메뉴 건너뛰기




Volumn 43, Issue 22, 2004, Pages 7143-7150

Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; MATHEMATICAL MODELS; MELTING; THERMODYNAMICS;

EID: 2642579966     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi036188r     Document Type: Article
Times cited : (42)

References (46)
  • 1
    • 84984934354 scopus 로고    scopus 로고
    • Molecular interactions on microarrays
    • Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays, Nat. Genet. 21, 5-9.
    • (1999) Nat. Genet. , vol.21 , pp. 5-9
    • Southern, E.1    Mir, K.2    Shchepinov, M.3
  • 2
    • 0035823170 scopus 로고    scopus 로고
    • Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology
    • Tillib, S. V., and Mirzabekov, A. D. (2001) Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology, Curr. Opin. Biotechnol. 12, 53-58.
    • (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 53-58
    • Tillib, S.V.1    Mirzabekov, A.D.2
  • 3
    • 0033578928 scopus 로고    scopus 로고
    • Universal DNA microarray method for multiplex detection of low abundance point mutations
    • Gerry, N. P., Witowski, N. E., Day, J., Hammer, R. P., Barany, G., and Barany, F. (1999) Universal DNA microarray method for multiplex detection of low abundance point mutations, J. Mol. Biol. 292, 251-262.
    • (1999) J. Mol. Biol. , vol.292 , pp. 251-262
    • Gerry, N.P.1    Witowski, N.E.2    Day, J.3    Hammer, R.P.4    Barany, G.5    Barany, F.6
  • 4
    • 0037011984 scopus 로고    scopus 로고
    • A robust DNA mechanical device controlled by hybridization topology
    • Yan, H., Zhang, X., Shen, Z., and Seeman, N. C. (2002) A robust DNA mechanical device controlled by hybridization topology, Nature 415, 62-65.
    • (2002) Nature , vol.415 , pp. 62-65
    • Yan, H.1    Zhang, X.2    Shen, Z.3    Seeman, N.C.4
  • 5
    • 0032490948 scopus 로고    scopus 로고
    • Design and self-assembly of two-dimensional DNA crystals
    • Winfree, E., Liu, F., Wenzler, L. A., and Seeman, N. C. (1998) Design and self-assembly of two-dimensional DNA crystals, Nature 394, 539-544.
    • (1998) Nature , vol.394 , pp. 539-544
    • Winfree, E.1    Liu, F.2    Wenzler, L.A.3    Seeman, N.C.4
  • 6
    • 0028114541 scopus 로고
    • Molecular computation of solutions to combinatorial problems
    • Adleman, L. M. (1994) Molecular computation of solutions to combinatorial problems, Science 266, 1021-1024.
    • (1994) Science , vol.266 , pp. 1021-1024
    • Adleman, L.M.1
  • 8
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes, Nucleic Acids Res. 24, 4501-4505.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 9
    • 0030875847 scopus 로고    scopus 로고
    • Thermodynamics and NMR of internal G·T mismatches in DNA
    • Allawi, H. T., and SantaLucia, J., Jr. (1997) Thermodynamics and NMR of internal G·T mismatches in DNA, Biochemistry 36, 10581-10594.
    • (1997) Biochemistry , vol.36 , pp. 10581-10594
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 10
    • 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. 26, 2694-2701.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2694-2701
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 11
    • 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., Jr. (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 Jr., J.4
  • 12
    • 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 37, 9435-9444.
    • (1998) Biochemistry , vol.37 , pp. 9435-9444
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 13
    • 0032562140 scopus 로고    scopus 로고
    • Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA
    • Allawi, H. T., and SantaLucia, J., Jr. (1998) Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA, Biochemistry 37, 2170-2179.
    • (1998) Biochemistry , vol.37 , pp. 2170-2179
    • Allawi, H.T.1    SantaLucia Jr., J.2
  • 14
    • 0025786033 scopus 로고
    • Thermodynamics of DNA duplexes with adjacent G·A mismatches
    • Li, Y., Zon, G., and Wilson, W. D. (1991) Thermodynamics of DNA duplexes with adjacent G·A mismatches, Biochemistry 30, 7566-7572.
