메뉴 건너뛰기




Volumn 260, Issue 2, 1996, Pages 135-146

Kinetic discrimination in the folding of intramolecular triple helices

Author keywords

DNA; Kinetics; Melting curves; Stopped flow; Triplex

Indexed keywords

OLIGONUCLEOTIDE; PALINDROMIC DNA; PURINE; PYRIMIDINE;

EID: 0030581146     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0388     Document Type: Editorial
Times cited : (16)

References (58)
  • 1
    • 0025942059 scopus 로고
    • A thermodynamic study of unusually stable RNA and DNA hairpins
    • Antao, V. P., Lai, S. Y. & Tinoco, I. J. (1991). A thermodynamic study of unusually stable RNA and DNA hairpins. Nucl. Acids Res. 19(21), 5901-5905.
    • (1991) Nucl. Acids Res. , vol.19 , Issue.21 , pp. 5901-5905
    • Antao, V.P.1    Lai, S.Y.2    Tinoco, I.J.3
  • 2
    • 0028315891 scopus 로고
    • Base-pairing and steric interactions between pyrimidine strand bridging loops and the purine strand in DNA pyrimidine·purine·pyrimidine triplexes
    • Booher, M. A., Wang, S. & Kool, E. T. (1994). Base-pairing and steric interactions between pyrimidine strand bridging loops and the purine strand in DNA pyrimidine·purine·pyrimidine triplexes. Biochemistry, 33, 4645-4651.
    • (1994) Biochemistry , vol.33 , pp. 4645-4651
    • Booher, M.A.1    Wang, S.2    Kool, E.T.3
  • 4
    • 0027081208 scopus 로고
    • A base-triple structural domain in RNA
    • Chastain, M. & Tinoco, I. J. (1992). A base-triple structural domain in RNA. Biochemistry, 31, 12733-12741.
    • (1992) Biochemistry , vol.31 , pp. 12733-12741
    • Chastain, M.1    Tinoco, I.J.2
  • 5
    • 0027753985 scopus 로고
    • Nucleoside triples from the group I intron
    • Chastain, M. & Tinoco, I. J. (1993). Nucleoside triples from the group I intron. Biochemistry, 32, 14220-14228.
    • (1993) Biochemistry , vol.32 , pp. 14220-14228
    • Chastain, M.1    Tinoco, I.J.2
  • 6
    • 0026437888 scopus 로고
    • Stabilities of double-and triple helical nucleic acids
    • Cheng, Y. K. & Pettitt, M. B. (1992). Stabilities of double-and triple helical nucleic acids. Prog. Biophys. Mol. Biol. 58, 225-257.
    • (1992) Prog. Biophys. Mol. Biol. , vol.58 , pp. 225-257
    • Cheng, Y.K.1    Pettitt, M.B.2
  • 7
    • 0022432308 scopus 로고
    • An unusually long poly-(purine)·poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene
    • Christophe, D., Cabrer, B., Bacolla, A., Targovnik, H. V. P. & Vassart, G. (1985). An unusually long poly-(purine)·poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. Nucl. Acids Res. 13(14), 5127-5144.
    • (1985) Nucl. Acids Res. , vol.13 , Issue.14 , pp. 5127-5144
    • Christophe, D.1    Cabrer, B.2    Bacolla, A.3    Targovnik, H.V.P.4    Vassart, G.5
  • 8
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly, M. L. (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 9
    • 0015223584 scopus 로고
    • Relaxation kinetics of dimer formation by self complementary oligoribonucleotides
    • Craig, M. E., Crothers, D. M. & Doty, P. (1971). Relaxation kinetics of dimer formation by self complementary oligoribonucleotides. J. Mol. Biol. 62, 383-401.
    • (1971) J. Mol. Biol. , vol.62 , pp. 383-401
    • Craig, M.E.1    Crothers, D.M.2    Doty, P.3
  • 10
    • 0012016975 scopus 로고
    • Protonated DNA structures
    • Eckstein, F. & Lilley, D. M. J. eds, Springer-Verlag, Berlin
    • Frank-Kamenetskii, M. D. (1990). Protonated DNA structures. In Nucleic Acids and Molecular Biology (Eckstein, F. & Lilley, D. M. J. eds), vol. 4, pp. 1-8, Springer-Verlag, Berlin.
