메뉴 건너뛰기




Volumn 87, Issue 1, 2004, Pages 215-226

Prediction of hybridization and melting for double-stranded nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DOUBLE STRANDED RNA; NUCLEIC ACID; RNA; SINGLE STRANDED DNA; SINGLE STRANDED RNA; UNCLASSIFIED DRUG;

EID: 3042735602     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.020743     Document Type: Article
Times cited : (185)

References (48)
  • 1
    • 0019883193 scopus 로고
    • Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide
    • Albergo, D., L. A. Marky, K. J. Breslauer, and D. H. Turner. 1981. Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 20:1409-1413.
    • (1981) Biochemistry , vol.20 , pp. 1409-1413
    • Albergo, D.1    Marky, L.A.2    Breslauer, K.J.3    Turner, D.H.4
  • 2
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal G-T mismatches in DNA
    • Allawi, H. T., and J. SantaLucia, Jr. 1997. Thermodynamics and NMR of internal G-T mismatches in DNA. Biochemistry. 97:10581-10594.
    • (1997) Biochemistry , vol.97 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 3
    • 0013769174 scopus 로고
    • Theory of effects of concentration and chain length on helix-coil equilibria in two-stranded nucleic acids
    • Applequist, J., and V. Damle. 1963. Theory of effects of concentration and chain length on helix-coil equilibria in two-stranded nucleic acids. J. Chem. Phys. 39:2719-2721.
    • (1963) J. Chem. Phys. , vol.39 , pp. 2719-2721
    • Applequist, J.1    Damle, V.2
  • 4
    • 0015257704 scopus 로고
    • ∞ from the dependence of the temperature of the helix-coil transition on oligomer concentrations
    • ∞ from the dependence of the temperature of the helix-coil transition on oligomer concentrations. Biopolymers. 11:913-933.
    • (1972) Biopolymers , vol.11 , pp. 913-933
    • Blake, R.D.1
  • 8
    • 0026687954 scopus 로고
    • Calorimetry: A tool for DNA and ligand-DNA studies
    • Breslauer, K. J., E. Freire, and M. Straume. 1992. Calorimetry: a tool for DNA and ligand-DNA studies. Methods Enzymol. 211:533-567.
    • (1992) Methods Enzymol. , vol.211 , pp. 533-567
    • Breslauer, K.J.1    Freire, E.2    Straume, M.3
  • 9
    • 0016656309 scopus 로고
    • Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7
    • Breslauer, K. J., J. M. Sturtevant, and I. Tinoco, Jr. 1975. Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. J. Mol. Biol. 99:549-565.
    • (1975) J. Mol. Biol. , vol.99 , pp. 549-565
    • Breslauer, K.J.1    Sturtevant, J.M.2    Tinoco Jr., I.3
  • 10
    • 0033529318 scopus 로고    scopus 로고
    • A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques
    • Chalikian, T. V., J. Volker, G. E. Plum, and K. J. Breslauer. 1999. A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. Proc. Natl. Acad. Sci. USA. 96:7853-7858.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 7853-7858
    • Chalikian, T.V.1    Volker, J.2    Plum, G.E.3    Breslauer, K.J.4
  • 11
    • 0025689277 scopus 로고
    • Thermodynamic stability of the 5′ dangling-ended DNA hairpins formed from sequences 5′-(XY)2GGATAC(T)4GTATCC-3′, where X,Y=A,T, G,C
    • Doktycz, M. J., T. M. Paner, M. Amaratunga, and A. S. Benight. 1990. Thermodynamic stability of the 5′ dangling-ended DNA hairpins formed from sequences 5′-(XY)2GGATAC(T)4GTATCC-3′, where X,Y=A,T, G,C. Biopolymers. 30:829-845.
    • (1990) Biopolymers , vol.30 , pp. 829-845
    • Doktycz, M.J.1    Paner, T.M.2    Amaratunga, M.3    Benight, A.S.4
  • 12
    • 0019886913 scopus 로고
    • A 300-MHz proton nuclear magnetic resonance investigation of deoxyribonucleic acid restriction fragments: Dynamic properties
    • Early, T. A., D. R. Kearns, W. Hillen, and R. D. Wells. 1981. A 300-MHz proton nuclear magnetic resonance investigation of deoxyribonucleic acid restriction fragments: dynamic properties. Biochemistry. 20:3764-3769.
    • (1981) Biochemistry , vol.20 , pp. 3764-3769
    • Early, T.A.1    Kearns, D.R.2    Hillen, W.3    Wells, R.D.4
  • 13
    • 0017587485 scopus 로고
    • Theory of DNA melting curves
    • Fixman, M., and J. J. Freire. 1977. Theory of DNA melting curves. Biopolymers. 16:2693-2704.
