Hammerhead redux: Does the new structure fit the old biochemical data?

被引：50

作者：

Nelson, Jennifer A. ^{[1
]}

Uhlenbeck, Olke C. ^{[1
]}

机构：

[1] Northwestern Univ, Dept Biochem Mol Biol & Cell Biol, Evanston, IL 60208 USA

来源：

RNA | 2008年 / 14卷 / 04期

关键词：

RNA dynamics; ribozyme; RNA crystal structure; RNA structure-function; catalytic core;

D O I：

10.1261/rna.912608

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The cleavage rates of 78 hammerhead ribozymes containing structurally conservative chemical modifications were collected from the literature and compared to the recently determined crystal structure of the Schistosoma mansoni hammerhead. With only a few exceptions, the biochemical data were consistent with the structure, indicating that the new structure closely resembles the transition state of the reaction. Since all the biochemical data were collected on minimal hammerheads that have a very different structure, the minimal hammerhead must be dynamic and occasionally adopt the quite different extended structure in order to cleave.

引用

页码：605 / 615

页数：11

共 57 条

[1] Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn [J].

Alam, S ;

Grum-Tokars, V ;

Krucinska, J ;

Kundracik, ML ;

Wedekind, JE .

BIOCHEMISTRY, 2005, 44 (44) :14396-14408

[2] Inter-strand C-H center dot center dot center dot O hydrogen bonds stabilizing four-stranded intercalated molecules: Stereoelectronic effects of 04' in cytosine-rich DNA [J].

Berger, I ;

Egli, M ;

Rich, A .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (22) :12116-12121

[3] The structure-function dilemma of the hammer head ribozyme [J].

Blount, KE ;

Uhlenbeck, OC .

ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 2005, 34 :415-440

[4] Steric interference modification of the hammerhead ribozyme [J].

Blount, KF ;

Grover, NL ;

Mokler, V ;

Beigelman, L ;

Uhlenbeck, OC .

CHEMISTRY & BIOLOGY, 2002, 9 (09) :1009-1016

[5] Chemically modified hammerhead ribozymes with improved catalytic rates [J].

Burgin, AB ;

Gonzalez, C ;

MatulicAdamic, J ;

Karpeisky, AM ;

Usman, N ;

McSwiggen, JA ;

Beigelman, L .

BIOCHEMISTRY, 1996, 35 (45) :14090-14097

[6] Efficient ligation of the Schistosoma hammerhead ribozyme [J].

Canny, Marella D. ;

Jucker, Fiona M. ;

Pardi, Arthur .

BIOCHEMISTRY, 2007, 46 (12) :3826-3834

[7] Fast cleavage kinetics of a natural hammerhead ribozyme [J].

Canny, MD ;

Jucker, FM ;

Kellogg, E ;

Khvorova, A ;

Jayasena, SD ;

Pardi, A .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (35) :10848-10849

[8] Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads:: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads [J].

Carbonell, Alberto ;

De la Pena, Marcos ;

Flores, Ricardo ;

Gago, Selma .

NUCLEIC ACIDS RESEARCH, 2006, 34 (19) :5613-5622

[9] General acid catalysis by the hepatitis delta virus ribozyme [J].

Das, SR ;

Piccirilli, JA .

NATURE CHEMICAL BIOLOGY, 2005, 1 (01) :45-52

[10] Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity [J].

De la Peña, M ;

Gago, S ;

Flores, R .

EMBO JOURNAL, 2003, 22 (20) :5561-5570

← 1 2 3 4 5 6 →