메뉴 건너뛰기




Volumn 345, Issue 5, 2005, Pages 987-1001

Secondary structure prediction of interacting RNA molecules

Author keywords

dynamic programming; interacting RNA molecules; ribozymes; RNA secondary structure prediction; sub optimal structures

Indexed keywords

DNA; NUCLEIC ACID; NUCLEOTIDE; RIBOZYME; RNA;

EID: 11844254846     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.10.082     Document Type: Article
Times cited : (159)

References (42)
  • 1
    • 0004052742 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • J. Barciszewski B.F.C. Clark RNA Biochemistry and Biotechnology Kluwer Academic Publishers Dodretch
    • M. Zuker, D.H. Mathews, and D.H. Turner Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide J. Barciszewski B.F.C. Clark RNA Biochemistry and Biotechnology NATO ASI Series 1999 Kluwer Academic Publishers Dodretch
    • (1999) NATO ASI Series
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3
  • 2
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • I.L. Hofacker, M. Fekete, and P.F. Stadler Secondary structure prediction for aligned RNA sequences J. Mol. Biol. 319 2002 1059 1066
    • (2002) J. Mol. Biol. , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 4
    • 0037401145 scopus 로고    scopus 로고
    • Modelling hybridization kinetics
    • J.-Y. Wang, and K. Drlica Modelling hybridization kinetics Math. Biosci. 183 2003 37 47
    • (2003) Math. Biosci. , vol.183 , pp. 37-47
    • Wang, J.-Y.1    Drlica, K.2
  • 5
    • 0032483347 scopus 로고    scopus 로고
    • Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes
    • Q. Yu, D.B. Pecchia, S.L. Kigsley, J.E. Heckman, and H.M. Burke Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes J. Biol. Chem. 273 1998 23524 23533
    • (1998) J. Biol. Chem. , vol.273 , pp. 23524-23533
    • Yu, Q.1    Pecchia, D.B.2    Kigsley, S.L.3    Heckman, J.E.4    Burke, H.M.5
  • 6
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucl. Acids Res. 31 2003 3406 3415
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 8
  • 9
    • 0035687548 scopus 로고    scopus 로고
    • Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library
    • A. Barroso-delJesus, and A. Berzal-Herranz Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library EMBO Rep. 2 2001 1112 1118
    • (2001) EMBO Rep. , vol.2 , pp. 1112-1118
    • Barroso-Deljesus, A.1    Berzal-Herranz, A.2
  • 10
    • 2642555548 scopus 로고    scopus 로고
    • An autonomous molecular computer for logical control of gene expression
    • Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, and E. Shapiro An autonomous molecular computer for logical control of gene expression Nature 429 2004 423 429
    • (2004) Nature , vol.429 , pp. 423-429
    • Benenson, Y.1    Gil, B.2    Ben-Dor, U.3    Adar, R.4    Shapiro, E.5
  • 11
  • 12
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 13
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbour thermodynamics
    • J. SantaLucia Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbour thermodynamics Proc. Natl Acad. Sci. USA 92 1998 1460 1465
    • (1998) Proc. Natl Acad. Sci. USA , vol.92 , pp. 1460-1465
    • Santalucia, J.1    Jr2
  • 14
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • M. Zuker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucl. Acids Res. 9 1981 133 148
    • (1981) Nucl. Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 15
    • 0025944267 scopus 로고
    • DNA probes: Applications of the principles of nucleic acid hybridization
    • J.G. Wetmur DNA probes: applications of the principles of nucleic acid hybridization Crit. Rev. Biochem. Mol. Biol. 26 1991 227 259
    • (1991) Crit. Rev. Biochem. Mol. Biol. , vol.26 , pp. 227-259
    • Wetmur, J.G.1
  • 16
    • 0033080745 scopus 로고    scopus 로고
    • Complete sub-optimal folding of RNA and the stability of secondary structures
