메뉴 건너뛰기




Volumn 31, Issue 24, 2003, Pages 7280-7301

A statistical sampling algorithm for RNA secondary structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; MESSENGER RNA; RIBOZYME; RNA; SMALL INTERFERING RNA; TRANSFER RNA;

EID: 0346888665     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg938     Document Type: Article
Times cited : (467)

References (33)
  • 1
    • 0043268903 scopus 로고    scopus 로고
    • The structural basis of large ribosomal subunit function
    • More,P.B. and Steitz,T.A. (2003). The structural basis of large ribosomal subunit function. Annu. Rev. Biochem., 72, 813-850.
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 813-850
    • More, P.B.1    Steitz, T.A.2
  • 3
    • 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
  • 4
    • 0027186090 scopus 로고
    • RNA multi-structure landscapes. A study based on temperature dependent partition functions
    • Bonhoeffer,S., McCaskill,J.S., Stadler,P.F. and Schuster,P. (1993) RNA multi-structure landscapes. A study based on temperature dependent partition functions. Eur. Biophys. J., 22, 13-24.
    • (1993) Eur. Biophys. J. , vol.22 , pp. 13-24
    • Bonhoeffer, S.1    McCaskill, J.S.2    Stadler, P.F.3    Schuster, P.4
  • 5
    • 0011883768 scopus 로고
    • Application of computational technologies to ribozyme biotechnology products
    • Christoffersen,R.E., McSwiggen,J.A. and Konings,D. (1994) Application of computational technologies to ribozyme biotechnology products. J. Mol. Struct. (Theochem.), 311, 273-284.
    • (1994) J. Mol. Struct. (Theochem.) , vol.311 , pp. 273-284
    • Christoffersen, R.E.1    McSwiggen, J.A.2    Konings, D.3
  • 6
    • 0017604507 scopus 로고
    • Does 5S RNA function by a switch between two secondary structures?
    • Weidner,H., Yuan,R. and Crothers,D.M. (1977) Does 5S RNA function by a switch between two secondary structures? Nature, 266, 193-194.
    • (1977) Nature , vol.266 , pp. 193-194
    • Weidner, H.1    Yuan, R.2    Crothers, D.M.3
  • 7
    • 0018829075 scopus 로고
    • A general model for the conformational switch in 5S RNA during protein synthesis
    • Jagadeeswaran,P. and Cherayil,J.D. (1980) A general model for the conformational switch in 5S RNA during protein synthesis. J. Theor. Biol., 83, 369-375.
    • (1980) J. Theor. Biol. , vol.83 , pp. 369-375
    • Jagadeeswaran, P.1    Cherayil, J.D.2
  • 8
    • 0024786853 scopus 로고
    • Alternative mRNA structures of the cIII gene of bacteriophage λ determine the rate of its translation initiation
    • Altuvia,S., Kornitzer,D., Teff,D. and Oppenheim,A.B. (1989) Alternative mRNA structures of the cIII gene of bacteriophage λ determine the rate of its translation initiation. J. Mol. Biol., 210, 265-280.
    • (1989) J. Mol. Biol. , vol.210 , pp. 265-280
    • Altuvia, S.1    Kornitzer, D.2    Teff, D.3    Oppenheim, A.B.4
  • 9
    • 0002250828 scopus 로고
    • Translation initiation
    • Reznikoff,W. and Golg,L. (eds), Butterworth Publishers, Stoneham, MA
    • Stormo,G. (1986) Translation initiation. In Reznikoff,W. and Golg,L. (eds), Maximizing Gene Expression. Butterworth Publishers, Stoneham, MA, pp. 195-224.
    • (1986) Maximizing Gene Expression , pp. 195-224
    • Stormo, G.1
  • 10
    • 0001562527 scopus 로고    scopus 로고
    • Transcription attentuation
    • Neidhardt,F.C., Curtiss,R. and Lin,E.C (eds), 2nd edn. American Society for Microbiology, Washington, DC
    • Landick,R., Turnbough,C.L. and Yanofsky,C. (1996) Transcription attentuation. In Neidhardt,F.C., Curtiss,R. and Lin,E.C (eds), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn. American Society for Microbiology, Washington, DC, pp. 1263-1286.
    • (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology , pp. 1263-1286
    • Landick, R.1    Turnbough, C.L.2    Yanofsky, C.3
  • 11
    • 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
  • 12
    • 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
  • 13
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 14
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty,S., Fontana,W., Hofacker,I.L. and Schuster,P. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-165.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 15
    • 0023045712 scopus 로고
    • A dynamic programming algorithm for finding alternative RNA secondary structures
    • Williams,A.L. and Tinoco,I.,Jr (1986) A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res., 14, 299-315.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 299-315
    • Williams, A.L.1    Tinoco Jr., I.2
  • 16
    • 0033563515 scopus 로고    scopus 로고
    • A Bayesian statistical algorithm for RNA secondary structure prediction
