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Volumn 73, Issue 6, 1997, Pages 2990-3003

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA; SOLVENT;

EID: 0030735002     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78328-0     Document Type: Article
Times cited : (27)

References (67)
  • 1
    • 0028864394 scopus 로고
    • The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein
    • Aboul-ela, F., J. Karn, and G. Varani. 1995. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253:313-332.
    • (1995) J. Mol. Biol. , vol.253 , pp. 313-332
    • Aboul-ela, F.1    Karn, J.2    Varani, G.3
  • 2
    • 0029852357 scopus 로고    scopus 로고
    • Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge
    • Aboul-ela, F., J. Karn, and G. Varani. 1996. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res. 24:3974-3981.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3974-3981
    • Aboul-ela, F.1    Karn, J.2    Varani, G.3
  • 3
    • 0024426629 scopus 로고
    • The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles)
    • Battacharyya, A., and D. M. J. Lilley. 1989. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids, Res. 17:6821-6840.
    • (1989) Nucleic Acids, Res. , vol.17 , pp. 6821-6840
    • Battacharyya, A.1    Lilley, D.M.J.2
  • 4
    • 0025171938 scopus 로고
    • RNA bulges and the helical periodicity of double stranded RNA
    • Battacharyya, A., A. I. H. Murchie, and D. M. J. Lilley. 1990. RNA bulges and the helical periodicity of double stranded RNA. Nature. 343: 484-487.
    • (1990) Nature , vol.343 , pp. 484-487
    • Battacharyya, A.1    Murchie, A.I.H.2    Lilley, D.M.J.3
  • 5
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics program
    • Davis, M. E., J. D. Madura, B. A. Luty, and J. A. McCammon. 1991. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comput. Phys. Commun. 62:187-198.
    • (1991) Comput. Phys. Commun. , vol.62 , pp. 187-198
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 6
    • 84986522972 scopus 로고
    • Dieleciric boundary smoothing in finite difference solutions of the Poisson equation: An approach to improve accuracy and convergence
    • Davis, M. E., and J. A. McCammon. 1991. Dieleciric boundary smoothing in finite difference solutions of the Poisson equation: an approach to improve accuracy and convergence. J. Comput. Chem. 12:909-912.
    • (1991) J. Comput. Chem. , vol.12 , pp. 909-912
    • Davis, M.E.1    McCammon, J.A.2
  • 8
    • 0026816545 scopus 로고
    • The electrostatic contribution to DNA base-stacking interactions
    • Friedman, R. A., and B. Honig. 1992. The electrostatic contribution to DNA base-stacking interactions. Biopolymers. 32:145-159.
    • (1992) Biopolymers , vol.32 , pp. 145-159
    • Friedman, R.A.1    Honig, B.2
  • 9
    • 0029118487 scopus 로고
    • A free energy analysis of nucleic acid base stacking in aqueous solution
    • Friedman, R. A., and B. Honig. 1995. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. 69:1528-1535.
    • (1995) Biophys. J. , vol.69 , pp. 1528-1535
    • Friedman, R.A.1    Honig, B.2
  • 10
    • 0028072693 scopus 로고
    • Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence energy transfer
    • Gohlke, C., A. I. H. Murchie, D. M. J. Lilley, and R. M. Clegg. 1994. Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence energy transfer. Proc. Natl. Acad. Sci. USA. 91: 11660-11664.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11660-11664
    • Gohlke, C.1    Murchie, A.I.H.2    Lilley, D.M.J.3    Clegg, R.M.4
  • 11
    • 0023052458 scopus 로고
    • Extra-helical adenosine stacks into right-handed DNA: Solution conformation of the d(CGCA-GAGCTCGCG) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra
    • Hare, D., L. Shapiro, and D. J. Patel. 1986. Extra-helical adenosine stacks into right-handed DNA: solution conformation of the d(CGCA-GAGCTCGCG) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. Biochemistry. 25:7456-7464.
