Beyond energy minimization:: approaches to the kinetic folding of RNA

被引：34

作者：

Flamm, Christoph ^{[1
]}

Hofacker, Ivo L. ^{[1
]}

机构：

[1] Univ Vienna, Inst Theoret Chem, A-1090 Vienna, Austria

来源：

MONATSHEFTE FUR CHEMIE | 2008年 / 139卷 / 04期

基金：

奥地利科学基金会;

关键词：

RNA folding kinetics; Co-transcriptional folding; folding pathway; metastable structures;

D O I：

10.1007/s00706-008-0895-3

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

The term RNA folding is often used synonymously with the prediction of equilibrium structures. Yet many RNAs function thanks to their ability to undergo structural changes. In this contribution we present a systematic overview of existing approaches to the prediction of RNA folding kinetics, and in particular discuss the strengths and limitations of each method.

引用

页码：447 / 457

页数：11

共 77 条

[1] Asymmetry in RNA pseudoknots: observation and theory [J].

Aalberts, DP ;

Hodas, NO .

NUCLEIC ACIDS RESEARCH, 2005, 33 (07) :2210-2214

[2] PREDICTION OF RNA SECONDARY STRUCTURE, INCLUDING PSEUDOKNOTTING, BY COMPUTER-SIMULATION [J].

ABRAHAMS, JP ;

VANDENBERG, M ;

VANBATENBURG, E ;

PLEIJ, C .

NUCLEIC ACIDS RESEARCH, 1990, 18 (10) :3035-3044

[3] Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals [J].

Artsimovitch, I ;

Landick, R .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (13) :7090-7095

[4] Sequence-dependent kinetic model for transcription elongation by RNA polymerase [J].

Bai, L ;

Shundrovsky, A ;

Wang, MD .

JOURNAL OF MOLECULAR BIOLOGY, 2004, 344 (02) :335-349

[5] Single-molecule analysis of RNA polymerase transcription [J].

Bai, Lu ;

Santangelo, Thomas J. ;

Wang, Michelle D. .

ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 2006, 35 :343-360

[6] Topological constraints in nucleic acid hybridization kinetics [J].

Bois, JS ;

Venkataraman, S ;

Choi, HM ;

Spakowitz, AJ ;

Wang, ZG ;

Pierce, NA .

NUCLEIC ACIDS RESEARCH, 2005, 33 (13) :4090-4095

[7] NEW ALGORITHM FOR MONTE-CARLO SIMULATION OF ISING SPIN SYSTEMS [J].

BORTZ, AB ;

KALOS, MH ;

LEBOWITZ, JL .

JOURNAL OF COMPUTATIONAL PHYSICS, 1975, 17 (01) :10-18

[8] Delocalization transitions of semiflexible manifolds -: art. no. 061502 [J].

Bundschuh, R ;

Lässig, M .

PHYSICAL REVIEW E, 2002, 65 (06)

[9] Predicting RNA folding thermodynamics with a reduced chain representation model [J].

Cao, S ;

Chen, SJ .

RNA, 2005, 11 (12) :1884-1897

[10] Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity [J].

Cao, Song ;

Chen, Shi-Jie .

JOURNAL OF MOLECULAR BIOLOGY, 2007, 367 (03) :909-924

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