-
1
-
-
0842281551
-
Principles of protein folding, misfolding and aggregation
-
C.M. Dobson Principles of protein folding, misfolding and aggregation Semin. Cell Dev. Biol. 15 2004 3 16
-
(2004)
Semin. Cell Dev. Biol.
, vol.15
, pp. 3-16
-
-
Dobson, C.M.1
-
3
-
-
0025367254
-
Self-splicing of group I introns
-
T.R. Cech Self-splicing of group I introns Annu. Rev. Biochem. 59 1990 543 568
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 543-568
-
-
Cech, T.R.1
-
7
-
-
0036864241
-
Folding mechanisms of group I ribozymes: Role of stability and contact order
-
S.A. Woodson Folding mechanisms of group I ribozymes: role of stability and contact order Biochem. Soc. Trans. 30 2001 1166 1169
-
(2001)
Biochem. Soc. Trans.
, vol.30
, pp. 1166-1169
-
-
Woodson, S.A.1
-
8
-
-
1842298212
-
From Levinthal to pathways to funnels
-
K.A. Dill, and H.S. Chan From Levinthal to pathways to funnels Nature Struct. Biol. 4 1997 10 19
-
(1997)
Nature Struct. Biol.
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
9
-
-
0027991626
-
Kinetic intermediates in RNA folding
-
P.P. Zarrinkar, and J.R. Williamson 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
-
11
-
-
0032549780
-
RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
-
B. Sclavi, M. Sullivan, M.R. Chance, M. Brenowitz, and S.A. Woodson 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
-
12
-
-
0034674420
-
A single-molecule study of RNA catalysis and folding
-
X. Zhuang, L.E. Bartley, H.P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu 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
-
13
-
-
0033520410
-
New pathways in folding of the Tetrahymena group I RNA enzyme
-
R. Russell, and D. Herschlag New pathways in folding of the Tetrahymena group I RNA enzyme J. Mol. Biol. 291 1999 1155 1167
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 1155-1167
-
-
Russell, R.1
Herschlag, D.2
-
14
-
-
0032575759
-
Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape
-
M.S. Rook, D.K. Treiber, and J.R. Williamson Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape J. Mol. Biol. 281 1998 609 620
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 609-620
-
-
Rook, M.S.1
Treiber, D.K.2
Williamson, J.R.3
-
15
-
-
0035946973
-
Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics
-
S.L. Heilman-Miller, J. Pan, D. Thirumalai, and S.A. Woodson Role of 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
-
17
-
-
0242636400
-
An alternative route for the folding of large RNAs: Apparent two-state folding by a group II intron ribozyme
-
L.J. Su, M. Brenowitz, and A.M. Pyle An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme J. Mol. Biol. 334 2003 639 652
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 639-652
-
-
Su, L.J.1
Brenowitz, M.2
Pyle, A.M.3
-
18
-
-
0029864990
-
The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme
-
P.P. Zarrinkar, and J.R. Williamson 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
-
19
-
-
0029874598
-
The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding [see comments]
-
P.P. Zarrinkar, and J.R. Williamson The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding [see comments] Nature Struct. Biol. 3 1996 432 438
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 432-438
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
-
20
-
-
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
-
B. Sclavi, S. Woodson, M. Sullivan, M.R. Chance, and M. Brenowitz 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
-
21
-
-
0037007009
-
Rapid compaction during RNA folding
-
R. Russell, I.S. Millett, M.W. Tate, L.W. Kwok, B. Nakatani, and S.M. Gruner Rapid compaction during RNA folding Proc Natl Acad. Sci. USA 99 2002 4266 4271
-
(2002)
Proc Natl Acad. Sci. USA
, vol.99
, pp. 4266-4271
-
-
Russell, R.1
Millett, I.S.2
Tate, M.W.3
Kwok, L.W.4
Nakatani, B.5
Gruner, S.M.6
-
22
-
-
0037039464
-
Exploring the folding landscape of a structured RNA
-
R. Russell, X. Zhuang, H.P. Babcock, I.S. Millett, S. Doniach, S. Chu, and D. Herschlag 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
-
23
-
-
0025361553
-
Predicting optimal and suboptimal secondary structure for RNA
-
J.A. Jaeger, D.H. Turner, and M. Zuker Predicting optimal and suboptimal secondary structure for RNA Methods Enzymol. 183 1990 281 306
-
(1990)
Methods Enzymol.
