Literature DB >> 10744018

RNA folding at elementary step resolution.

C Flamm1, W Fontana, I L Hofacker, P Schuster.   

Abstract

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational landscape and the folding kinetics for a number of examples based on artificial and natural sequences, including the influence of base modification in tRNAs.

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Year:  2000        PMID： 10744018      PMCID： PMC1369916          DOI： 10.1017/s1355838200992161

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


  13 in total

1.  Complete suboptimal folding of RNA and the stability of secondary structures.

Authors:  S Wuchty; W Fontana; I L Hofacker; P Schuster
Journal:  Biopolymers       Date:  1999-02       Impact factor: 2.505

2.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure.

Authors:  J S McCaskill
Journal:  Biopolymers       Date:  1990 May-Jun       Impact factor: 2.505

3.  The computer simulation of RNA folding pathways using a genetic algorithm.

Authors:  A P Gultyaev; F H van Batenburg; C W Pleij
Journal:  J Mol Biol       Date:  1995-06-30       Impact factor: 5.469

4.  A computer model of evolutionary optimization.

Authors:  W Fontana; P Schuster
Journal:  Biophys Chem       Date:  1987-05-09       Impact factor: 2.352

5.  Model calculations on the kinetics of oligonucleotide double helix coil transitions. Evidence for a fast chain sliding reaction.

Authors:  D Pörschke
Journal:  Biophys Chem       Date:  1974-08       Impact factor: 2.352

6.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.

Authors:  M Zuker; P Stiegler
Journal:  Nucleic Acids Res       Date:  1981-01-10       Impact factor: 16.971

7.  Fast algorithm for predicting the secondary structure of single-stranded RNA.

Authors:  R Nussinov; A B Jacobson
Journal:  Proc Natl Acad Sci U S A       Date:  1980-11       Impact factor: 11.205

8.  Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.

Authors:  A R Banerjee; J A Jaeger; D H Turner
Journal:  Biochemistry       Date:  1993-01-12       Impact factor: 3.162

9.  Description of RNA folding by "simulated annealing".

Authors:  M Schmitz; G Steger
Journal:  J Mol Biol       Date:  1996-01-12       Impact factor: 5.469

10.  Statistical description of nucleic acid secondary structure folding.

Authors:  A A Suvernev; P A Frantsuzov
Journal:  J Biomol Struct Dyn       Date:  1995-08
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  94 in total

1.  Design of multistable RNA molecules.

Authors:  C Flamm; I L Hofacker; S Maurer-Stroh; P F Stadler; M Zehl
Journal:  RNA       Date:  2001-02       Impact factor: 4.942

2.  RNA hairpin-folding kinetics.

Authors:  Wenbing Zhang; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-12       Impact factor: 11.205

3.  Small worlds in RNA structures.

Authors:  Stefan Wuchty
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

4.  Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.

Authors:  Eric J Sorin; Young Min Rhee; Bradley J Nakatani; Vijay S Pande
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

5.  Paradigms for computational nucleic acid design.

Authors:  Robert M Dirks; Milo Lin; Erik Winfree; Niles A Pierce
Journal:  Nucleic Acids Res       Date:  2004-02-27       Impact factor: 16.971

6.  Predicting secondary structural folding kinetics for nucleic acids.

Authors:  Peinan Zhao; Wen-Bing Zhang; Shi-Jie Chen
Journal:  Biophys J       Date:  2010-04-21       Impact factor: 4.033

7.  BarMap: RNA folding on dynamic energy landscapes.

Authors:  Ivo L Hofacker; Christoph Flamm; Christian Heine; Michael T Wolfinger; Gerik Scheuermann; Peter F Stadler
Journal:  RNA       Date:  2010-05-26       Impact factor: 4.942

8.  Computational approaches for RNA energy parameter estimation.

Authors:  Mirela Andronescu; Anne Condon; Holger H Hoos; David H Mathews; Kevin P Murphy
Journal:  RNA       Date:  2010-10-12       Impact factor: 4.942

9.  Understanding the kinetic mechanism of RNA single base pair formation.

Authors:  Xiaojun Xu; Tao Yu; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-22       Impact factor: 11.205

10.  Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.

Authors:  Eric A Josephs; D Dewran Kocak; Christopher J Fitzgibbon; Joshua McMenemy; Charles A Gersbach; Piotr E Marszalek
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971
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