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Volumn 201, Issue 2, 1999, Pages 113-140

Mean free energy topology for nucleotide sequences of varying composition based on secondary structure calculations

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; RNA;

EID: 0033592775     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1999.1018     Document Type: Article
Times cited : (5)

References (47)
  • 1
    • 0030596731 scopus 로고    scopus 로고
    • Approximate scaling properties of RNA free energy landscapes
    • BASKARAN S., STADLER P. F., SCHUSTER P. Approximate scaling properties of RNA free energy landscapes. J. theor. Biol. 181:1996;299-310.
    • (1996) J. Theor. Biol. , vol.181 , pp. 299-310
    • Baskaran, S.1    Stadler, P.F.2    Schuster, P.3
  • 4
    • 0015070886 scopus 로고
    • Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty
    • BRITTEN R. J., DAVIDSON E. H. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quart. Rev. Biol. 46:1971;111-138.
    • (1971) Quart. Rev. Biol. , vol.46 , pp. 111-138
    • Britten, R.J.1    Davidson, E.H.2
  • 5
    • 0025329872 scopus 로고
    • A computational procedure for assessing the significance of RNA secondary structure
    • CHEN J.-H., LE SH.-Y., SHAPIRO B., CURREY K. M., MAIZEL J. V. A computational procedure for assessing the significance of RNA secondary structure. CABIOS. 6:1990;7-18.
    • (1990) CABIOS , vol.6 , pp. 7-18
    • Chen, J.-H.1    Le, Sh.-Y.2    Shapiro, B.3    Currey, K.M.4    Maizel, J.V.5
  • 6
    • 0026748179 scopus 로고
    • A procedure for RNA pseudo-knot prediction
    • CHEN J.-H., LE SH.-Y., MAIZEL J. V. A procedure for RNA pseudo-knot prediction. CABIOS. 8:1992;243-248.
    • (1992) CABIOS , vol.8 , pp. 243-248
    • Chen, J.-H.1    Le, Sh.-Y.2    Maizel, J.V.3
  • 7
    • 0026748176 scopus 로고
    • An algorithm for comparing RNA secondary structures and searching for similar substructures
    • CHEVALET C., MICHOT B. An algorithm for comparing RNA secondary structures and searching for similar substructures. CABIOS. 8:1992;215-225.
    • (1992) CABIOS , vol.8 , pp. 215-225
    • Chevalet, C.1    Michot, B.2
  • 8
    • 0007525268 scopus 로고    scopus 로고
    • Evidence of structural order in globin intron sequences of messenger RNA
    • S. Miyano, Takagi T. Tokyo: Universal Academy Press, Inc.
    • DAWSON W. K., YAMAMOTO K. Evidence of structural order in globin intron sequences of messenger RNA. Miyano S., Takagi T. Genome Informatics Series No. 9. 1998;49-61 Universal Academy Press, Inc. Tokyo.
    • (1998) Genome Informatics Series No. 9 , pp. 49-61
    • Dawson, W.K.1    Yamamoto, K.2
  • 9
    • 0003240784 scopus 로고    scopus 로고
    • Evidence of structural information in cytochrome P450 family intron sequences of messenger RNA
    • S. Istrail, P. Pevzner, Waterman M. ACM, Inc.
    • DAWSON W. K., YAMAMOTO K. Evidence of structural information in cytochrome P450 family intron sequences of messenger RNA. Istrail S., Pevzner P., Waterman M. RECOMB 99. 1999;ACM, Inc.
    • (1999) RECOMB 99
    • Dawson, W.K.1    Yamamoto, K.2
  • 15
    • 0032577365 scopus 로고    scopus 로고
    • Continuity in evolution: On the nature of transitions
    • FONTANA W., SCHUSTER P. Continuity in evolution: on the nature of transitions. Science. 280:1998a;1451-1455.
    • (1998) Science , vol.280 , pp. 1451-1455
    • Fontana, W.1    Schuster, P.2
  • 16
    • 0032556237 scopus 로고    scopus 로고
    • The possible and the attainable in RNA genotype-phenotype mapping
    • FONTANA W., SCHUSTER P. The possible and the attainable in RNA genotype-phenotype mapping. J. theor. Biol. 194:1998b;491-515.
    • (1998) J. Theor. Biol. , vol.194 , pp. 491-515
    • Fontana, W.1    Schuster, P.2
  • 17
    • 0028979822 scopus 로고
    • A stem-loop 'kissing' model for the initiation of recombination and the origin of introns
    • FORSDYKE D. R. A stem-loop 'kissing' model for the initiation of recombination and the origin of introns. Mol. Biol. Evol. 12:1995;949-958.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 949-958
    • Forsdyke, D.R.1