    • S. Wuchty, W. Fontana, I.L. Hofacker, and P. Schuster Complete sub-optimal folding of RNA and the stability of secondary structures Biopolymers 49 1999 145 165
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 17
    • 0036606177 scopus 로고    scopus 로고
    • 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
    • Y. Kasai, H. Shizuku, Y. Takagi, M. Warashina, and K. Taira 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 Nucl. Acids Res. 30 2002 2383 2389
    • (2002) Nucl. Acids Res. , vol.30 , pp. 2383-2389
    • Kasai, Y.1    Shizuku, H.2    Takagi, Y.3    Warashina, M.4    Taira, K.5
  • 18
    • 0032403146 scopus 로고    scopus 로고
    • Recent developments in the hammerhead ribozyme field
    • N.K. Vaish, A.R. Kore, and F. Eckstein Recent developments in the hammerhead ribozyme field Nucl. Acids Res. 26 1998 5237 5242
    • (1998) Nucl. Acids Res. , vol.26 , pp. 5237-5242
    • Vaish, N.K.1    Kore, A.R.2    Eckstein, F.3
  • 20
    • 0034651754 scopus 로고    scopus 로고
    • RNA double cleavage by a hairpin-derived twin ribozyme
    • C. Schmidt, R. Welz, and S. Miller RNA double cleavage by a hairpin-derived twin ribozyme Nucl. Acids Res. 28 2000 886 894
    • (2000) Nucl. Acids Res. , vol.28 , pp. 886-894
    • Schmidt, C.1    Welz, R.2    Miller, S.3
  • 21
    • 0035848837 scopus 로고    scopus 로고
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
    • P.B. Rupert, and A.R. Ferre-d'Amare Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410 2001 780 786
    • (2001) Nature , vol.410 , pp. 780-786
    • Rupert, P.B.1    Ferre-D'Amare, A.R.2
  • 22
    • 0034004464 scopus 로고    scopus 로고
    • Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer
    • D. Vitiello, D.B. Pecchia, and J.M. Burke Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer RNA 6 2000 628 637
    • (2000) RNA , vol.6 , pp. 628-637
    • Vitiello, D.1    Pecchia, D.B.2    Burke, J.M.3
  • 23
    • 0035957257 scopus 로고    scopus 로고
    • A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis
    • K.J. Hampel, and J.M. Burke A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis Biochemistry 40 2001 3723 3729
    • (2001) Biochemistry , vol.40 , pp. 3723-3729
    • Hampel, K.J.1    Burke, J.M.2
  • 24
    • 0038475923 scopus 로고    scopus 로고
    • Substrate specificity and reaction kinetics of an X-motif ribozyme
    • D. Lazarev, I. Puskarz, and R.R. Breaker Substrate specificity and reaction kinetics of an X-motif ribozyme RNA 9 2003 688 697
    • (2003) RNA , vol.9 , pp. 688-697
    • Lazarev, D.1    Puskarz, I.2    Breaker, R.R.3
  • 25
    • 0032530868 scopus 로고    scopus 로고
    • Mechanism for allosteric inhibition of an ATP-sensitive ribozyme
    • J. Tang, and R.R. Breaker Mechanism for allosteric inhibition of an ATP-sensitive ribozyme Nucl. Acids Res. 26 1998 4214 4221
    • (1998) Nucl. Acids Res. , vol.26 , pp. 4214-4221
    • Tang, J.1    Breaker, R.R.2
  • 26
    • 0035671634 scopus 로고    scopus 로고
    • Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: Structure probing of an mRNA bound to its cognate gRNA
    • S.S. Leung, and D.J. Koslowsky Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA RNA 7 2001 1803 1816
    • (2001) RNA , vol.7 , pp. 1803-1816
    • Leung, S.S.1    Koslowsky, D.J.2
  • 27
    • 0032832044 scopus 로고    scopus 로고
    • Ribozyme cleavage of a 2′,5′-phosphodiester linkage: Mechanism and a restricted divalent metal-ion requirement
    • I.-H. Shih, and M.D. Been Ribozyme cleavage of a 2′,5′- phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement RNA 5 1999 1140 1148
    • (1999) RNA , vol.5 , pp. 1140-1148
    • Shih, I.-H.1    Been, M.D.2
  • 28
    • 0035504748 scopus 로고    scopus 로고
    • Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions
