-
1
-
-
0003604405
-
-
3 rd ed., Cold Spring Harbor Laboratory Press, New York
-
Gesteland, R. F., Cech, T. R., and Atkins, J. F. (2006) The RNA World, 3 rd ed., Cold Spring Harbor Laboratory Press, New York.
-
(2006)
The RNA World
-
-
Gesteland, R.F.1
Cech, T.R.2
Atkins, J.F.3
-
2
-
-
0029163563
-
RNA chaperones and the RNA folding problem
-
Herschlag, D. (1995) RNA chaperones and the RNA folding problem J. Biol. Chem. 270, 20871-20874
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 20871-20874
-
-
Herschlag, D.1
-
3
-
-
0030916948
-
Protein-facilitated RNA folding
-
Weeks, K. M. (1997) Protein-facilitated RNA folding Curr. Opin. Struct. Biol. 7, 336-342
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 336-342
-
-
Weeks, K.M.1
-
4
-
-
8444229753
-
Strategies for RNA folding and assembly
-
Schroeder, R., Barta, A., and Semrad, K. (2004) Strategies for RNA folding and assembly Nat. Rev. Mol. Cell Biol. 5, 908-919
-
(2004)
Nat. Rev. Mol. Cell Biol.
, vol.5
, pp. 908-919
-
-
Schroeder, R.1
Barta, A.2
Semrad, K.3
-
7
-
-
0027173194
-
The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms
-
LeCuyer, K. A. and Crothers, D. M. (1993) The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms Biochemistry 32, 5301-5311
-
(1993)
Biochemistry
, vol.32
, pp. 5301-5311
-
-
Lecuyer, K.A.1
Crothers, D.M.2
-
8
-
-
0027932176
-
Thermodynamics of folding a pseudoknotted mRNA fragment
-
Gluick, T. C. and Draper, D. E. (1994) Thermodynamics of folding a pseudoknotted mRNA fragment J. Mol. Biol. 241, 246-262
-
(1994)
J. Mol. Biol.
, vol.241
, pp. 246-262
-
-
Gluick, T.C.1
Draper, D.E.2
-
9
-
-
0032578472
-
RNA folding causes secondary structure rearrangement
-
Wu, M. and Tinoco, I., Jr. (1998) RNA folding causes secondary structure rearrangement Proc. Natl. Acad. Sci. U.S.A. 95, 11555-11560
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 11555-11560
-
-
Wu, M.1
Tinoco, Jr.I.2
-
10
-
-
0034103611
-
A collapsed non-native RNA folding state
-
Buchmueller, K. L., Webb, A. E., Richardson, D. A., and Weeks, K. M. (2000) A collapsed non-native RNA folding state Nat. Struct. Biol. 7, 362-366
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 362-366
-
-
Buchmueller, K.L.1
Webb, A.E.2
Richardson, D.A.3
Weeks, K.M.4
-
11
-
-
0035957327
-
Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group i ribozyme
-
Zheng, M., Wu, M., and Tinoco, I., Jr. (2001) Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme Proc. Natl. Acad. Sci. U.S.A. 98, 3695-3700
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 3695-3700
-
-
Zheng, M.1
Wu, M.2
Tinoco, Jr.I.3
-
12
-
-
27144451444
-
RNA tertiary interactions mediate native collapse of a bacterial group i ribozyme
-
Chauhan, S., Caliskan, G., Briber, R. M., Perez-Salas, U., Rangan, P., Thirumalai, D., and Woodson, S. A. (2005) RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme J. Mol. Biol. 353, 1199-1209
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 1199-1209
-
-
Chauhan, S.1
Caliskan, G.2
Briber, R.M.3
Perez-Salas, U.4
Rangan, P.5
Thirumalai, D.6
Woodson, S.A.7
-
14
-
-
38649085954
-
Tertiary interactions determine the accuracy of RNA folding
-
Chauhan, S. and Woodson, S. A. (2008) Tertiary interactions determine the accuracy of RNA folding J. Am. Chem. Soc. 130, 1296-1303
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 1296-1303
-
-
Chauhan, S.1
Woodson, S.A.2
-
15
-
-
40849118189
-
Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry
-
Wang, B., Wilkinson, K. A., and Weeks, K. M. (2008) Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry Biochemistry 47, 3454-3461
-
(2008)
Biochemistry
, vol.47
, pp. 3454-3461
-
-
Wang, B.1
Wilkinson, K.A.2
Weeks, K.M.3
-
16
-
-
39049131090
-
RNA chaperones, RNA annealers and RNA helicases
-
Rajkowitsch, L., Chen, D., Stampfl, S., Semrad, K., Waldsich, C., Mayer, O., Jantsch, M. F., Konrat, R., Blasi, U., and Schroeder, R. (2007) RNA chaperones, RNA annealers and RNA helicases RNA Biol. 4, 118-130
-
(2007)
RNA Biol.