    • (1977) Biopolymers , vol.16 , pp. 2693-2704
    • Fixman, M.1    Freire, J.J.2
  • 14
    • 0001613489 scopus 로고
    • Contribution of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes
    • Freier, S. M., D. Alkema, A. Sinclair, T. Neilson, and D. H. Turner. 1983. Contribution of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry. 22:6198-6206.
    • (1983) Biochemistry , vol.22 , pp. 6198-6206
    • Freier, S.M.1    Alkema, D.2    Sinclair, A.3    Neilson, T.4    Turner, D.H.5
  • 15
    • 0019883234 scopus 로고
    • Solvent effects on the kinetics and thermodynamics of stacking in poly (cytidylic acid)
    • Freier, S. M., K. O. Hill, T. G. Dewey, L. A. Marky, K. J. Breslauer, and D. H. Turner. 1981. Solvent effects on the kinetics and thermodynamics of stacking in poly (cytidylic acid). Biochemistry. 20:1419-1426.
    • (1981) Biochemistry , vol.20 , pp. 1419-1426
    • Freier, S.M.1    Hill, K.O.2    Dewey, T.G.3    Marky, L.A.4    Breslauer, K.J.5    Turner, D.H.6
  • 16
    • 0015914592 scopus 로고
    • Free energy of imperfect nucleic acid helices. II. Small hairpin loops
    • Gralla, J., and D. M. Crothers. 1973. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol. 73:497-511.
    • (1973) J. Mol. Biol. , vol.73 , pp. 497-511
    • Gralla, J.1    Crothers, D.M.2
  • 19
    • 0033614819 scopus 로고    scopus 로고
    • Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices
    • Holbrook, J. A., M. W. Capp, R. M. Saecker, and M. T. Record. 1999. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry. 38:8409-8422.
    • (1999) Biochemistry , vol.38 , pp. 8409-8422
    • Holbrook, J.A.1    Capp, M.W.2    Saecker, R.M.3    Record, M.T.4
  • 22
    • 0025729926 scopus 로고
    • Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges
    • LeBlanc, D. A., and K. M. Morden. 1991. Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry. 30:4042-4047.
    • (1991) Biochemistry , vol.30 , pp. 4042-4047
    • LeBlanc, D.A.1    Morden, K.M.2
  • 23
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 87:911-940.
    • (1999) J. Mol. Biol. , vol.87 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 24
    • 0029955048 scopus 로고    scopus 로고
    • RNAdraw: An integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
    • Matzura, O., and A. Wennborg. 1996. RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. Comput. Appl. Biosci. 12:247-249.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 247-249
    • Matzura, O.1    Wennborg, A.2
  • 25
    • 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
  • 27
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contribution to helix stability: Thermodynamic of double-helix formation with CCGG, CCGGp, CCGGAp, CCGGUp, and ACCGGUp
    • Petersheim, M., and D. H. Turner. 1983. Base-stacking and base-pairing contribution to helix stability: Thermodynamic of double-helix formation with CCGG, CCGGp, CCGGAp, CCGGUp, and ACCGGUp. Biochemistry. 22:256-263.
    • (1983) Biochemistry , vol.22 , pp. 256-263
    • Petersheim, M.1    Turner, D.H.2
  • 28
    • 0028783875 scopus 로고
    • Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex
    • Plum, G. E., A. P. Grollman, F. Johnson, and K. J. Breslauer. 1995. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry. 34:16148-16160.
    • (1995) Biochemistry , vol.34 , pp. 16148-16160
    • Plum, G.E.1    Grollman, A.P.2    Johnson, F.3    Breslauer, K.J.4
  • 29
    • 0015846852 scopus 로고
    • Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC basepairs
    • Poerschke, D., O. C. Uhlenbeck, and F. H. Martin. 1973. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC basepairs. Biopolymers. 12:1313-1335.
    • (1973) Biopolymers , vol.12 , pp. 1313-1335
    • Poerschke, D.1    Uhlenbeck, O.C.2    Martin, F.H.3
  • 30
    • 0016266885 scopus 로고
    • Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations
    • Poland, D. 1974. Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations. Biopolymers. 13:1859-1871.
    • (1974) Biopolymers , vol.13 , pp. 1859-1871
    • Poland, D.1
  • 32
    • 0024804759 scopus 로고
    • Absorbance melting curves of RNA
    • Puglisi, J. D., and I. Tinoco, Jr. 1989. Absorbance melting curves of RNA. Methods Enzymol. 180:304-325.