, vol.183
, pp. 281-306
-
-
Jaeger, J.A.1
Turner, D.H.2
Zuker, M.3
-
24
-
-
0032563297
-
Folding intermediates of a self-splicing RNA: Mispairing of the catalytic core
-
J. Pan, and S.A. Woodson 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
-
25
-
-
0034635353
-
Fast folding of a ribozyme by stabilizing core interactions: Evidence for multiple folding pathways in RNA
-
J. Pan, M.L. Deras, and S.A. Woodson 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
-
26
-
-
0034633940
-
Multiple folding pathways for the P4-P6 RNA domain
-
S.K. Silverman, M.L. Deras, S.A. Woodson, S.A. Scaringe, and T.R. Cech 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
-
27
-
-
0034641668
-
Folding mechanism of the Tetrahymena ribozyme P4-P6 domain
-
M.L. Deras, M. Brenowitz, C.Y. Ralston, M.R. Chance, and S.A. Woodson 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
-
28
-
-
0037466333
-
Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme
-
T. Uchida, K. Takamoto, Q. He, M.R. Chance, and M. Brenowitz Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme J. Mol. Biol. 328 2003 463 478
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 463-478
-
-
Uchida, T.1
Takamoto, K.2
He, Q.3
Chance, M.R.4
Brenowitz, M.5
-
29
-
-
0036894697
-
Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme
-
K. Takamoto, Q. He, S. Morris, M.R. Chance, and M. Brenowitz Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme Nature Struct. Biol. 9 2002 928 933
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 928-933
-
-
Takamoto, K.1
He, Q.2
Morris, S.3
Chance, M.R.4
Brenowitz, M.5
-
30
-
-
0042009114
-
The fastest global events in RNA folding: Electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme
-
R. Das, L.W. Kwok, I.S. Millett, Y. Bai, T.T. Mills, and J. Jacob The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme J. Mol. Biol. 332 2003 311 319
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 311-319
-
-
Das, R.1
Kwok, L.W.2
Millett, I.S.3
Bai, Y.4
Mills, T.T.5
Jacob, J.6
-
31
-
-
0024359787
-
Defining the inside and outside of a catalytic RNA molecule
-
J.A. Latham, and T.R. Cech 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
-
32
-
-
0025963132
-
Visualizing the higher order folding of a catalytic RNA molecule
-
D.W. Celander, and T.R. Cech 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
-
33
-
-
0029820625
-
Crystal structure of a group I ribozyme domain: Principles of RNA packing [see comments]
-
J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, and C.E. Kundrot Crystal structure of a group I ribozyme domain: principles of RNA packing [see comments] Science 273 1996 1678 1685
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
-
34
-
-
0034680558
-
A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding
-
N. Pastor, H. Weinstein, E. Jamison, and M. Brenowitz A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding J. Mol. Biol. 304 2000 55 68
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 55-68
-
-
Pastor, N.1
Weinstein, H.2
Jamison, E.3
Brenowitz, M.4
-
35
-
-
0033644180
-
Time-resolved synchrotron X-ray footprinting and its application to RNA folding
-
C.Y. Ralston, B. Sclavi, M. Sullivan, M.L. Deras, S.A. Woodson, M.R. Chance, and M. Brenowitz 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
-
36
-
-
0031013756
-
Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches
-
V. Petri, and M. Brenowitz Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches Curr. Opin. Biotechnol. 8 1997 36 44
-
(1997)
Curr. Opin. Biotechnol.
, vol.8
, pp. 36-44
-
-
Petri, V.1
Brenowitz, M.2
-
37
-
-
4444235862
-
Kinetics analysis of DNA-protein interactions by time resolved synchrotron X-ray footprinting
-
K.A. Johnson IRL Press at Oxford University Press Oxford
-
G.M. Dhavan, M.R. Chance, and M. Brenowitz Kinetics analysis of DNA-protein interactions by time resolved synchrotron X-ray footprinting K.A. Johnson Analysis of Macromolecules: A Practical Approach 2003 IRL Press at Oxford University Press Oxford 75 86
-
(2003)
Analysis of Macromolecules: A Practical Approach
, pp. 75-86
-
-
Dhavan, G.M.1
Chance, M.R.2
Brenowitz, M.3
-
38
-
-
0036816641
-
Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting"
-
M. Brenowitz, M.R. Chance, G. Dhavan, and K. Takamoto Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting" Curr. Opin. Struct. Biol. 12 2002 648 653
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 648-653
-
-
Brenowitz, M.1
Chance, M.R.2
Dhavan, G.3
Takamoto, K.4
-
39
-
-
4444384354
-
Data on the metal requirements on Tetrahymena pyriformis
-
R.P. Hall Data on the metal requirements on Tetrahymena pyriformis Trans. N Y Acad. Sci. 16 1954 418 419
-
(1954)
Trans. N Y Acad. Sci.
, vol.16
, pp. 418-419
-
-
Hall, R.P.1
-
40
-
-
0031790171
-
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor [see comments]
-
S. Basu, R.P. Rambo, J. Strauss-Soukup, J.H. Cate, A.R. Ferre-D'Amare, S.A. Strobel, and J.A. Doudna A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor [see comments] Nature Struct. Biol. 5 1998 986 992
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 986-992
-
-
Basu, S.1
Rambo, R.P.2
Strauss-Soukup, J.3
Cate, J.H.4
Ferre-D'Amare, A.R.5
Strobel, S.A.6
Doudna, J.A.7
-
41
-
-
1242274330
-
A guide to ions and RNA structure
-
D.E. Draper A guide to ions and RNA structure Rna 10 2004 335 343
-
(2004)
Rna
, vol.10
, pp. 335-343
-
-
Draper, D.E.1
-
42
-
-
0032192761
-
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
-
J.B. Murray, A.A. Seyhan, N.G. Walter, J.M. Burke, and W.G. Scott The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone Chem. Biol. 5 1998 587 595
-
(1998)
Chem. Biol.
