Secondary structure prediction of interacting RNA molecules.

[1]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[2]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[3]  J. Wetmur.  DNA probes: applications of the principles of nucleic acid hybridization. , 1991, Critical reviews in biochemistry and molecular biology.

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

[5]  D. Turner,et al.  Predicting thermodynamic properties of RNA. , 1995, Methods in enzymology.

[6]  E. Jankowsky,et al.  Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme. , 1996, Nucleic acids research.

[7]  I. H. Öğüş,et al.  NATO ASI Series , 1997 .

[8]  I. Tinoco,et al.  The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement. , 1997, Journal of molecular biology.

[9]  G. Sczakiel,et al.  The subcellular localization and length of hammerhead ribozymes determine efficacy in human cells. , 1997, Nucleic acids research.

[10]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Breaker,et al.  Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. , 1998, Nucleic acids research.

[12]  N. Vaish,et al.  Recent developments in the hammerhead ribozyme field. , 1998, Nucleic acids research.

[13]  Q. Yu,et al.  Cleavage of Highly Structured Viral RNA Molecules by Combinatorial Libraries of Hairpin Ribozymes , 1998, The Journal of Biological Chemistry.

[14]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[15]  B. Séraphin,et al.  A role for U2/U6 helix Ib in 5' splice site selection. , 1998, RNA.

[16]  I. Shih,et al.  Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement. , 1999, RNA.

[17]  E Rivas,et al.  A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.

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

[19]  D. Turner,et al.  Predicting oligonucleotide affinity to nucleic acid targets. , 1999, RNA.

[20]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .

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

[22]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. , 1999, Biochemistry.

[23]  S. Müller,et al.  RNA double cleavage by a hairpin-derived twin ribozyme. , 2000, Nucleic acids research.

[24]  D. Pecchia,et al.  Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer. , 2000, RNA.

[25]  John M. Burke,et al.  A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis. , 2001, Biochemistry.

[26]  M. Legiewicz,et al.  Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions. , 2001, Nucleic acids research.

[27]  A. Ferré-D’Amaré,et al.  Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis , 2001, Nature.

[28]  F. Major,et al.  Functional involvement of G8 in the hairpin ribozyme cleavage mechanism , 2001, The EMBO journal.

[29]  A. Barroso-deljesús,et al.  Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self‐cleaving RNA library , 2001, EMBO reports.

[30]  Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure , 2002, DNA.

[31]  R. Lührmann,et al.  Direct probing of RNA structure and RNA-protein interactions in purified HeLa cell's and yeast spliceosomal U4/U6.U5 tri-snRNP particles. , 2002, Journal of molecular biology.

[32]  D. Turner,et al.  Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. , 2002, Biochemistry.

[33]  K. Taira,et al.  Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity. , 2002, Nucleic acids research.

[34]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[35]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[36]  Niles A. Pierce,et al.  A partition function algorithm for nucleic acid secondary structure including pseudoknots , 2003, J. Comput. Chem..

[37]  Mirela Andronescu,et al.  Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands , 2003 .

[38]  A D Tsodikov,et al.  Thermodynamic criteria for high hit rate antisense oligonucleotide design. , 2003, Nucleic acids research.

[39]  Jian-Ying Wang,et al.  Modeling hybridization kinetics. , 2003, Mathematical biosciences.

[40]  Substrate specificity and reaction kinetics of an X-motif ribozyme. , 2003, RNA.

[41]  Weixiong Zhang,et al.  An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots , 2004, Bioinform..

[42]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[43]  D. Koslowsky,et al.  Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of a gRNA bound to its cognate mRNA. , 2006, RNA.