    • (1990) Nucleic Acids and Molecular Biology , vol.4 , pp. 1-8
    • Frank-Kamenetskii, M.D.1
  • 12
    • 0027958767 scopus 로고
    • In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sun Y group I self-splicing intron
    • Green, R. & Szostak, J. W. (1994). In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sun Y group I self-splicing intron. J. Mol. Biol. 235, 140-155.
    • (1994) J. Mol. Biol. , vol.235 , pp. 140-155
    • Green, R.1    Szostak, J.W.2
  • 13
    • 0024295554 scopus 로고
    • Characterization of RNA hairpin loop stability
    • Groebe, D. R. & Uhlenbeck, O. C. (1988). Characterization of RNA hairpin loop stability. Nucl. Acids Res. 16, 11725-11735.
    • (1988) Nucl. Acids Res. , vol.16 , pp. 11725-11735
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 14
    • 0022719007 scopus 로고
    • Higher order structure in ribosomal RNA
    • Gutell, R. R., Noller, H. F. & Woese, C. R. (1986). Higher order structure in ribosomal RNA. EMBO J. 5, 1111-1113.
    • (1986) EMBO J. , vol.5 , pp. 1111-1113
    • Gutell, R.R.1    Noller, H.F.2    Woese, C.R.3
  • 16
    • 0025027735 scopus 로고
    • Single-strand DNA triple-helix formation
    • Häner, R. & Dervan, P. B. (1990). Single-strand DNA triple-helix formation. Biochemistry, 29, 9761-9765.
    • (1990) Biochemistry , vol.29 , pp. 9761-9765
    • Häner, R.1    Dervan, P.B.2
  • 17
    • 0011204402 scopus 로고
    • Intramolecular DNA triplexes in supercoiled plasmids
    • Hanvey, J. C., Shimizu, M. & Wells, R. D. (1988). Intramolecular DNA triplexes in supercoiled plasmids. Proc. Natl Acad. Sci. USA, 85, 6292-6296.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 6292-6296
    • Hanvey, J.C.1    Shimizu, M.2    Wells, R.D.3
  • 18
    • 0024295576 scopus 로고
    • DNA stem-loop structures in oligopurine-oligopyrimidine triplexes
    • Harvey, S. C., Luo, J. & Lavery, R. (1988). DNA stem-loop structures in oligopurine-oligopyrimidine triplexes. Nucl. Acids Res. 16(24), 11795-11809.
    • (1988) Nucl. Acids Res. , vol.16 , Issue.24 , pp. 11795-11809
    • Harvey, S.C.1    Luo, J.2    Lavery, R.3
  • 19
    • 0023780437 scopus 로고
    • Single strands, triple strands, and kinks in H-DNA
    • Htun, H. & Dahlberg, J. E. (1988). Single strands, triple strands, and kinks in H-DNA. Science, 241, 1791-1796.
    • (1988) Science , vol.241 , pp. 1791-1796
    • Htun, H.1    Dahlberg, J.E.2
  • 20
    • 0024510279 scopus 로고
    • Topology and formation of riple-stranded H-DNA
    • Htun, H. & Dahlberg, J. E. (1989). Topology and formation of riple-stranded H-DNA. Science, 243, 1571-1576.
    • (1989) Science , vol.243 , pp. 1571-1576
    • Htun, H.1    Dahlberg, J.E.2
  • 21
    • 0012080627 scopus 로고
    • The structure and formation of triple-stranded H-DNA
    • Sarma, R. H. & Sarma, M. H., eds, Adenine Press, New York
    • Htun, H. & Dahlberg, J. E. (1990). The structure and formation of triple-stranded H-DNA. In Structure and Methods: DNA and RNA (Sarma, R. H. & Sarma, M. H., eds), vol. 3, pp. 185-205, Adenine Press, New York.
    • (1990) Structure and Methods: DNA and RNA , vol.3 , pp. 185-205
    • Htun, H.1    Dahlberg, J.E.2
  • 22
    • 0024300366 scopus 로고
    • n: Chemical evidence for a three-stranded structure in plasmids
    • n: chemical evidence for a three-stranded structure in plasmids. Science, 241, 1800-1804.
    • (1988) Science , vol.241 , pp. 1800-1804
    • Johnston, B.H.1
  • 23
    • 0024327955 scopus 로고
    • Quantitative, analysis of DNA secondary structure from solvent-accessible surfaces: The B-to Z-DNA transition as a model
    • Kagawa, T. F., Stoddard, D., Zhou, G. & Ho, P. S. (1989). Quantitative, analysis of DNA secondary structure from solvent-accessible surfaces: the B-to Z-DNA transition as a model. Biochemistry, 28, 6642-6651.
