메뉴 건너뛰기




Volumn 32, Issue 22, 2004, Pages 6636-6642

Efficient computation of optimal oligo-RNA binding

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA; SMALL NUCLEAR RNA;

EID: 13544277162     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh1008     Document Type: Article
Times cited : (17)

References (38)
  • 1
    • 0019887799 scopus 로고
    • The identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) The identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 3
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 5
    • 0034070995 scopus 로고    scopus 로고
    • Calculating nucleic acid secondary structure
    • Zuker,M. (2000) Calculating nucleic acid secondary structure. Curr. Opin. Struct. Biol., 10, 303-310.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 303-310
    • Zuker, M.1
  • 6
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 7
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas,E. and Eddy,S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 8
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia,T., SantaLucia,J.,Jr, Burkard,M.E., Kierzek,R., Schroeder,S.J., Jiao,X., Cox,C. and Turner,D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 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    Cox, C.7    Turner, D.H.8
  • 9
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 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
  • 11
    • 0032787871 scopus 로고    scopus 로고
    • Fast evaluation of internal loops in RNA secondary structure prediction
    • Lyngsø,R.B., Zuker,M. and Pedersen,C.N.S. (1999) Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics, 15, 440-445.
    • (1999) Bioinformatics , vol.15 , pp. 440-445
    • Lyngsø, R.B.1    Zuker, M.2    Pedersen, C.N.S.3
  • 12
    • 42749106244 scopus 로고    scopus 로고
    • Thermodynamic modeling of donor splice site recognition in pre-mRNA
    • Garland,J.A. and Aalberts,D.P. (2004) Thermodynamic modeling of donor splice site recognition in pre-mRNA. Phys. Rev. E, 69 041903.
    • (2004) Phys. Rev. E , vol.69 , pp. 41903
    • Garland, J.A.1    Aalberts, D.P.2
  • 14
    • 0037146606 scopus 로고    scopus 로고
    • Small RNAs make big splash
    • Couzin,J. (2002) Small RNAs make big splash. Science, 298, 2296-2297.
    • (2002) Science , vol.298 , pp. 2296-2297
    • Couzin, J.1
  • 15
    • 0035887005 scopus 로고    scopus 로고
    • Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans
    • Ketting,R.F., Fischer,S.E.J., Bernstein,E., Sijen,T., Hannon,G.J. and Plasterk,R.H.A. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev., 15, 2654-2659.
    • (2001) Genes Dev. , vol.15 , pp. 2654-2659
    • Ketting, R.F.1    Fischer, S.E.J.2    Bernstein, E.3    Sijen, T.4    Hannon, G.J.5    Plasterk, R.H.A.6
  • 16
    • 0037827862 scopus 로고    scopus 로고
    • 2nd edn. Wiley, NY
    • Brown,T.A. (2002) Genomes, 2nd edn. Wiley, NY.
    • (2002) Genomes
    • Brown, T.A.1
  • 17
    • 0036886327 scopus 로고    scopus 로고
    • Retrotransposition of the Ll. LtrB group II intron proceeds predominantly via reverse splicing into DNA targets
    • Ichiyanagi,K., Beauregard,A., Lawrence,S., Smith,D., Cousineau,B. and Belfort,M. (2002) Retrotransposition of the Ll. LtrB group II intron proceeds predominantly via reverse splicing into DNA targets. Mol. Microbiol., 46, 1259-1272.
    • (2002) Mol. Microbiol. , vol.46 , pp. 1259-1272
    • Ichiyanagi, K.1    Beauregard, A.2    Lawrence, S.3    Smith, D.4    Cousineau, B.5    Belfort, M.6
  • 19
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe,T.M. and Eddy,S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1173.
    • (1999) Science , vol.283 , pp. 1168-1173
    • Lowe, T.M.1    Eddy, S.R.2
  • 20
    • 0042622372 scopus 로고    scopus 로고
    • RNAsoft: A suite of RNA secondary structure prediction and design software tools
    • Andronescu,M., Aguirre-Hernández,R., Condon,A. and Hoos,H.H. (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res., 31, 3416-3422.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3416-3422
