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3
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0033150677
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Structure, folding and catalysis of the small nucleolytic ribozymes
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Lilley D.M. Structure, folding and catalysis of the small nucleolytic ribozymes. Curr Opin Struct Biol. 9:1999;330-338.
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Lilley, D.M.1
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Mechanisms of ribozyme-mediated RNA cleavage
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Kuimelis R.G., McLaughlin L.W. Mechanisms of ribozyme-mediated RNA cleavage. Chem Rev. 98:1998;1027-1044.
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Chem Rev
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Kuimelis, R.G.1
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6
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0027183545
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Pyle A.M. Ribozymes: a distinct class of metalloenzymes. Science. 261:1993;709-714.
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Pyle, A.M.1
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A general two-metal-ion mechanism for catalytic RNA
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Steitz T.A., Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA. 90:1993;6498-6502.
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Steitz, T.A.1
Steitz, J.A.2
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8
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0033607225
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Three metal ions at the active site of the Tetrahymena group I ribozyme
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The authors have developed a quantitative fingerprinting approach to distinguish individual identities of critical metal ions in the group I intron.
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Shan S., Yoshida A., Sun S., Piccirilli J.A., Herschlag D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc Natl Acad Sci USA. 96:1999;12299-12304. The authors have developed a quantitative fingerprinting approach to distinguish individual identities of critical metal ions in the group I intron.
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Proc Natl Acad Sci USA
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Shan, S.1
Yoshida, A.2
Sun, S.3
Piccirilli, J.A.4
Herschlag, D.5
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11
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0033150681
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A chemogenetic approach to RNA function/structure analysis
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Strobel S.A. A chemogenetic approach to RNA function/structure analysis. Curr Opin Struct Biol. 9:1999;346-352.
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Curr Opin Struct Biol
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Strobel, S.A.1
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12
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0033102218
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A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme
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Through use of the powerful nucleotide analog interference mapping technique, the transition state of the Tetrahymena group I intron was found to be stabilized by a hydrogen-bonding base triad.
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Strobel S.A., Ortoleva-Donnelly L. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem Biol. 6:1999;153-165. Through use of the powerful nucleotide analog interference mapping technique, the transition state of the Tetrahymena group I intron was found to be stabilized by a hydrogen-bonding base triad.
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(1999)
Chem Biol
, vol.6
, pp. 153-165
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Strobel, S.A.1
Ortoleva-Donnelly, L.2
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13
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0032893740
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A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution
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Using phosphorothioate substitution, the authors found that a metal-ion interaction with a non-bridging oxygen position at the active site of the group I intron contributes to catalysis.
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Yoshida A., Sun S., Piccirilli J.A. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nat Struct Biol. 6:1999;318-321. Using phosphorothioate substitution, the authors found that a metal-ion interaction with a non-bridging oxygen position at the active site of the group I intron contributes to catalysis.
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(1999)
Nat Struct Biol
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Yoshida, A.1
Sun, S.2
Piccirilli, J.A.3
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14
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0032192761
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The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
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This study showed that three small ribozymes do not require divalent ions to function in the presence of high concentrations of monovalent cations. The exact role for monovalent ions in catalysis is undetermined.
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Murray J.B., Seyhan A.A., Walter N.G., Burke J.M., Scott W.G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol. 5:1998;587-595. This study showed that three small ribozymes do not require divalent ions to function in the presence of high concentrations of monovalent cations. The exact role for monovalent ions in catalysis is undetermined.
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(1998)
Chem Biol
, vol.5
, pp. 587-595
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Murray, J.B.1
Seyhan, A.A.2
Walter, N.G.3
Burke, J.M.4
Scott, W.G.5
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15
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0032497521
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Crystal structure of a hepatitis delta virus ribozyme
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The crystal structure of the product form of the genomic HDV ribozyme shows the active site cleft. It is proposed that Cys75 is involved in the catalytic scheme.
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Ferre-D'Amare A.R., Zhou K., Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature. 395:1998;567-574. The crystal structure of the product form of the genomic HDV ribozyme shows the active site cleft. It is proposed that Cys75 is involved in the catalytic scheme.