  • 18
    • 0032555046 scopus 로고    scopus 로고
    • An alternative way of thinking about stem-loops in DNA. A case study of the human GOS2 gene
    • FORSDYKE D. R. An alternative way of thinking about stem-loops in DNA. A case study of the human GOS2 gene. J. theor. Biol. 192:1998;489-504.
    • (1998) J. Theor. Biol. , vol.192 , pp. 489-504
    • Forsdyke, D.R.1
  • 19
    • 0031708076 scopus 로고    scopus 로고
    • The energy landscape in non-biological and biological molecules
    • FRAUENFELDER H., DAAN THORN L. The energy landscape in non-biological and biological molecules. Nature Struct. Biol. 5:1998;757-759.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 757-759
    • Frauenfelder, H.1    Daan Thorn, L.2
  • 21
    • 0003380323 scopus 로고    scopus 로고
    • Predicting disordered regions from amino acid sequence: Common themes despite differing structural characterization
    • S. Miyano, Takagi T. Tokyo: Universal Academy Press, Inc.
    • GARNER E., CANNON P., ROMERO P., OBRADOVIC Z., DUNKER A. K. Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Miyano S., Takagi T. Genome Informatics Series No. 9. 1998;201-213 Universal Academy Press, Inc. Tokyo.
    • (1998) Genome Informatics Series No. 9 , pp. 201-213
    • Garner, E.1    Cannon, P.2    Romero, P.3    Obradovic, Z.4    Dunker, A.K.5
  • 22
    • 0027377681 scopus 로고
    • Multiple coding and the evolutionary properties of RNA secondary structure
    • HUYNEN M. A., KONINGS D. A. M., HOGEWEG P. Multiple coding and the evolutionary properties of RNA secondary structure. J. theor. Biol. 165:1993;251-267.
    • (1993) J. Theor. Biol. , vol.165 , pp. 251-267
    • Huynen, M.A.1    Konings, D.A.M.2    Hogeweg, P.3
  • 23
    • 0025361553 scopus 로고
    • Predicting optimal and suboptimal secondary structure for RNA
    • JAEGER J. A., TURNER D. H., ZUKER M. Predicting optimal and suboptimal secondary structure for RNA. Meth. Enzymol. 183:1990;281-306.
    • (1990) Meth. Enzymol. , vol.183 , pp. 281-306
    • Jaeger, J.A.1    Turner, D.H.2    Zuker, M.3
  • 25
    • 0031252604 scopus 로고    scopus 로고
    • A snapshot of a dynamic nuclear building block
    • KINGSTON R. E. A snapshot of a dynamic nuclear building block. Nature Struct. Biol. 4:1997;763-766.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 763-766
    • Kingston, R.E.1
  • 26
    • 0031976753 scopus 로고    scopus 로고
    • Remarks on discrete and continuous large-scale models of DNA dynamics
    • KLAPPER I., QIAN H. Remarks on discrete and continuous large-scale models of DNA dynamics. Biophys. J. 74:1997;2504-2514.
    • (1997) Biophys. J. , vol.74 , pp. 2504-2514
    • Klapper, I.1    Qian, H.2
  • 27
    • 0032555056 scopus 로고    scopus 로고
    • Giant hairpins formed by CUG repeats in myotonic dystrophy messenger RNAs might sterically block RNA export through nuclear pores
    • KOCH K. S., LEFFERT H. L. Giant hairpins formed by CUG repeats in myotonic dystrophy messenger RNAs might sterically block RNA export through nuclear pores. J. theor. Biol. 192:1998;505-514.
    • (1998) J. Theor. Biol. , vol.192 , pp. 505-514
    • Koch, K.S.1    Leffert, H.L.2
  • 28
    • 0000341183 scopus 로고
    • Sequences and codes: Fundamentals of biomolecular cryptology
    • Smith E. W. New York: Academic Press, Inc.
    • KONOPKA A. K. Sequences and codes: fundamentals of biomolecular cryptology. Smith E. W. Biocomputing, Informatics and Genome Projects. 1994;119-174 Academic Press, Inc. New York.
    • (1994) Biocomputing, Informatics and Genome Projects , pp. 119-174
    • Konopka, A.K.1
  • 29
    • 0024381773 scopus 로고
    • A method for assessing the statistical significance of RNA folding
    • LE S.-Y., MAIZEL J. V. JR. A method for assessing the statistical significance of RNA folding. J. theor. Biol. 138:1989;495-510.
    • (1989) J. Theor. Biol. , vol.138 , pp. 495-510
    • Le, S.-Y.1    Maizel J.V., Jr.2
  • 30
    • 0028799521 scopus 로고
    • Constraints on intron evolution in the gene encoding the myosin alkali light chain in drosophila