    • J. Wrzesinski, M. Legiewicz, B. Smólska, and J. Ciesiolka Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions Nucl. Acids Res. 29 2001 4482 4492
    • (2001) Nucl. Acids Res. , vol.29 , pp. 4482-4492
    • Wrzesinski, J.1    Legiewicz, M.2    Smólska, B.3    Ciesiolka, J.4
  • 29
    • 0031591383 scopus 로고    scopus 로고
    • The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement
    • K.-Y. Chang, and I. Tinoco Jr The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement J. Mol. Biol. 269 1997 52 66
    • (1997) J. Mol. Biol. , vol.269 , pp. 52-66
    • Chang, K.-Y.1    Tinoco Jr., I.2
  • 30
    • 0344474519 scopus 로고    scopus 로고
    • A role for U2/U6 helix lb in 5′ splice site selection
    • B.G.M. Luukkonen, and B. Séraphin A role for U2/U6 helix lb in 5′ splice site selection RNA 4 1998 915 927
    • (1998) RNA , vol.4 , pp. 915-927
    • Luukkonen, B.G.M.1    Séraphin, B.2
  • 31
    • 0036297657 scopus 로고    scopus 로고
    • Direct probing of RNA structure and RNA-protein interactions in purified HeLa cells and yeast spliceosomal U4/U6.U5 tri-snRNP particles
    • A. Mougin, A. Gottschalk, P. Fabrizio, R. Lührmann, and C. Branlant Direct probing of RNA structure and RNA-protein interactions in purified HeLa cells and yeast spliceosomal U4/U6.U5 tri-snRNP particles J. Mol. Biol. 317 2002 631 649
    • (2002) J. Mol. Biol. , vol.317 , pp. 631-649
    • Mougin, A.1    Gottschalk, A.2    Fabrizio, P.3    Lührmann, R.4    Branlant, C.5
  • 32
    • 0033596964 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G and T·T mismatches
    • N. Peyret, A.P. Seneviratne, H.T. Allawi, and J. SantaLucia Jr Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G and T·T mismatches Biochemistry 38 1999 3468 3477
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, A.P.2    Allawi, H.T.3    SantaLucia Jr., J.4
  • 33
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base-pairs
    • T. Xia, J. SantaLucia Jr, M.E. Burkard, R. Kierzek, S.J. Schroeder, and X. Jiao Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base-pairs Biochemistry 37 1998 14719 14735
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6
  • 35
    • 0029868499 scopus 로고    scopus 로고
    • Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme
    • E. Jankowsky, and B. Schwenzer Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme Nucl. Acids Res. 24 1996 423 429
    • (1996) Nucl. Acids Res. , vol.24 , pp. 423-429
    • Jankowsky, E.1    Schwenzer, B.2
  • 36
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • J. Ruan, G.D. Stormo, and W. Zhang An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots Bioinformatics 20 2004 58 66
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 37
    • 0037154101 scopus 로고    scopus 로고
    • Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops
    • D.H. Mathews, and D.H. Turner Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops Bioinformatics 41 2002 869 880
    • (2002) Bioinformatics , vol.41 , pp. 869-880
    • Mathews, D.H.1    Turner, D.H.2
  • 40
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • R.M. Dirks, and N.A. Pierce A partition function algorithm for nucleic acid secondary structure including pseudoknots J. Comput. Chem. 24 2003 1664 1677
    • (2003) J. Comput. Chem. , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 41
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • E. Rivas, and S.R. Eddy A dynamic programming algorithm for RNA structure prediction including pseudoknots J. Mol. Biol. 285 1999 2053 2068
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 42
    • 0025264854 scopus 로고
    • The equilibrium partition function and base-pair binding probabilities for RNA secondary structure
    • J.S. McCaskill The equilibrium partition function and base-pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.