, vol.4
, pp. 118-130
-
-
Rajkowitsch, L.1
Chen, D.2
Stampfl, S.3
Semrad, K.4
Waldsich, C.5
Mayer, O.6
Jantsch, M.F.7
Konrat, R.8
Blasi, U.9
Schroeder, R.10
-
17
-
-
38449108345
-
RNA misfolding and the action of chaperones
-
Russell, R. (2008) RNA misfolding and the action of chaperones Front. Biosci. 13, 1-20
-
(2008)
Front. Biosci.
, vol.13
, pp. 1-20
-
-
Russell, R.1
-
18
-
-
0035933312
-
Protein-dependent transition states for ribonucleoprotein assembly
-
Webb, A. E., Rose, M. A., Westhof, E., and Weeks, K. M. (2001) Protein-dependent transition states for ribonucleoprotein assembly J. Mol. Biol. 309, 1087-1100
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 1087-1100
-
-
Webb, A.E.1
Rose, M.A.2
Westhof, E.3
Weeks, K.M.4
-
19
-
-
0025678737
-
Modelling of the three-dimensional architecture of group i catalytic introns based on comparative sequence analysis
-
Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis J. Mol. Biol. 216, 585-610
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
-
20
-
-
0025367254
-
Self-splicing of group i introns
-
Cech, T. R. (1990) Self-splicing of group I introns Annu. Rev. Biochem. 59, 543-568
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 543-568
-
-
Cech, T.R.1
-
21
-
-
20444496805
-
Structure and assembly of group i introns
-
Woodson, S. A. (2005) Structure and assembly of group I introns Curr. Opin. Struct. Biol. 15, 324-330
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 324-330
-
-
Woodson, S.A.1
-
22
-
-
30944458838
-
Atomic level architecture of group i introns revealed
-
Vicens, Q. and Cech, T. R. (2006) Atomic level architecture of group I introns revealed Trends Biochem. Sci. 31, 41-51
-
(2006)
Trends Biochem. Sci.
, vol.31
, pp. 41-51
-
-
Vicens, Q.1
Cech, T.R.2
-
23
-
-
0037039310
-
Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group i intron RNA
-
Bassi, G. S., de Oliveira, D. M., White, M. F., and Weeks, K. M. (2002) Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA Proc. Natl. Acad. Sci. U.S.A. 99, 128-133
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 128-133
-
-
Bassi, G.S.1
De Oliveira, D.M.2
White, M.F.3
Weeks, K.M.4
-
24
-
-
0041972557
-
Kinetic and thermodynamic framework for assembly of the six-component bI3 group i intron ribonucleoprotein catalyst
-
Bassi, G. S. and Weeks, K. M. (2003) Kinetic and thermodynamic framework for assembly of the six-component bI3 group I intron ribonucleoprotein catalyst Biochemistry 42, 9980-9988
-
(2003)
Biochemistry
, vol.42
, pp. 9980-9988
-
-
Bassi, G.S.1
Weeks, K.M.2
-
25
-
-
26944447183
-
Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase
-
Longo, A., Leonard, C. W., Bassi, G. S., Berndt, D., Krahn, J. M., Hall, T. M., and Weeks, K. M. (2005) Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase Nat. Struct. Mol. Biol. 12, 779-787
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 779-787
-
-
Longo, A.1
Leonard, C.W.2
Bassi, G.S.3
Berndt, D.4
Krahn, J.M.5
Hall, T.M.6
Weeks, K.M.7
-
26
-
-
77749337616
-
The Mrs1 splicing factor binds the bI3 group i intron at each of two tetraloop-receptor motifs
-
Duncan, C. D. and Weeks, K. M. (2010) The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs PLoS One 5, e8983
-
(2010)
PLoS One
, vol.5
, pp. 8983
-
-
Duncan, C.D.1
Weeks, K.M.2
-
27
-
-
49749103581
-
SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group i intron RNA
-
Duncan, C. D. and Weeks, K. M. (2008) SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA Biochemistry 47, 8504-8513
-
(2008)
Biochemistry
, vol.47
, pp. 8504-8513
-
-
Duncan, C.D.1
Weeks, K.M.2
-
28
-
-
34247162792
-
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
-
Mortimer, S. A. and Weeks, K. M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry J. Am. Chem. Soc. 129, 4144-4145
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 4144-4145
-
-
Mortimer, S.A.1
Weeks, K.M.2
-
29
-
-
52949152433
-
ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