    • (1989) Biochemistry , vol.28 , pp. 6642-6651
    • Kagawa, T.F.1    Stoddard, D.2    Zhou, G.3    Ho, P.S.4
  • 24
    • 0026757199 scopus 로고
    • Central non-Pur·Pyr sequences in oligo(dG·dC) tracts and metal ions influence the formation of intramolecular DNA triplex isomers
    • Kang, S. & Wells, R. D. (1992). Central non-Pur·Pyr sequences in oligo(dG·dC) tracts and metal ions influence the formation of intramolecular DNA triplex isomers. J. Biol. Chem. 267, 20887-20891.
    • (1992) J. Biol. Chem. , vol.267 , pp. 20887-20891
    • Kang, S.1    Wells, R.D.2
  • 25
    • 0026703204 scopus 로고
    • GC-rich flanking tracts decrease the kinetics of intramolecular DNA triplex formation
    • Kang, S., Wohlrab, F. & Wells, R. D. (1992a). GC-rich flanking tracts decrease the kinetics of intramolecular DNA triplex formation. J. Biol. Chem. 267, 19435-19442.
    • (1992) J. Biol. Chem. , vol.267 , pp. 19435-19442
    • Kang, S.1    Wohlrab, F.2    Wells, R.D.3
  • 26
    • 0026570255 scopus 로고
    • Metal ions cause the isomerization of certain intramolecular DNA triplex isomers
    • Kang, S., Wohlrab, F. & Wells, R. D. (1992b). Metal ions cause the isomerization of certain intramolecular DNA triplex isomers. J. Biol. Chem. 267, 1259-1264.
    • (1992) J. Biol. Chem. , vol.267 , pp. 1259-1264
    • Kang, S.1    Wohlrab, F.2    Wells, R.D.3
  • 27
    • 0022407361 scopus 로고
    • A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA
    • Lyamichev, V. I., Mirkin, S. M. & Frank-Kamenetskii, M. D. (1985). A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struct. Dynam. 3(2), 327-338.
    • (1985) J. Biomol. Struct. Dynam. , vol.3 , Issue.2 , pp. 327-338
    • Lyamichev, V.I.1    Mirkin, S.M.2    Frank-Kamenetskii, M.D.3
  • 29
    • 0026723480 scopus 로고
    • Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex
    • Macaya, R., Wang, F., Schultze, P. & Feigon, J. (1992). Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. J. Mol. Biol. 225, 755-773.
    • (1992) J. Mol. Biol. , vol.225 , pp. 755-773
    • Macaya, R.1    Wang, F.2    Schultze, P.3    Feigon, J.4
  • 30
    • 0025166762 scopus 로고
    • Kinetic analysis of oligodeoxyribonucleotide-directed triple-helix formation on DNA
    • Maher, L. J. I., Dervan, P. B. & Wold, B. J. (1990). Kinetic analysis of oligodeoxyribonucleotide-directed triple-helix formation on DNA. Biochemistry, 29, 8820-8826.
    • (1990) Biochemistry , vol.29 , pp. 8820-8826
    • Maher, L.J.I.1    Dervan, P.B.2    Wold, B.J.3
  • 31
    • 0026216741 scopus 로고
    • Oligonucleotide-directed DNA triple helix formation: An approach to artificial repressers?
    • Maher, L. J. I., Wold, B. & Dervan, P. B. (1991). Oligonucleotide-directed DNA triple helix formation: an approach to artificial repressers? Anti-sense Res. Devel. 1(3), 227-281.
    • (1991) Anti-sense Res. Devel. , vol.1 , Issue.3 , pp. 227-281
    • Maher, L.J.I.1    Wold, B.2    Dervan, P.B.3
  • 32
    • 0025678737 scopus 로고
    • Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel, F. & Westhoff, E. (1990). Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585-610.
    • (1990) J. Mol. Biol. , vol.216 , pp. 585-610
    • Michel, F.1    Westhoff, E.2
  • 33
    • 0020198881 scopus 로고
    • Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure
    • Michel, F., Jacquier, A. & Dujon, B. (1982). Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie, 64, 867-881.