    • (1986) Biochemistry , vol.25 , pp. 7456-7464
    • Hare, D.1    Shapiro, L.2    Patel, D.J.3
  • 12
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions: Biological and chemical applications
    • Honig, B., K. A. Sharp, and A.-S. Yang. 1993. Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97:1101-1109.
    • (1993) J. Phys. Chem. , vol.97 , pp. 1101-1109
    • Honig, B.1    Sharp, K.A.2    Yang, A.-S.3
  • 13
    • 0001690587 scopus 로고
    • Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: Possible relevance to the folding of single-stranded nucleic acids
    • Hsieh, C.-H., and J. D. Griffith. 1989. Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids. Proc. Natl. Acad. Sci. U.S.A. 86:4833-4837.
    • (1989) Proc. Natl. Acad. Sci. U.S.A. , vol.86 , pp. 4833-4837
    • Hsieh, C.-H.1    Griffith, J.D.2
  • 14
    • 0024580271 scopus 로고
    • The electrostatic potential of B-DNA
    • Jayaram, B., K. A. Sharp, and B. Honig. 1989. The electrostatic potential of B-DNA. Biopolymers. 28:975-993.
    • (1989) Biopolymers , vol.28 , pp. 975-993
    • Jayaram, B.1    Sharp, K.A.2    Honig, B.3
  • 15
    • 85022423714 scopus 로고
    • Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations
    • Jean-Charles, A., A. Nicolls, K. A. Sharp A., B. Honig, B. Tempzyck, B. Hendrikson, and W. C. Still. 1991. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations. J. Am. Chem. Soc. 113:1454-1455.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 1454-1455
    • Jean-Charles, A.1    Nicolls, A.2    Sharp A., K.A.3    Honig, B.4    Tempzyck, B.5    Hendrikson, B.6    Still, W.C.7
  • 17
    • 0023951245 scopus 로고
    • The three-dimensional structure of a DNA duplex containing looped-out bases
    • Joshua-Tor, L., D. Rabinovich, H. Hope, F. Frolow, E. Appela, and J. L. Sussman. 1988. The three-dimensional structure of a DNA duplex containing looped-out bases. Nature. 334:82-84.
    • (1988) Nature , vol.334 , pp. 82-84
    • Joshua-Tor, L.1    Rabinovich, D.2    Hope, H.3    Frolow, F.4    Appela, E.5    Sussman, J.L.6
  • 18
    • 0027487292 scopus 로고
    • Molecular modelling of the 3D structure of RNA tetraloops with different nucleotide sequences
    • Kajava, A., and H. Rüterjans. 1993. Molecular modelling of the 3D structure of RNA tetraloops with different nucleotide sequences. Nucleic Acids Res. 21:4557-4562.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 4557-4562
    • Kajava, A.1    Rüterjans, H.2
  • 19
    • 0025037779 scopus 로고
    • Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes
    • Kalnik, M. W., D. G. Norman, P. F. Swann, and D. J. Patel. 1990. Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. J. Biol. Chem. 265:636-647.
    • (1990) J. Biol. Chem. , vol.265 , pp. 636-647
    • Kalnik, M.W.1    Norman, D.G.2    Swann, P.F.3    Patel, D.J.4
  • 20
    • 0024965969 scopus 로고
    • Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: Extra cytidine equilibrates between looped out (low temperatures) and stacked (elevated temperature) conformation in solution
    • Kalnik, M. W., D. G. Norman, M. G. Zagorski, P. F. Swann, and D. J. Patel. 1989. Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperatures) and stacked (elevated temperature) conformation 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
  • 21
    • 0029286439 scopus 로고
    • Triad DNA: A model for trinucleotide repeats
    • Kuryavyi, V. V., and T. M. Jovin. 1995. Triad DNA: a model for trinucleotide repeats. Nature Genet. 9:339-341.