    • LEICHT B. G., MUSE S. V., HANCZYC M., CLARK A. G. Constraints on intron evolution in the gene encoding the myosin alkali light chain in drosophila. Genetics. 139:1995;299-308.
    • (1995) Genetics , vol.139 , pp. 299-308
    • Leicht, B.G.1    Muse, S.V.2    Hanczyc, M.3    Clark, A.G.4
  • 31
    • 0004279283 scopus 로고    scopus 로고
    • New York: Oxford University Press, Inc.
    • LEWIN B. Genes VI. 1997;Oxford University Press, Inc. New York.
    • (1997) Genes VI
    • Lewin, B.1
  • 32
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates, Inc., Publishers
    • LI W.-H. Molecular Evolution. 1997;Sinauer Associates, Inc., Publishers.
    • (1997) Molecular Evolution
    • Li, W.-H.1
  • 33
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • MALAKAUSKAS S. M., MAYO S. L. Design, structure and stability of a hyperthermophilic protein variant. Nature Struct. Biol. 5:1998;470-475.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 37
    • 0030869663 scopus 로고    scopus 로고
    • A method for identifying splice sites and translational star sites in eukaryotic mRNA
    • SALZBERG S. L. A method for identifying splice sites and translational star sites in eukaryotic mRNA. CABIOS. 13:1997;365-376.
    • (1997) CABIOS , vol.13 , pp. 365-376
    • Salzberg, S.L.1
  • 38
    • 0001894975 scopus 로고
    • Evolution of functional structures of RNA
    • Cold Springs Harbor: Cold Springs Harbor Laboratory Press. p. 419-445
    • TOMIZAWA J. Evolution of functional structures of RNA. The RNA World. 1993;Cold Springs Harbor Laboratory Press, Cold Springs Harbor. p. 419-445.
    • (1993) The RNA World
    • Tomizawa, J.1
  • 40
    • 0023045712 scopus 로고
    • A dynamic programming algorithm for finding alternate RNA secondary structures
    • WILLIAMS A. L. JR., TINOCO I. JR. A dynamic programming algorithm for finding alternate RNA secondary structures. Nucl. Acids Res. 14:1986;299-315.
    • (1986) Nucl. Acids Res. , vol.14 , pp. 299-315
    • Williams A.L., Jr.1    Tinoco I., Jr.2
  • 41
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • WU M., TINOCO I. JR. RNA folding causes secondary structure rearrangement. Proc. Nat. Acad. Sci. U.S.A. 95:1998;11555-11560.
    • (1998) Proc. Nat. Acad. Sci. U.S.A. , vol.95 , pp. 11555-11560
    • Wu, M.1    Tinoco I., Jr.2
  • 42
    • 0032578390 scopus 로고    scopus 로고
    • Native secondary structure formation in RNA may be a slave to tertiary folding
    • THIRUMALAI D. Native secondary structure formation in RNA may be a slave to tertiary folding. Proc. Nat. Acad. Sci. U.S.A. 95:1998;11506-11508.
    • (1998) Proc. Nat. Acad. Sci. U.S.A. , vol.95 , pp. 11506-11508
    • Thirumalai, D.1
  • 43
    • 0002176755 scopus 로고
    • RNA structure elements and RNA function
    • Cold Springs Harbor: Cold Springs Harbor Laboratory Press. p. 465-596
    • WYATT J. R., TINOCO I. JR. RNA structure elements and RNA function. The RNA World. 1993;Cold Springs Harbor Laboratory Press, Cold Springs Harbor. p. 465-596.
    • (1993) The RNA World
    • Wyatt, J.R.1    Tinoco I., Jr.2
  • 44
    • 0343180338 scopus 로고
    • RNA folding and evolution
    • Pickover C. A. London: World Scientific
    • YAMAMOTO K., YOSHIKURA K. RNA folding and evolution. Pickover C. A. Visualizing biological information. 1995;158-164 World Scientific, London.
    • (1995) Visualizing Biological Information , pp. 158-164
    • Yamamoto, K.1    Yoshikura, K.2
  • 45
    • 0028024432 scopus 로고
    • Influence of slight sequence changes on the free energy of the single stranded ribonucleic acid molecule
    • YOUHEI F., YAMAMOTO K. Influence of slight sequence changes on the free energy of the single stranded ribonucleic acid molecule. J. theor. Biol. 171:1994;151-161.
    • (1994) J. Theor. Biol. , vol.171 , pp. 151-161
    • Youhei, F.1    Yamamoto, K.2
  • 46
    • 0024477261 scopus 로고
    • On Finding All Suboptimal Foldings of an RNA Molecule
    • ZUKER M. On Finding All Suboptimal Foldings of an RNA Molecule. Science. 244:1989;48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1


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