-
Vasa, S. M., Guex, N., Wilkinson, K. A., Weeks, K. M., and Giddings, M. C. (2008) ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis RNA 14, 1979-1990
-
(2008)
RNA
, vol.14
, pp. 1979-1990
-
-
Vasa, S.M.1
Guex, N.2
Wilkinson, K.A.3
Weeks, K.M.4
Giddings, M.C.5
-
30
-
-
58549109608
-
Accurate SHAPE-directed RNA structure determination
-
Deigan, K. E., Li, T. W., Mathews, D. H., and Weeks, K. M. (2009) Accurate SHAPE-directed RNA structure determination Proc. Natl. Acad. Sci. U.S.A. 106, 97-102
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 97-102
-
-
Deigan, K.E.1
Li, T.W.2
Mathews, D.H.3
Weeks, K.M.4
-
31
-
-
44149101971
-
Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
-
Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E., and Dokholyan, N. V. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms RNA 14, 1164-1173
-
(2008)
RNA
, vol.14
, pp. 1164-1173
-
-
Ding, F.1
Sharma, S.2
Chalasani, P.3
Demidov, V.V.4
Broude, N.E.5
Dokholyan, N.V.6
-
32
-
-
67849127180
-
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics
-
Gherghe, C. M., Leonard, C. W., Ding, F., Dokholyan, N. V., and Weeks, K. M. (2009) Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics J. Am. Chem. Soc. 131, 2541-2546
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 2541-2546
-
-
Gherghe, C.M.1
Leonard, C.W.2
Ding, F.3
Dokholyan, N.V.4
Weeks, K.M.5
-
34
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
-
Merino, E. J., Wilkinson, K. A., Coughlan, J. L., and Weeks, K. M. (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE) J. Am. Chem. Soc. 127, 4223-4231
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
35
-
-
33947720028
-
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
-
Wilkinson, K. A., Merino, E. J., and Weeks, K. M. (2006) Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Nat. Protoc. 1, 1610-1616
-
(2006)
Nat. Protoc.
, vol.1
, pp. 1610-1616
-
-
Wilkinson, K.A.1
Merino, E.J.2
Weeks, K.M.3
-
37
-
-
0001268975
-
Hydroxyl radical footprinting: High-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein
-
Tullius, T. D. and Dombroski, B. A. (1986) Hydroxyl radical footprinting: high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein Proc. Natl. Acad. Sci. U.S.A. 83, 5469-5473
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 5469-5473
-
-
Tullius, T.D.1
Dombroski, B.A.2
-
38
-
-
0024359787
-
Defining the inside and outside of a catalytic RNA molecule
-
Latham, J. A. and Cech, T. R. (1989) Defining the inside and outside of a catalytic RNA molecule Science 245, 276-282
-
(1989)
Science
, vol.245
, pp. 276-282
-
-
Latham, J.A.1
Cech, T.R.2
-
39
-
-
16244389281
-
Mapping nucleic acid structure by hydroxyl radical cleavage
-
Tullius, T. D. and Greenbaum, J. A. (2005) Mapping nucleic acid structure by hydroxyl radical cleavage Curr. Opin. Chem. Biol. 9, 127-134
-
(2005)
Curr. Opin. Chem. Biol.
, vol.9
, pp. 127-134
-
-
Tullius, T.D.1
Greenbaum, J.A.2
-
40
-
-
0032544035
-
DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone
-
Balasubramanian, B., Pogozelski, W. K., and Tullius, T. D. (1998) DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone Proc. Natl. Acad. Sci. U.S.A. 95, 9738-9743
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 9738-9743
-
-
Balasubramanian, B.1
Pogozelski, W.K.2
Tullius, T.D.3
-
41
-
-
39449112406
-
Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting
-
Shcherbakova, I. and Brenowitz, M. (2008) Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting Nat. Protoc. 3, 288-302
-
(2008)
Nat. Protoc.
, vol.3
, pp. 288-302
-
-
Shcherbakova, I.1
Brenowitz, M.2
-
42
-
-
77954183805
-
High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly
-
McGinnis, J. L., Duncan, C. D. S., and Weeks, K. M. (2009) High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly Methods Enzymol. 468, 67-89
-
(2009)
Methods Enzymol.
, vol.468
, pp. 67-89
-
-
McGinnis, J.L.1
Duncan, C.D.S.2
Weeks, K.M.3
|