    • Andronescu, M.1    Aguirre-Hernández, R.2    Condon, A.3    Hoos, H.H.4
  • 21
    • 0032729689 scopus 로고    scopus 로고
    • Predicting oligonucleotide affinity to nucleic acid targets
    • Mathews,D.H., Burkard,M.E., Freier,S.M., Wyatt,J.R. and Turner,D.H. (1999) Predicting oligonucleotide affinity to nucleic acid targets. RNA, 5, 1458-1469.
    • (1999) RNA , vol.5 , pp. 1458-1469
    • Mathews, D.H.1    Burkard, M.E.2    Freier, S.M.3    Wyatt, J.R.4    Turner, D.H.5
  • 22
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 23
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh,O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
    • (1982) J. Mol. Biol. , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 25
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra,M.J. and Turner,D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.
    • (1995) Methods Enzymol. , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 26
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson,H. and Stockmayer,W.H. (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys., 18, 1600-1606.
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 28
    • 0034622514 scopus 로고    scopus 로고
    • Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA
    • Schroeder,S.J. and Turner,D.H. (2000) Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. Biochemistry, 39, 9257-9274.
    • (2000) Biochemistry , vol.39 , pp. 9257-9274
    • Schroeder, S.J.1    Turner, D.H.2
  • 32
    • 0001468848 scopus 로고    scopus 로고
    • Splicing of precursors to mRNAs by the splicesomes
    • Gesteland,R.F., Cech,T.R. and Atkins,J.F. (eds) 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • Burge,C.B., Tuschl,T. and Sharp,P.A. (1999) Splicing of precursors to mRNAs by the splicesomes. In Gesteland,R.F., Cech,T.R. and Atkins,J.F. (eds) The RNA World, 2nd Edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1999) The RNA World
    • Burge, C.B.1    Tuschl, T.2    Sharp, P.A.3
  • 33
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • SantaLucia,J., Allawi,H.T. and Senevirante,A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35, 3555-3562.
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia, J.1    Allawi, H.T.2    Senevirante, A.3
  • 34
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal GT mismatches in DNA
    • Allawi,H.T. and SantaLucia,J.,Jr (1997) Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry, 34, 10581-10594.
    • (1997) Biochemistry , vol.34 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 35
    • 0032562140 scopus 로고    scopus 로고
    • Nearest neighbor thermodynamic parameters for internal G · A mismatches in DNA
    • Allawi,H.T. and SantaLucia,J.,Jr (1997) Nearest neighbor thermodynamic parameters for internal G · A mismatches in DNA. Biochemistry, 37, 2170-2179.
    • (1997) Biochemistry , vol.37 , pp. 2170-2179
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 36
    • 0032102940 scopus 로고    scopus 로고
    • Thermodynamics of internal C · T mismatches in DNA
    • Allawi,H.T. and SantaLucia,J.,Jr (1998) Thermodynamics of internal C · T mismatches in DNA. Nucleic Acids Res., 11, 2694-2701.
    • (1998) Nucleic Acids Res. , vol.11 , pp. 2694-2701
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 37
    • 0032581024 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics of internal A · C mismatches in DNA: Sequence dependence and pH effects
    • Allawi,H.T. and SantaLucia,J.,Jr (1998) Nearest-neighbor thermodynamics of internal A · C mismatches in DNA: sequence dependence and pH effects. Biochemistry, 26, 9435-9444.
    • (1998) Biochemistry , vol.26 , pp. 9435-9444
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 38
    • 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
    • Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G, and T·T mismatches. Biochemistry, 38 3468-3477.
    • (1999) Biochemistry , vol.38 , pp. 3468-3477
    • Peyret, N.1    Seneviratne, P.A.2    Allawi, H.T.3    SantaLucia, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.