    • (1995) Nature Genet. , vol.9 , pp. 339-341
    • Kuryavyi, V.V.1    Jovin, T.M.2
  • 22
    • 0001063425 scopus 로고
    • Junctions and bends in nucleic acids: A new theoretical modelling approach
    • W. K. Olson, R. H. Sarma, M. H. Sarma, and M. Sundaralingam, editors. Adenine Press, New York
    • Lavery, R. 1988. Junctions and bends in nucleic acids: a new theoretical modelling approach. In Structure and Expression. W. K. Olson, R. H. Sarma, M. H. Sarma, and M. Sundaralingam, editors. Adenine Press, New York. 121-211.
    • (1988) Structure and Expression , pp. 121-211
    • Lavery, R.1
  • 23
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery, R., and H. Sklenar. 1988. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:63-91.
    • (1988) J. Biomol. Struct. Dyn. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 24
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R., and H. Sklenar. 1989. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6: 655-667.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 25
    • 0022691669 scopus 로고
    • The flexibility of nucleic acids. II. The calculation of internal energy and applications to mononucleotide repeats in DNA
    • Lavery, R., H. Sklenar, K. Zakrzewska, and A. Pullman. 1986. The flexibility of nucleic acids. II. The calculation of internal energy and applications to mononucleotide repeats in DNA. J. Biomol. Struct. Dyn. 3:989-1014.
    • (1986) J. Biomol. Struct. Dyn. , vol.3 , pp. 989-1014
    • Lavery, R.1    Sklenar, H.2    Zakrzewska, K.3    Pullman, A.4
  • 26
    • 84988106802 scopus 로고
    • Optimized monopole expansions for the representation of the electrostatic properties of the nucleic acids
    • Lavery, R., K. Zakrzewska, and A. Pullman. 1984. Optimized monopole expansions for the representation of the electrostatic properties of the nucleic acids. J. Comput. Chem. 5:363-373.
    • (1984) J. Comput. Chem. , vol.5 , pp. 363-373
    • Lavery, R.1    Zakrzewska, K.2    Pullman, A.3
  • 28
    • 84986532558 scopus 로고
    • Solving the finite-difference non-linear Poisson-Boltzmann equation
    • Luty, B. A., M. E. Davis, and J. A. McCammon. 1992. Solving the finite-difference non-linear Poisson-Boltzmann equation. J. Comput. Chem. 13:768-771.
    • (1992) J. Comput. Chem. , vol.13 , pp. 768-771
    • Luty, B.A.1    Davis, M.E.2    McCammon, J.A.3
  • 30
    • 0023897732 scopus 로고
    • Crystal structure of 15-mer DNA duplex containing unpaired bases
    • Miller, M., R. W. Harritson, A. Woldaver, E. Appela, and J. L. Sussman. 1988. Crystal structure of 15-mer DNA duplex containing unpaired bases. Nature. 334:85-86.
    • (1988) Nature , vol.334 , pp. 85-86
    • Miller, M.1    Harritson, R.W.2    Woldaver, A.3    Appela, E.4    Sussman, J.L.5
  • 31
    • 0028239626 scopus 로고
    • Salt effects on protein-DNA interactions: The cI repressor and EcoRI endonuclease
    • Misra, V. K., J. L. Hecht, K. A. Sharp, R. A. Friedman, and B. Honig. 1994b. Salt effects on protein-DNA interactions: the cI repressor and EcoRI endonuclease. J. Mol. Biol. 238:264-280.
    • (1994) J. Mol. Biol. , vol.238 , pp. 264-280
    • Misra, V.K.1    Hecht, J.L.2    Sharp, K.A.3    Friedman, R.A.4    Honig, B.5
  • 32
    • 0029047968 scopus 로고
    • On the magnitude of electrostatic contribution to ligand-DNA interactions
    • Misra, V. K., and B. Honig. 1995. On the magnitude of electrostatic contribution to ligand-DNA interactions. Proc. Natl. Acad. Sci. USA. 92:4691-4695.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 4691-4695
    • Misra, V.K.1    Honig, B.2
  • 33
    • 0030032805 scopus 로고    scopus 로고
    • Electrostatic contribution to the B to Z transition of DNA
    • Misra, V. K., and B. Honig. 1996. Electrostatic contribution to the B to Z transition of DNA. Biochemistry. 35:1115-1124.
