Folding kinetics of large RNAs.

[1]  I. Hofacker,et al.  Beyond energy minimization: approaches to the kinetic folding of RNA , 2008 .

[2]  Tao Pan,et al.  Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures , 2007, Proceedings of the National Academy of Sciences.

[3]  C. Yanofsky,et al.  RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria. , 2007, RNA.

[4]  Rolf Backofen,et al.  Variations on RNA folding and alignment: lessons from Benasque , 2007, Journal of mathematical biology.

[5]  Lydia Tapia,et al.  Tools for Simulating and Analyzing RNA Folding Kinetics , 2007, RECOMB.

[6]  Shi-Jie Chen,et al.  Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. , 2007, Journal of molecular biology.

[7]  Tao Pan,et al.  RNA folding during transcription. , 2006, Annual review of biophysics and biomolecular structure.

[8]  Andrey A. Mironov,et al.  Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA , 2006, J. Bioinform. Comput. Biol..

[9]  Song Cao,et al.  Predicting RNA folding thermodynamics with a reduced chain representation model. , 2005, RNA.

[10]  Paul Gollnick,et al.  Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. , 2005, Annual review of genetics.

[11]  D. Crothers,et al.  The kinetics of ligand binding by an adenine-sensing riboswitch. , 2005, Biochemistry.

[12]  Michael T. Wolfinger,et al.  Efficient computation of RNA folding dynamics , 2004 .

[13]  R. Micura,et al.  On Secondary Structure Rearrangements and Equilibria of Small RNAs , 2003, Chembiochem : a European journal of chemical biology.

[14]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[15]  C. Pleij,et al.  Self-induced structural switches in RNA. , 2002, Biochimie.

[16]  C. Yanofsky,et al.  Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[17]  Michael T. Wolfinger,et al.  Barrier Trees of Degenerate Landscapes , 2002 .

[18]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[19]  J. van Duin,et al.  Translational control by delayed RNA folding: identification of the kinetic trap. , 2001, RNA.

[20]  P. Higgs RNA secondary structure: physical and computational aspects , 2000, Quarterly Reviews of Biophysics.

[21]  D. Bartel,et al.  One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.

[22]  E. Siggia,et al.  Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[23]  P. Schuster,et al.  RNA folding at elementary step resolution. , 1999, RNA.

[24]  C. Pleij,et al.  Metastable structures and refolding kinetics in hok mRNA of plasmid R1. , 1999, RNA.

[25]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[26]  M Cieplak,et al.  Energy landscapes, supergraphs, and "folding funnels" in spin systems. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[27]  J. Doye,et al.  Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters , 1999, cond-mat/9903305.

[28]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[29]  Mark A. Miller,et al.  Archetypal energy landscapes , 1998, Nature.

[30]  A. T. Perrotta,et al.  A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation. , 1998, Journal of molecular biology.

[31]  P. Higgs,et al.  Barrier heights between ground states in a model of RNA secondary structure , 1998 .

[32]  A. Gultyaev,et al.  Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3'-end triggers structural rearrangements that allow translation and antisense RNA binding. , 1997, Journal of molecular biology.

[33]  R. Poot,et al.  RNA folding kinetics regulates translation of phage MS2 maturation gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Detlev Riesner,et al.  Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation , 1997, The EMBO journal.

[35]  M. Karplus,et al.  The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics , 1997 .

[36]  Paul Higgs,et al.  Evidence for kinetic effects in the folding of large RNA molecules , 1996 .

[37]  J. van Duin,et al.  RNA phage KU1 has an insertion of 18 nucleotides in the start codon of its lysis gene. , 1996, Virology.

[38]  G. Steger,et al.  Description of RNA folding by "simulated annealing". , 1996, Journal of molecular biology.

[39]  K. Dill,et al.  Statistical thermodynamics of double‐stranded polymer molecules , 1995 .

[40]  P. Frantsuzov,et al.  Statistical description of nucleic acid secondary structure folding. , 1995, Journal of biomolecular structure & dynamics.

[41]  C. Pleij,et al.  The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.

[42]  J. van Duin,et al.  Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? , 1995, RNA.

[43]  T. H. Klotz,et al.  "Valley structures" in the phase space of a finite 3d ISING spin glass with , 1994 .

[44]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[45]  J. Duin,et al.  Translational control by a long range RNA-RNA interaction; a basepair substitution analysis. , 1993 .

[46]  R. Luce,et al.  In vitro recombination and terminal elongation of RNA by Q beta replicase. , 1992, The EMBO journal.

[47]  A. Gultyaev,et al.  The computer simulation of RNA folding involving pseudoknot formation. , 1991, Nucleic acids research.

[48]  J. Abrahams,et al.  Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. , 1990, Nucleic acids research.

[49]  J. van Duin,et al.  Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. , 1990, Journal of molecular biology.

[50]  M. Zuker On finding all suboptimal foldings of an RNA molecule. , 1989, Science.

[51]  B. Berkhout,et al.  Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene. , 1987, Journal of molecular biology.

[52]  S. Molin,et al.  Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A A Mironov,et al.  A kinetic approach to the prediction of RNA secondary structures. , 1985, Journal of biomolecular structure & dynamics.

[54]  H. M. Martinez,et al.  An RNA folding rule , 1984, Nucleic Acids Res..

[55]  R. Contreras,et al.  A-Protein gene of bacteriophage MS2 , 1975, Nature.

[56]  W. Olson,et al.  Configurational statistics of polynucleotide chains. A single virtual bond treatment. , 1975, Macromolecules.

[57]  D. Crothers,et al.  The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. , 1974, Journal of molecular biology.

[58]  W. Fiers,et al.  Nucleotide Sequence of the Gene Coding for the Bacteriophage MS2 Coat Protein , 1972, Nature.

[59]  M. Eigen,et al.  Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. , 1971, Journal of molecular biology.

[60]  M. Eigen,et al.  Co-operative non-enzymic base recognition. I. Thermodynamics of the helix-coil transition of oligoriboadenylic acids at ACIDIC PH. , 1970, Journal of molecular biology.

[61]  E. Wagner,et al.  RNA antitoxins. , 2007, Current opinion in microbiology.

[62]  P. Schuster,et al.  Statistics of RNA melting kinetics , 2004, European Biophysics Journal.

[63]  M. Gelfand,et al.  Riboswitches: the oldest mechanism for the regulation of gene expression? , 2004, Trends in genetics : TIG.

[64]  Peter F. Stadler,et al.  Exact Folding Dynamics of RNA Secondary Structures , 2003 .

[65]  D. Thirumalai,et al.  Early events in RNA folding. , 2001, Annual review of physical chemistry.

[66]  E. Westhof,et al.  Hierarchy and dynamics of RNA folding. , 1997, Annual review of biophysics and biomolecular structure.

[67]  P. Higgs Thermodynamic properties of transfer RNA: a computational study , 1995 .

[68]  T. H. Klotz,et al.  "valley Structures" in the Phase Space of a Nite 3d Ising Spin Glass with I Inter- Actions , 1993 .

[69]  J. van Duin,et al.  Translational control by a long range RNA-RNA interaction; a basepair substitution analysis. , 1993, Nucleic acids research.

[70]  L. Frost,et al.  The physiology and biochemistry of pili. , 1988, Advances in microbial physiology.

[71]  D. Sankoff,et al.  RNA secondary structures and their prediction , 1984 .