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(1998)
Nature
, vol.395
, pp. 567-574
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Ferre-D'Amare, A.R.1
Zhou, K.2
Doudna, J.A.3
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16
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0033215448
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Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
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Imidazole was found to rescue activity of a mutant antigenomic HDV ribozyme, which supports the theory that the missing nucleobase (Cys76) might be acting as a general base in the reaction mechanism. Mechanistic models are presented.
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Perrotta A.T., Shih I., Been M.D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science. 286:1999;123-126. Imidazole was found to rescue activity of a mutant antigenomic HDV ribozyme, which supports the theory that the missing nucleobase (Cys76) might be acting as a general base in the reaction mechanism. Mechanistic models are presented.
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(1999)
Science
, vol.286
, pp. 123-126
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Perrotta, A.T.1
Shih, I.2
Been, M.D.3
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17
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0030747007
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a shift at the active site of a lead-dependent ribozyme
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a shift at the active site of a lead-dependent ribozyme. J Am Chem Soc. 119:1997;6621-6628.
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(1997)
J Am Chem Soc
, vol.119
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Legault, P.1
Pardi, A.2
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18
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0032773132
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Enhancement of RNA self-cleavage by micellar catalysis
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The authors used the hydrophobic interior or micelles to simulate the possible effects of a intramolecular environment and found that the reaction rate of a self-cleaving motif was increased compared with the rate in aqueous solution.
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Riepe A., Beier H., Gross H.J. Enhancement of RNA self-cleavage by micellar catalysis. FEBS Lett. 457:1999;193-199. The authors used the hydrophobic interior or micelles to simulate the possible effects of a intramolecular environment and found that the reaction rate of a self-cleaving motif was increased compared with the rate in aqueous solution.
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(1999)
FEBS Lett
, vol.457
, pp. 193-199
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Riepe, A.1
Beier, H.2
Gross, H.J.3
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19
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0030476765
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Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
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Scott W.G., Murray J.B., Arnold J.R.P., Stoddard B.L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:1996;2065-2069.
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Science
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Scott, W.G.1
Murray, J.B.2
Arnold, J.R.P.3
Stoddard, B.L.4
Klug, A.5
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20
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0032489357
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The structural basis of hammerhead ribozyme self-cleavage
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Murray J.B., Terwey D.P., Maloney L., Karpeisky A., Usman N., Beigelman L., Scott W.G. The structural basis of hammerhead ribozyme self-cleavage. Cell. 92:1998;665-673.
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(1998)
Cell
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Murray, J.B.1
Terwey, D.P.2
Maloney, L.3
Karpeisky, A.4
Usman, N.5
Beigelman, L.6
Scott, W.G.7
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21
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0031882388
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A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate
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2+. Implications of site preference in conjunction with possible ion roles are discussed.
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2+. Implications of site preference in conjunction with possible ion roles are discussed.
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(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 542-547
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Lott, W.B.1
Pontius, B.W.2
Von Hippel, P.H.3
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22
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0033555778
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A re-investigation of the thio effect at the hammerhead cleavage site
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Following recent doubts about the interpretation of phosphorothioate substitution experiments, this paper pioneers a careful way of designing and analyzing thioate substitution experiments.
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Scott E.C., Uhlenbeck O.C. A re-investigation of the thio effect at the hammerhead cleavage site. Nucleic Acids Res. 27:1999;479-484. Following recent doubts about the interpretation of phosphorothioate substitution experiments, this paper pioneers a careful way of designing and analyzing thioate substitution experiments.
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(1999)
Nucleic Acids Res
, vol.27
, pp. 479-484
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Scott, E.C.1
Uhlenbeck, O.C.2
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23
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0033607198
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Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate
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Wang S., Karbstein K., Peracchi A., Beigelman L., Herschlag D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry. 38:1999;14363-14378.
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(1999)
Biochemistry
, vol.38
, pp. 14363-14378
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Wang, S.1
Karbstein, K.2
Peracchi, A.3
Beigelman, L.4
Herschlag, D.5
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24
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0033178245
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Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme
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Lafontaine D.A., Ananvoranich S., Perreault J.P. Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme. Nucleic Acids Res. 27:1999;3236-3243.
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(1999)
Nucleic Acids Res
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Lafontaine, D.A.1
Ananvoranich, S.2
Perreault, J.P.3
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25
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0032832044
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Ribozyme cleavage of a 2,5-phosphodiester linkage: Mechanism and a restricted divalent metal-ion requirement
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2+ is used. This metal preference suggests that there is an important metal coordination to the active site. Implications of this catalytic promiscuity are also discussed.