    • (1982) Biochimie , vol.64 , pp. 867-881
    • Michel, F.1    Jacquier, A.2    Dujon, B.3
  • 34
    • 0025134897 scopus 로고
    • Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns
    • Michel, F., Ellington, A. D., Couture, S. & Szostak, J. W. (1990). Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature, 347, 578-580.
    • (1990) Nature , vol.347 , pp. 578-580
    • Michel, F.1    Ellington, A.D.2    Couture, S.3    Szostak, J.W.4
  • 36
    • 0000539166 scopus 로고
    • Stereospecific detection and modification of double helix DNA by oligonucleotides
    • Nguyen, T. T. & Hélène, C. (1993). Stereospecific detection and modification of double helix DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 105, 666-690.
    • (1993) Angew. Chem. Int. Ed. Engl. , vol.105 , pp. 666-690
    • Nguyen, T.T.1    Hélène, C.2
  • 39
    • 0021760007 scopus 로고
    • An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules
    • Papanicolaou, C., Gouy, M. & Ninio, J. (1984). An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucl. Acids Res. 12, 31-44.
    • (1984) Nucl. Acids Res. , vol.12 , pp. 31-44
    • Papanicolaou, C.1    Gouy, M.2    Ninio, J.3
  • 40
    • 0024505223 scopus 로고
    • Complex structural behavior of oligopurine-oligopyrimidine sequence cloned within the supercoiled plasmid
    • Parniewski, P., Galazaka, G., Wilk, A. & Klysik, J. (1989). Complex structural behavior of oligopurine-oligopyrimidine sequence cloned within the supercoiled plasmid. Nucl. Acids Res. 17, 617-629.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 617-629
    • Parniewski, P.1    Galazaka, G.2    Wilk, A.3    Klysik, J.4
  • 41
    • 0015223587 scopus 로고
    • Co-operative non-enzymatic base recognition. III. Kinetics of the helix-coil transition of the oligoribouridylic·oligoriboadenylic acid alone at acidic pH
    • Pörschke, D. & Eigen, M. (1971). Co-operative non-enzymatic base recognition. III. Kinetics of the helix-coil transition of the oligoribouridylic·oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62, 361-381.
    • (1971) J. Mol. Biol. , vol.62 , pp. 361-381
    • Pörschke, D.1    Eigen, M.2
  • 42
    • 11944257696 scopus 로고
    • Structural effects in the recognition of DNA by circular oligonucleotides
    • Prakash, G. & Kool, E. T. (1992). Structural effects in the recognition of DNA by circular oligonucleotides. J. Am. Chem. Soc. 114, 3523-3527.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3523-3527
    • Prakash, G.1    Kool, E.T.2
  • 43
    • 0026651395 scopus 로고
    • Conformation of the TAR RNA-arginine complex by NMR spectroscopy
    • Puglisi, J. D., Tan, R., Calnan, B. J., Frankel, A. D. & Williamson, J. R. (1992). Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science, 257, 76-80.
    • (1992) Science , vol.257 , pp. 76-80
    • Puglisi, J.D.1    Tan, R.2    Calnan, B.J.3    Frankel, A.D.4    Williamson, J.R.5
  • 44
    • 0027485989 scopus 로고
    • NMR structural studies on a nonnatural deoxyribonucleoside which mediates recognition of GC base pairs in pyrimidine·purine· pyrimidine DNA triplexes
    • Radhakrishnan, I., Patel, D. J., Priestley, E. S., Nash, H. M. & Dervan, P. B. (1993). NMR structural studies on a nonnatural deoxyribonucleoside which mediates recognition of GC base pairs in pyrimidine·purine· pyrimidine DNA triplexes. Biochemistry, 32, 11228-11234.
    • (1993) Biochemistry , vol.32 , pp. 11228-11234
    • Radhakrishnan, I.1    Patel, D.J.2    Priestley, E.S.3    Nash, H.M.4    Dervan, P.B.5
  • 45
    • 0016912825 scopus 로고
    • Transfer RNA: Molecular structure, sequence, and properties
    • Rich, A. & RajBhandary, U. L. (1976). Transfer RNA: molecular structure, sequence, and properties. Annu. Rev. Biochem. 45, 805-860.