, vol.5
, pp. 587-595
-
-
Murray, J.B.1
Seyhan, A.A.2
Walter, N.G.3
Burke, J.M.4
Scott, W.G.5
-
44
-
-
0030929889
-
A magnesium ion core at the heart of a ribozyme domain [see comments]
-
J.H. Cate, R.L. Hanna, and J.A. Doudna A magnesium ion core at the heart of a ribozyme domain [see comments] Nature Struct. Biol. 4 1997 553 558
-
(1997)
Nature Struct. Biol.
, vol.4
, pp. 553-558
-
-
Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
-
45
-
-
0032319210
-
Following the folding of RNA with time-resolved synchrotron X-ray footprinting
-
B. Sclavi, S. Woodson, M. Sullivan, M. Chance, and M. Brenowitz 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
-
46
-
-
0037035555
-
Linkage of monovalent and divalent ion binding in the folding of the p4-p6 domain of the Tetrahymena ribozyme
-
T. Uchida, Q. He, C.Y. Ralston, M. Brenowitz, and M.R. Chance Linkage of monovalent and divalent ion binding in the folding of the p4-p6 domain of the Tetrahymena ribozyme Biochemistry 41 2002 5799 5806
-
(2002)
Biochemistry
, vol.41
, pp. 5799-5806
-
-
Uchida, T.1
He, Q.2
Ralston, C.Y.3
Brenowitz, M.4
Chance, M.R.5
-
47
-
-
1642380887
-
Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures
-
R. Owczarzy, Y. You, B.G. Moreira, J.A. Manthey, L. Huang, M.A. Behlke, and J.A. Walder Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures Biochemistry 43 2004 3537 3554
-
(2004)
Biochemistry
, vol.43
, pp. 3537-3554
-
-
Owczarzy, R.1
You, Y.2
Moreira, B.G.3
Manthey, J.A.4
Huang, L.5
Behlke, M.A.6
Walder, J.A.7
-
48
-
-
0033565267
-
Nucleic acid duplex stability: Influence of base composition on cation effects
-
S. Nakano, M. Fujimoto, H. Hara, and N. Sugimoto Nucleic acid duplex stability: influence of base composition on cation effects Nucl. Acids Res. 27 1999 2957 2965
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 2957-2965
-
-
Nakano, S.1
Fujimoto, M.2
Hara, H.3
Sugimoto, N.4
-
49
-
-
0032549735
-
Kinetic intermediates trapped by native interactions in RNA folding
-
D.K. Treiber, M.S. Rook, P.P. Zarrinkar, and J.R. Williamson Kinetic intermediates trapped by native interactions in RNA folding Science 279 1998 1943 1946
-
(1998)
Science
, vol.279
, pp. 1943-1946
-
-
Treiber, D.K.1
Rook, M.S.2
Zarrinkar, P.P.3
Williamson, J.R.4
-
50
-
-
0033544723
-
The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
-
J. Pan, and S.A. Woodson The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA J. Mol. Biol. 294 1999 955 965
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 955-965
-
-
Pan, J.1
Woodson, S.A.2
-
51
-
-
0033607181
-
An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme
-
M.S. Rook, D.K. Treiber, and J.R. Williamson An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme Proc Natl Acad. Sci. USA 96 1999 12471 12476
-
(1999)
Proc Natl Acad. Sci. USA
, vol.96
, pp. 12471-12476
-
-
Rook, M.S.1
Treiber, D.K.2
Williamson, J.R.3
-
52
-
-
0024285808
-
Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes
-
A.J. Zaug, C.A. Grosshans, and T.R. Cech Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes Biochemistry 27 1988 8924 8931
-
(1988)
Biochemistry
, vol.27
, pp. 8924-8931
-
-
Zaug, A.J.1
Grosshans, C.A.2
Cech, T.R.3
-
53
-
-
0029963656
-
A simple method for 3′-labeling of RNA
-
Z. Huang, and J.W. Szostak A simple method for 3′-labeling of RNA Nucl. Acids Res. 24 1996 4360 4361
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 4360-4361
-
-
Huang, Z.1
Szostak, J.W.2
-
54
-
-
0022437260
-
Quantitative DNase footprint titration: A method for studying protein-DNA interactions
-
M. Brenowitz, D.F. Senear, M.A. Shea, and G.K. Ackers Quantitative DNase footprint titration: a method for studying protein-DNA interactions Methods Enzymol. 130 1986 132 181
-
(1986)
Methods Enzymol.
, vol.130
, pp. 132-181
-
-
Brenowitz, M.1
Senear, D.F.2
Shea, M.A.3
Ackers, G.K.4
-
55
-
-
0028441183
-
Representation of the secondary and tertiary structure of group I introns
-
T.R. Cech, S.H. Damberger, and R.R. Gutell Representation of the secondary and tertiary structure of group I introns Nature Struct. Biol. 1 1994 273 280
-
(1994)
Nature Struct. Biol.
, vol.1
, pp. 273-280
-
-
Cech, T.R.1
Damberger, S.H.2
Gutell, R.R.3
|