    • (1989) Methods Enzymol. , vol.180 , pp. 304-325
    • Puglisi, J.D.1    Tinoco Jr., I.2
  • 34
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J., Jr. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 35
    • 0035070585 scopus 로고    scopus 로고
    • Immobilized RNA switches for the analysis of complex chemical and biological mixture
    • Seetharaman, S., M. Zivarats, N. Sudarsan, and R. R. Braker. 2001. Immobilized RNA switches for the analysis of complex chemical and biological mixture. Nat. Biotechnol. 19:336-341.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 336-341
    • Seetharaman, S.1    Zivarats, M.2    Sudarsan, N.3    Braker, R.R.4
  • 37
    • 0000826487 scopus 로고
    • Biochemical applications of differential scanning calorimetry
    • Sturtevant, J. M. 1987. Biochemical applications of differential scanning calorimetry. Annu. Rev. Phys. Chem. 38:463-488.
    • (1987) Annu. Rev. Phys. Chem. , vol.38 , pp. 463-488
    • Sturtevant, J.M.1
  • 38
    • 0023653195 scopus 로고
    • Sequence dependence for the energetics of dangling ends terminal base pairs in ribonucleic acid
    • Sugimoto, N., R. Kierzek, and D. H. Turner. 1987. Sequence dependence for the energetics of dangling ends terminal base pairs in ribonucleic acid. Biochemistry. 26:4554-4558.
    • (1987) Biochemistry , vol.26 , pp. 4554-4558
    • Sugimoto, N.1    Kierzek, R.2    Turner, D.H.3
  • 39
    • 0013549381 scopus 로고
    • Sequence alignment in the neighborhood of the optimum with general application to dynamic programming
    • Waterman, M. S. 1983. Sequence alignment in the neighborhood of the optimum with general application to dynamic programming. Proc. Natl. Acad. Sci. USA. 80:3123-3124.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3123-3124
    • Waterman, M.S.1
  • 40
    • 0022380106 scopus 로고
    • A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
    • Waterman, M. S., and T. H. Byers. 1985. A dynamic programming algorithm to find all solutions in a neighborhood of the optimum. Math. Biosci. 77:179-188.
    • (1985) Math. Biosci. , vol.77 , pp. 179-188
    • Waterman, M.S.1    Byers, T.H.2
  • 41
    • 0023045712 scopus 로고
    • A dynamic programing algorithm for finding alternate RNA secondary structures
    • Williams, A. L., and I. Tinoco, Jr. 1986. A dynamic programing algorithm for finding alternate 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
  • 42
    • 0025896047 scopus 로고
    • Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides
    • Zieba, K., T. M. Chu, D. W. Kupke, and L. A. Marky. 1991. Differential hydration of dA-dT base pairing and dA and dT bulges in deoxyoligonucleotides. Biochemistry. 30:8018-8026.
    • (1991) Biochemistry , vol.30 , pp. 8018-8026
    • Zieba, K.1    Chu, T.M.2    Kupke, D.W.3    Marky, L.A.4
  • 43
    • 0000754002 scopus 로고
    • "Theory of melting" of the helical form in double chains of the DNA type
    • Zimm, B. H. 1960. "Theory of melting" of the helical form in double chains of the DNA type. J. Chem. Phys. 33:1349-1356.
    • (1960) J. Chem. Phys. , vol.33 , pp. 1349-1356
    • Zimm, B.H.1
  • 44
    • 0024806949 scopus 로고
    • Computer prediction of RNA structure
    • Zuker, M. 1989a. Computer prediction of RNA structure. Methods Enzymol. 180:262-288.
    • (1989) Methods Enzymol. , vol.180 , pp. 262-288
    • Zuker, M.1
  • 45
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker, M. 1989b. On finding all suboptimal foldings of an RNA molecule. Science. 244:48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 46
    • 0000616205 scopus 로고
    • RNA secondary structures and their prediction
    • Zuker, M., and D. Sankoff. 1984. RNA secondary structures and their prediction. Bull. Math. Biol. 46:591-621.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 591-621
    • Zuker, M.1    Sankoff, D.2
  • 47
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., and P. Stiegler. 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
  • 48
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • J. Barciszewski, and B. F. C. Clark, editors. NATO ASI Series. Kluwer Academic Publishers. Dordrecht, the Netherlands
    • Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA Biochemistry and Biotechnology. J. Barciszewski, and B. F. C. Clark, editors. NATO ASI Series. Kluwer Academic Publishers. Dordrecht, the Netherlands. 11-43.
    • (1999) RNA Biochemistry and Biotechnology , pp. 11-43
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.