    • (1996) Biochemistry , vol.35 , pp. 1115-1124
    • Misra, V.K.1    Honig, B.2
  • 34
    • 0028246710 scopus 로고
    • Salt effects on ligand-DNA binding: Minor groove binding antibiotics
    • Misra, V. K., K. A. Sharp, R. A. Friedman, and B. Honig. 1994a. Salt effects on ligand-DNA binding: minor groove binding antibiotics. J. Mol. Biol. 238:245-263.
    • (1994) J. Mol. Biol. , vol.238 , pp. 245-263
    • Misra, V.K.1    Sharp, K.A.2    Friedman, R.A.3    Honig, B.4
  • 35
    • 0010928616 scopus 로고
    • Continuum model calculations of solvation free energies: Accurate evaluation of electrostatic contributions
    • Mohan, V., M. E. Davis, J. A. McCammon, and B. M. Pettitt. 1992. Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions. J. Phvs. Chem. 96:428-6431.
    • (1992) J. Phvs. Chem. , vol.96 , pp. 428-6431
    • Mohan, V.1    Davis, M.E.2    McCammon, J.A.3    Pettitt, B.M.4
  • 38
    • 0024471947 scopus 로고
    • 31P NMR spectra and restrained molecular dynamics structure of an extra-helical adenosine tridecamer oligodeoxyribonucleotide
    • 31P NMR spectra and restrained molecular dynamics structure of an extra-helical adenosine tridecamer oligodeoxyribonucleotide. Biochemistry. 28:8714-8725.
    • (1989) Biochemistry , vol.28 , pp. 8714-8725
    • Nikonowicz, E.1    Roongta, V.2    Jones, C.R.3    Gorenstein, D.G.4
  • 40
    • 0026699291 scopus 로고
    • Conformational substates in B-DNA
    • Poncin, M., B. Hartmann, and R. Lavery. 1992. Conformational substates in B-DNA. J. Mol. Biol. 226:775-794.
    • (1992) J. Mol. Biol. , vol.226 , pp. 775-794
    • Poncin, M.1    Hartmann, B.2    Lavery, R.3
  • 41
    • 0030090986 scopus 로고    scopus 로고
    • Crystal structures of an A-form duplex with single-adenosine bulges and conformational basis for site-specific RNA self-cleavage
    • Portmann, S., S. Grimm, C. Workman, N. Usman, and M. Egli. 1996. Crystal structures of an A-form duplex with single-adenosine bulges and conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3:173-184.
    • (1996) Chem. Biol. , vol.3 , pp. 173-184
    • Portmann, S.1    Grimm, S.2    Workman, C.3    Usman, N.4    Egli, M.5
  • 42
    • 0025728614 scopus 로고
    • OPLS potential functions for nucleotide bases: Relative association constants of hydrogen bonded pairs in chloroform
    • Pranata, J. S. G., S. G. Wierschke, and W. L. Jorgensen. 1991. OPLS potential functions for nucleotide bases: relative association constants of hydrogen bonded pairs in chloroform. J. Am. Chem. Soc. 113: 2810-2819.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 2810-2819
    • Pranata, J.S.G.1    Wierschke, S.G.2    Jorgensen, W.L.3
  • 43
    • 0026651395 scopus 로고
    • Conformation of the TAR RNA-arginine complex by NMR spectroscopy
    • Puglisi, J. D., R. Tan, B. J. Calnan, A. D. Frankel, and J. R. Williamson. 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
    • 0031012579 scopus 로고    scopus 로고
    • Enzyme inhibitor association thermodynamics: Explicit and continuum solvent studies
    • Resat, H., T. J. Marrone, and J. A. McCammon. 1997. Enzyme inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys. J. 72:522-532.