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2+ is used. This metal preference suggests that there is an important metal coordination to the active site. Implications of this catalytic promiscuity are also discussed.
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(1999)
RNA
, vol.5
, pp. 1140-1148
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Shih, I.H.1
Been, M.D.2
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26
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0033607181
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An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme
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This study leads to a discussion examining the possibility that cations can be harmful as well as helpful to the folding process.
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Rook M.S., Treiber D.K., Williamson J.R. An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme. Proc Natl Acad Sci USA. 96:1999;12471-12476. This study leads to a discussion examining the possibility that cations can be harmful as well as helpful to the folding process.
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(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 12471-12476
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Rook, M.S.1
Treiber, D.K.2
Williamson, J.R.3
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27
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0033065083
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Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics
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Pan J., Thirumalai D., Woodson S.A. Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics, and kinetics. Proc Natl Acad Sci USA. 96:1999;6149-6154.
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(1999)
Proc Natl Acad Sci USA
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, pp. 6149-6154
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Pan, J.1
Thirumalai, D.2
Woodson, S.A.3
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28
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0032549735
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Kinetic intermediates trapped by native interactions in RNA folding
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Kinetic traps are typically thought of as non-native structures. This study finds that early stable formation of native structure can lead to a folding barrier.
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Treiber D.K., Rook M.S., Zarrinkar P.P., Williamson J.R. Kinetic intermediates trapped by native interactions in RNA folding. Science. 279:1998;1943-1946. Kinetic traps are typically thought of as non-native structures. This study finds that early stable formation of native structure can lead to a folding barrier.
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(1998)
Science
, vol.279
, pp. 1943-1946
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Treiber, D.K.1
Rook, M.S.2
Zarrinkar, P.P.3
Williamson, J.R.4
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29
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0029820625
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Crystal structure of a group I ribozyme domain: Principles of RNA packing
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Cate J.H., Gooding A.R., Podell E., Zhou K., Golden B.L., Kundrot C.E., Cech T.R., Doudna J.A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
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(1996)
Science
, vol.273
, pp. 1678-1685
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Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
Cech, T.R.7
Doudna, J.A.8
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30
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0032549780
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RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting
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Sclavi B., Sullivan M., Chance M.R., Brenowitz M., Woodson S.A. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science. 279:1998;1940-1943.
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(1998)
Science
, vol.279
, pp. 1940-1943
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Sclavi, B.1
Sullivan, M.2
Chance, M.R.3
Brenowitz, M.4
Woodson, S.A.5
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31
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0030929889
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A magnesium ion core at the heart of a ribozyme domain
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Cate J.H., Hanna R.L., Doudna J.A. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 4:1997;553-558.
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(1997)
Nat Struct Biol
, vol.4
, pp. 553-558
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Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
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32
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0033520410
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New pathways in folding of the Tetrahymena group I RNA enzyme
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The authors discuss alternate folding pathways of the group I intron in terms of folding landscapes and discuss the implications of this model.
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Russell R., Herschlag D. New pathways in folding of the Tetrahymena group I RNA enzyme. J Mol Biol. 291:1999;1155-1167. The authors discuss alternate folding pathways of the group I intron in terms of folding landscapes and discuss the implications of this model.
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(1999)
J Mol Biol
, vol.291
, pp. 1155-1167
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Russell, R.1
Herschlag, D.2
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33
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0032575759
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Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape
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It was found in this study that fast-folding variants of the group I intron included mutations in the P5abc region that destabilize the native structure of this metal-binding subdomain of the ribozyme.
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Rook M.S., Treiber D.K., Williamson J.R. Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape. J Mol Biol. 281:1998;609-620. It was found in this study that fast-folding variants of the group I intron included mutations in the P5abc region that destabilize the native structure of this metal-binding subdomain of the ribozyme.
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(1998)
J Mol Biol
, vol.281
, pp. 609-620
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Rook, M.S.1
Treiber, D.K.2
Williamson, J.R.3
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34
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0031465967
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'New view' of protein folding reconciled with the old through multiple unfolding simulations
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Lazaridis T., Karplus M. 'New view' of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1997;1928-1931.
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(1997)
Science
, vol.278
, pp. 1928-1931
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Lazaridis, T.1
Karplus, M.2
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