-
0035819201
-
Loop dependence of the dynamics of DNA hairpins
-
Shen Y., Kuznetsov S.V., and Ansari A. Loop dependence of the dynamics of DNA hairpins. J. Phys. Chem. B 105 (2001) 12202-12211
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 12202-12211
-
-
Shen, Y.1
Kuznetsov, S.V.2
Ansari, A.3
-
66
-
-
0033578330
-
Folding of a large ribozyme during transcription and the effect of the elongation factor NusA
-
Pan T., Artsimovitch I., Fang X.W., Landick R., and Sosnick T.R. Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl Acad. Sci. USA 96 (1999) 9545-9550
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 9545-9550
-
-
Pan, T.1
Artsimovitch, I.2
Fang, X.W.3
Landick, R.4
Sosnick, T.R.5
-
67
-
-
4644266762
-
Intracellular folding of the Tetrahymena group I intron depends on exon sequence and promoter choice
-
Koduvayur S.P., and Woodson S.A. Intracellular folding of the Tetrahymena group I intron depends on exon sequence and promoter choice. RNA 10 (2004) 1526-1532
-
(2004)
RNA
, vol.10
, pp. 1526-1532
-
-
Koduvayur, S.P.1
Woodson, S.A.2
-
68
-
-
0033605081
-
Pathway modulation, circular permutation and rapid RNA folding under kinetic control
-
Pan T., Fang X., and Sosnick T. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J. Mol. Biol. 286 (1999) 721-731
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 721-731
-
-
Pan, T.1
Fang, X.2
Sosnick, T.3
-
69
-
-
21244459458
-
Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast
-
Mahen E.M., Harger J.W., Calderon E.M., and Fedor M.J. Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol. Cell 19 (2005) 27-37
-
(2005)
Mol. Cell
, vol.19
, pp. 27-37
-
-
Mahen, E.M.1
Harger, J.W.2
Calderon, E.M.3
Fedor, M.J.4
-
70
-
-
0032319210
-
Following the folding of RNA with time-resolved synchrotron X-ray footprinting
-
Sclavi B., Woodson S., Sullivan M., Chance M., and Brenowitz M. Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol. 295 (1998) 379-402
-
(1998)
Methods Enzymol.
, vol.295
, pp. 379-402
-
-
Sclavi, B.1
Woodson, S.2
Sullivan, M.3
Chance, M.4
Brenowitz, M.5
-
71
-
-
0029806242
-
Quantitative kinetic footprinting of protein-DNA association reactions
-
Hsieh M., and Brenowitz M. Quantitative kinetic footprinting of protein-DNA association reactions. Methods Enzymol. 274 (1996) 478-492
-
(1996)
Methods Enzymol.
, vol.274
, pp. 478-492
-
-
Hsieh, M.1
Brenowitz, M.2
-
72
-
-
9244253711
-
Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA
-
Lease R.A., and Woodson S.A. Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J. Mol. Biol. 344 (2004) 1211-1223
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 1211-1223
-
-
Lease, R.A.1
Woodson, S.A.2
-
73
-
-
8644229237
-
Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site
-
Guo F., Gooding A., and Cech R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol. Cell 16 (2004) 351-362
-
(2004)
Mol. Cell
, vol.16
, pp. 351-362
-
-
Guo, F.1
Gooding, A.2
Cech, R.3
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