    • (1997) Biophys. J. , vol.72 , pp. 522-532
    • Resat, H.1    Marrone, T.J.2    McCammon, J.A.3
  • 45
    • 0024375698 scopus 로고
    • DNA bending by the bulge defect
    • Rice, J. A., and D. M. Crothers. 1989. DNA bending by the bulge defect. Biochemistry. 28:4512-4516.
    • (1989) Biochemistry , vol.28 , pp. 4512-4516
    • Rice, J.A.1    Crothers, D.M.2
  • 46
    • 33751552991 scopus 로고
    • Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
    • Sharp, K. A., and B. Honig. 1990. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94: 7684-7692.
    • (1990) J. Phys. Chem. , vol.94 , pp. 7684-7692
    • Sharp, K.A.1    Honig, B.2
  • 47
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms: Lysozyme and insulin
    • Shrake, A., and J. A. Rupley. 1973. Environment and exposure to solvent of protein atoms: lysozyme and insulin. J. Mol. Biol. 79:351-365.
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-365
    • Shrake, A.1    Rupley, J.A.2
  • 48
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 49
    • 0022691672 scopus 로고
    • The flexibility of nucleic acids. I. "SIR", a novel approach to the variation of polymer geometry in constraint systems
    • Sklenar, H., R. Lavery, and B. Pullman. 1986. The flexibility of nucleic acids. I. "SIR", a novel approach to the variation of polymer geometry in constraint systems. J. Biomol. Struct. Dyn. 3:967-987.
    • (1986) J. Biomol. Struct. Dyn. , vol.3 , pp. 967-987
    • Sklenar, H.1    Lavery, R.2    Pullman, B.3
  • 50
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith, K. C., and B. Honig. 1994. Evaluation of the conformational free energies of loops in proteins. Proteins Struct. Fund. Genet. 18:119-132.
    • (1994) Proteins Struct. Fund. Genet. , vol.18 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 51
    • 0001008706 scopus 로고
    • Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations
    • Smith, P. E., R. M. Brunne, A. E. Mark, and W. F. van Gunsteren. 1993. Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations. J. Phys. Chem. 97:2009-2014.
    • (1993) J. Phys. Chem. , vol.97 , pp. 2009-2014
    • Smith, P.E.1    Brunne, R.M.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 54
    • 0025802093 scopus 로고
    • Effects of bulge composition and flanking sequence on the kinking of DNA by bulges
    • Wang, Y. H., and J. Griffith. 1991. Effects of bulge composition and flanking sequence on the kinking of DNA by bulges. Biochemistry. 30:1358-1363.
    • (1991) Biochemistry , vol.30 , pp. 1358-1363
    • Wang, Y.H.1    Griffith, J.2
  • 55
    • 0023127913 scopus 로고
    • Proton-nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence
    • Woodson, S. A., and D. M. Crothers. 1988a. Proton-nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence. Biochemistry. 26:904-912.
    • (1988) Biochemistry , vol.26 , pp. 904-912
    • Woodson, S.A.1    Crothers, D.M.2
  • 56
    • 0024276818 scopus 로고
    • Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization
    • Woodson, S. A., and D. M Crothers. 1988b. 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
  • 57
    • 0024686721 scopus 로고
    • Conformation of a bulge-containing oligomer from a hot spot sequence by NMR and energy minimization
    • Woodson, S. A., and D. M. Crothers. 1989. Conformation of a bulge-containing oligomer from a hot spot sequence by NMR and energy minimization. Biopolymers. 28:1149-1177.
    • (1989) Biopolymers , vol.28 , pp. 1149-1177
    • Woodson, S.A.1    Crothers, D.M.2
  • 58
    • 0023657074 scopus 로고
    • Role of a bulged A residue in a specific RNA protein interaction
    • Wu, H.-N., and O. C. Uhlenbeck. 1987. Role of a bulged A residue in a specific RNA protein interaction. Biochemistry. 26:8221-8227.