    • (1991) Biochemistry , vol.30 , pp. 7566-7572
    • Li, Y.1    Zon, G.2    Wilson, W.D.3
  • 15
    • 0029116756 scopus 로고
    • Oligonucleotides containing G·A pairs: Effect of flanking sequences on structure and stability
    • Li, Y., and Agrawal, S. (1995) Oligonucleotides containing G·A pairs: effect of flanking sequences on structure and stability, Biochemistry 34, 10056-10062.
    • (1995) Biochemistry , vol.34 , pp. 10056-10062
    • Li, Y.1    Agrawal, S.2
  • 16
    • 0022423486 scopus 로고
    • Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T)
    • Aboul-ela, F., Koh, D., Tinoco, I., Jr., and Martin, F. H. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T), Nucleic Acids Res. 13, 4811-4824.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 4811-4824
    • Aboul-Ela, F.1    Koh, D.2    Tinoco Jr., I.3    Martin, F.H.4
  • 17
    • 0034194135 scopus 로고    scopus 로고
    • Thermodynamic parameters for DNA sequences with dangling ends
    • Bommarito, S., Peyret, N., and SantaLucia, J., Jr. (2000) Thermodynamic parameters for DNA sequences with dangling ends, Nucleic Acids Res. 28, 1929-1934.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1929-1934
    • Bommarito, S.1    Peyret, N.2    SantaLucia Jr., J.3
  • 18
    • 0024290403 scopus 로고
    • Influence of dangling thymidine residues on the stability and structure of two DNA duplexes
    • Senior, M., Jones, R. A., and Breslauer, K. J. (1988) Influence of dangling thymidine residues on the stability and structure of two DNA duplexes, Biochemistry 27, 3879-3885.
    • (1988) Biochemistry , vol.27 , pp. 3879-3885
    • Senior, M.1    Jones, R.A.2    Breslauer, K.J.3
  • 19
    • 0025729926 scopus 로고
    • Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges
    • LeBlanc, D. A., and Morden, K. M. (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
  • 20
    • 0034703715 scopus 로고    scopus 로고
    • Kinetic property of bulged helix formation: Analysis of kinetic behavior using nearest-neighbor parameters
    • Ohmichi, T., Nakamuta, H., Yasuda, K., and Sugimoto, N. (2000) Kinetic property of bulged helix formation: analysis of kinetic behavior using nearest-neighbor parameters, J. Am. Chem. Soc. 122, 11286-11294.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 11286-11294
    • Ohmichi, T.1    Nakamuta, H.2    Yasuda, K.3    Sugimoto, N.4
  • 22
    • 0028969367 scopus 로고
    • Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment
    • Ke, S. H., and Wartell, R. M. (1995) Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment, Biochemistry 34, 4593-4600.
    • (1995) Biochemistry , vol.34 , pp. 4593-4600
    • Ke, S.H.1    Wartell, R.M.2
  • 23
    • 0033619687 scopus 로고    scopus 로고
    • The effect of base sequence on the stability of RNA and DNA single base bulges
    • Zhu, J., and Wartell, R. M. (1999) The effect of base sequence on the stability of RNA and DNA single base bulges, Biochemistry 38, 15986-15993.
    • (1999) Biochemistry , vol.38 , pp. 15986-15993
    • Zhu, J.1    Wartell, R.M.2
  • 24
    • 0025186882 scopus 로고
    • Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
    • Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides, Biochemistry 29, 278-285.
    • (1990) Biochemistry , vol.29 , pp. 278-285
    • Longfellow, C.E.1    Kierzek, R.2    Turner, D.H.3
  • 25
    • 0037143573 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges
    • Znosko, B. M., Silvestri, S. B., Volkman, H., Boswell, B., and Serra, M. J. (2002) Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges, Biochemistry 41, 10406-10417.