    • (1976) Annu. Rev. Biochem. , vol.45 , pp. 805-860
    • Rich, A.1    Rajbhandary, U.L.2
  • 46
    • 0000977766 scopus 로고
    • Thermodynamics and kinetics of conformational transitions in oligonucleotides and tRNA
    • Duchesne, J., ed., Academic Press, New York
    • Riesner, D. & Romer, R. (1973). Thermodynamics and kinetics of conformational transitions in oligonucleotides and tRNA. In Physio-chemical Properties of Nucleic Acids (Duchesne, J., ed.), vol. 2, pp. 237-318, Academic Press, New York.
    • (1973) Physio-chemical Properties of Nucleic Acids , vol.2 , pp. 237-318
    • Riesner, D.1    Romer, R.2
  • 48
    • 0025944799 scopus 로고
    • Specificity and stringency in DNA triplex formation
    • Roberts, R. W. & Crothers, D. M. (1991). Specificity and stringency in DNA triplex formation. Proc. Natl Acad. Sci. USA, 88, 9397-9401.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 9397-9401
    • Roberts, R.W.1    Crothers, D.M.2
  • 50
    • 0026562625 scopus 로고
    • Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin
    • SantaLucia, J. J., Kierzek, R. & Turner, D. H. (1992). Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science, 256, 217-219.
    • (1992) Science , vol.256 , pp. 217-219
    • Santalucia, J.J.1    Kierzek, R.2    Turner, D.H.3
  • 51
    • 0025301201 scopus 로고
    • Multiple non-B-DNA conformations of polypurine-polypyrimidine sequences in plasmids
    • Shimizu, M., Hanvey, J. C. & Wells, R. D. (1990). Multiple non-B-DNA conformations of polypurine-polypyrimidine sequences in plasmids. Biochemistry, 29, 4704-4713.
    • (1990) Biochemistry , vol.29 , pp. 4704-4713
    • Shimizu, M.1    Hanvey, J.C.2    Wells, R.D.3
  • 52
    • 0028090797 scopus 로고
    • The loop sequence plays crucial roles for the isomerization of intramolecular DNA triplexes in supercoiled plasmids
    • Shimizu, M., Kubo, K., Matsumoto, U. & Shindo, H. (1993). The loop sequence plays crucial roles for the isomerization of intramolecular DNA triplexes in supercoiled plasmids. J. Mol. Biol. 235, 185-197.
    • (1993) J. Mol. Biol. , vol.235 , pp. 185-197
    • Shimizu, M.1    Kubo, K.2    Matsumoto, U.3    Shindo, H.4
  • 53
    • 0001191247 scopus 로고
    • DNA flexibility studied by covalent closure of short fragments into circles
    • Shore, D., Langowski, J. & Baldwin, R. L. (1981). DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl Acad. Sci. USA, 78, 4833-4837.
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , pp. 4833-4837
    • Shore, D.1    Langowski, J.2    Baldwin, R.L.3
  • 54
    • 0025345246 scopus 로고
    • Formation of a stable triplex from a single DNA strand
    • Sklenar, V. & Feigon, J. (1990). Formation of a stable triplex from a single DNA strand. Nature, 345, 836-838.
    • (1990) Nature , vol.345 , pp. 836-838
    • Sklenar, V.1    Feigon, J.2
  • 56
    • 0028280187 scopus 로고
    • Stabilities of nucleotide loops bridging the pyrimidine strands in DNA pyrimidine·purine·pyrimidine triplexes: Special stability of the CTTTG loop
    • Wang, S., Booher, M. A. & Kool, E. T. (1994). Stabilities of nucleotide loops bridging the pyrimidine strands in DNA pyrimidine·purine·pyrimidine triplexes: special stability of the CTTTG loop. Biochemistry, 33, 4639-4644.
    • (1994) Biochemistry , vol.33 , pp. 4639-4644
    • Wang, S.1    Booher, M.A.2    Kool, E.T.3
  • 57
    • 0027370486 scopus 로고
    • Major groove accessibility of RNA
    • Weeks, K. M. & Crothers, D. M. (1993). Major groove accessibility of RNA. Science, 261, 1574-1577.
    • (1993) Science , vol.261 , pp. 1574-1577
    • Weeks, K.M.1    Crothers, D.M.2
  • 58
    • 0025369611 scopus 로고
    • Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH
    • Xodo, L. E., Manzini, G. & Quadrifoglio, F. (1990). Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH. Nucl. Acids Res. 18(12), 3557-3564.
    • (1990) Nucl. Acids Res. , vol.18 , Issue.12 , pp. 3557-3564
    • Xodo, L.E.1    Manzini, G.2    Quadrifoglio, F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.