    • (1987) Biochemistry , vol.26 , pp. 8221-8227
    • Wu, H.-N.1    Uhlenbeck, O.C.2
  • 59
    • 0029121068 scopus 로고
    • Free energy determinants of secondary structure formation. I. α-Helices
    • Yang, A.-S., and B. Honig. 1995a. Free energy determinants of secondary structure formation. I. α-Helices. J. Mol. Biol 252:251-265.
    • (1995) J. Mol. Biol , vol.252 , pp. 251-265
    • Yang, A.-S.1    Honig, B.2
  • 60
    • 0029150955 scopus 로고
    • Free energy determinants of secondary structure formation. II. Anti-parallel β-sheets
    • Yang, A.-S., and B. Honig. 1995b. Free energy determinants of secondary structure formation. II. Anti-parallel β-sheets. J. Mol. Biol. 252: 366-376.
    • (1995) J. Mol. Biol. , vol.252 , pp. 366-376
    • Yang, A.-S.1    Honig, B.2
  • 61
    • 0030596522 scopus 로고    scopus 로고
    • Free energy determinants of secondary structure formation. III. β-Turns and their role in protein folding
    • Yang, A.-S., and B. Honig. 1996. Free energy determinants of secondary structure formation. III. β-Turns and their role in protein folding. J. Mol. Biol. 259:873-882.
    • (1996) J. Mol. Biol. , vol.259 , pp. 873-882
    • Yang, A.-S.1    Honig, B.2
  • 62
    • 0029148986 scopus 로고
    • Dielectric response of triplex DNA in ionic solution from simulations
    • Yang, L., S. Weerasinghe, P. E. Smith, and B. M. Pettitt. 1995. Dielectric response of triplex DNA in ionic solution from simulations. Biophys. J. 69:1519-1527.
    • (1995) Biophys. J. , vol.69 , pp. 1519-1527
    • Yang, L.1    Weerasinghe, S.2    Smith, P.E.3    Pettitt, B.M.4
  • 63
    • 0028969693 scopus 로고
    • Bulge-Induced bends in RNA: Quantification by transient electric birefringence
    • Zacharias, M., and P. J. Hagerman. 1995a. Bulge-Induced bends in RNA: quantification by transient electric birefringence. J. Mol. Biol. 247: 486-500.
    • (1995) J. Mol. Biol. , vol.247 , pp. 486-500
    • Zacharias, M.1    Hagerman, P.J.2
  • 64
    • 0029032837 scopus 로고
    • The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide
    • Zacharias, M., and P. J. Hagerman. 1995b. The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc. Natl. Acad. Sci. USA. 92:6052-6056.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 6052-6056
    • Zacharias, M.1    Hagerman, P.J.2
  • 65
    • 0030989905 scopus 로고    scopus 로고
    • The influence of static and dynamic bends on the birefringence decay profiles of RNA helices: Brownian dynamics simulations
    • Zacharias, M., and P. J. Hagerman. 1997. The influence of static and dynamic bends on the birefringence decay profiles of RNA helices: Brownian dynamics simulations. Biophys. J. 73:318-332.
    • (1997) Biophys. J. , vol.73 , pp. 318-332
    • Zacharias, M.1    Hagerman, P.J.2
  • 66
    • 0026619551 scopus 로고
    • Poisson-Boltzmann analysis of the λ-repressor-operator interaction
    • Zacharias, M., B. A. Luty, M. E. Davis, and J. A. McCammon. 1992. Poisson-Boltzmann analysis of the λ-repressor-operator interaction. Biophys. J. 63:1280-1285.
    • (1992) Biophys. J. , vol.63 , pp. 1280-1285
    • Zacharias, M.1    Luty, B.A.2    Davis, M.E.3    McCammon, J.A.4
  • 67
    • 0028339543 scopus 로고
    • Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking
    • Zacharias, M., B. A. Luty, M. E. Davis, and J. A. McCammon. 1994. Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. J. Mol. Biol. 238:455-465.
    • (1994) J. Mol. Biol. , vol.238 , pp. 455-465
    • Zacharias, M.1    Luty, B.A.2    Davis, M.E.3    McCammon, J.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.