    • (2002) Biochemistry , vol.41 , pp. 10406-10417
    • Znosko, B.M.1    Silvestri, S.B.2    Volkman, H.3    Boswell, B.4    Serra, M.J.5
  • 26
    • 0028945546 scopus 로고
    • Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes
    • Gray, D. M., Hung, S. H., and Johnson, K. H. (1995) Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes, Methods Enzymol. 246, 19-34.
    • (1995) Methods Enzymol. , vol.246 , pp. 19-34
    • Gray, D.M.1    Hung, S.H.2    Johnson, K.H.3
  • 33
    • 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
  • 34
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • SantaLucia, J., Jr., Allawi, H. T., and Seneviratne, P. A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability, Biochemistry 35, 3555-3562.
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia Jr., J.1    Allawi, H.T.2    Seneviratne, P.A.3
  • 36
    • 0021760007 scopus 로고
    • An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules
    • Papanicolaou, C., Gouy, M., and Ninio, J. (1984) An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules, Nucleic Acids Res. 12, 31-44.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 31-44
    • Papanicolaou, C.1    Gouy, M.2    Ninio, J.3
  • 37
    • 0025042737 scopus 로고
    • NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA)·oligo(dT) tract
    • Morden, K. M., Gunn, B. M., and Maskos, K. (1990) NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA)·oligo(dT) tract, Biochemistry 29, 8835-8845.
    • (1990) Biochemistry , vol.29 , pp. 8835-8845
    • Morden, K.M.1    Gunn, B.M.2    Maskos, K.3
  • 39
    • 0024516799 scopus 로고
    • Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. Extra adenosine stacks into duplex independent of flanking sequence and temperature
    • Kalnik, M. W., Norman, D. G., Swann, P. F., and Patel, D. J. (1989) Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. Extra adenosine stacks into duplex independent of flanking sequence and temperature, J. Biol. Chem. 264, 3702-3712.
    • (1989) J. Biol. Chem. , vol.264 , pp. 3702-3712
    • Kalnik, M.W.1    Norman, D.G.2    Swann, P.F.3    Patel, D.J.4
  • 40
    • 0025037779 scopus 로고
    • Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states
    • Kalnik, M. W., Norman, D. G., Li, B. F., Swann, P. F., and Patel, D. J. (1990) Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states, J. Biol. Chem. 265, 636-647.
    • (1990) J. Biol. Chem. , vol.265 , pp. 636-647
    • Kalnik, M.W.1    Norman, D.G.2    Li, B.F.3    Swann, P.F.4    Patel, D.J.5
  • 41
    • 0024965969 scopus 로고
    • Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: Extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution
    • Kalnik, M. W., Norman, D. G., Zagorski, M. G., Swann, P. F., and Patel, D. J. (1989) Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution, Biochemistry 28, 294-303.
    • (1989) Biochemistry , vol.28 , pp. 294-303
    • Kalnik, M.W.1    Norman, D.G.2    Zagorski, M.G.3    Swann, P.F.4    Patel, D.J.5
  • 42
    • 0024276818 scopus 로고
    • Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization
    • Woodson, S. A., and Crothers, D. M. (1988) Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization, Biochemistry 27, 3130-3141.
    • (1988) Biochemistry , vol.27 , pp. 3130-3141
    • Woodson, S.A.1    Crothers, D.M.2
  • 43
    • 0029805937 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and simulated annealing
    • 2 by two-dimensional NMR and simulated annealing, Biochemistry 35, 14077-14089.
    • (1996) Biochemistry , vol.35 , pp. 14077-14089
    • McDowell, J.A.1    Turner, D.H.2
  • 44
    • 0031462334 scopus 로고    scopus 로고
    • Measuring the thermodynamics of RNA secondary structure formation
    • SantaLucia, J., Jr., and Turner, D. H. (1997) Measuring the thermodynamics of RNA secondary structure formation, Biopolymers 44, 309-319.
    • (1997) Biopolymers , vol.44 , pp. 309-319
    • SantaLucia Jr., J.1    Turner, D.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.