    • Ding,Y. and Lawrence,C.E. (1999) A Bayesian statistical algorithm for RNA secondary structure prediction. Comput. Chem., 23, 387-400.
    • (1999) Comput. Chem. , vol.23 , pp. 387-400
    • Ding, Y.1    Lawrence, C.E.2
  • 17
    • 0036012373 scopus 로고    scopus 로고
    • Rational statistical design of antisense oligonucleotides for high throughput functional genomics and drug target validation
    • Ding,Y. (2002) Rational statistical design of antisense oligonucleotides for high throughput functional genomics and drug target validation. Stat. Sin., 12, 273-296.
    • (2002) Stat. Sin. , vol.12 , pp. 273-296
    • Ding, Y.1
  • 18
    • 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
  • 19
    • 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
  • 20
    • 0027173194 scopus 로고
    • The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms
    • LeCuyer,K.A. and Crothers,D.M. (1993) The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry, 32, 5301-5311.
    • (1993) Biochemistry , vol.32 , pp. 5301-5311
    • LeCuyer, K.A.1    Crothers, D.M.2
  • 22
    • 0018876711 scopus 로고
    • Secondary structure of mRNA and efficiency of translation initiation
    • Iserentant,D. and Fiers,W. (1980) Secondary structure of mRNA and efficiency of translation initiation. Gene, 9, 1-12.
    • (1980) Gene , vol.9 , pp. 1-12
    • Iserentant, D.1    Fiers, W.2
  • 23
    • 0035283171 scopus 로고    scopus 로고
    • Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
    • Ding,Y. and Lawrence,C.E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res., 29, 1034-1046.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1034-1046
    • Ding, Y.1    Lawrence, C.E.2
  • 24
    • 0034739611 scopus 로고    scopus 로고
    • Selecting optimal antisense reagents
    • Sohail,M. and Southern,E.M. (2000) Selecting optimal antisense reagents. Adv. Drug Deliv. Rev., 44, 23-34.
    • (2000) Adv. Drug Deliv. Rev. , vol.44 , pp. 23-34
    • Sohail, M.1    Southern, E.M.2
  • 25
    • 0030632073 scopus 로고    scopus 로고
    • Density of states, metastable states and saddle points exploring the energy landscape of an RNA molecule
    • Cupal,J., Flamm,C., Renner,A. and Stadler,P.F. (1997) Density of states, metastable states and saddle points exploring the energy landscape of an RNA molecule. Proceedings of ISMB97, pp. 88-91.
    • (1997) Proceedings of ISMB97 , pp. 88-91
    • Cupal, J.1    Flamm, C.2    Renner, A.3    Stadler, P.F.4
  • 26
    • 37049089723 scopus 로고
    • Thermodynamic properties of transfer RNA: A computational study
    • Higgs,P.G. (1995) Thermodynamic properties of transfer RNA: a computational study. J. Chem. Soc. Faraday Trans., 91, 2531-2540.
    • (1995) J. Chem. Soc. Faraday Trans. , vol.91 , pp. 2531-2540
    • Higgs, P.G.1
  • 27
    • 0028502408 scopus 로고
    • Landscapes: Complex optimization problems and biopolymer structures
    • Schuster,P. and Stadler,P.F. (1994) Landscapes: complex optimization problems and biopolymer structures. Comput. Chem., 18, 295-324.
    • (1994) Comput. Chem. , vol.18 , pp. 295-324
    • Schuster, P.1    Stadler, P.F.2
  • 29
    • 0037470145 scopus 로고    scopus 로고
    • Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis
    • Vickers,T.A., Koo,S., Bennett,C.F., Crooke,S.T., Dean,N.M. and Baker,B. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem., 278, 7108-7118.
    • (2003) J. Biol. Chem. , vol.278 , pp. 7108-7118
    • Vickers, T.A.1    Koo, S.2    Bennett, C.F.3    Crooke, S.T.4    Dean, N.M.5    Baker, B.6
  • 30
    • 0038521255 scopus 로고    scopus 로고
    • The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript
    • Bohula,E.A., Salisbury,A.J., Sohail,M., Playford,M.P., Riedemann,J., Southern,E.M. and Macaulay,V.M. (2003) The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem., 278, 15991-15997.
    • (2003) J. Biol. Chem. , vol.278 , pp. 15991-15997
    • Bohula, E.A.1    Salisbury, A.J.2    Sohail, M.3    Playford, M.P.4    Riedemann, J.5    Southern, E.M.6    Macaulay, V.M.7
  • 31
    • 0042161890 scopus 로고    scopus 로고
    • The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides
    • Far,R.K. and Sczakiel,G. (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. Nucleic Acids Res., 31, 4417-4424.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4417-4424
    • Far, R.K.1    Sczakiel, G.2
  • 32
    • 0029670262 scopus 로고    scopus 로고
    • Molecular beacons: Probes that fluoresce upon hybridization
    • Tyagi,S. and Kramer,F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
    • (1996) Nat. Biotechnol. , vol.14 , pp. 303-308
    • Tyagi, S.1    Kramer, F.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.