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Volumn 285, Issue 4, 1999, Pages 1563-1575

Resolving the discrepancies among nucleic acid conformational analyses

Author keywords

Base pair geometry; Conflicting rise values; Dimer step parameters; Nucleic acid conformational analysis; Nucleic acid structure

Indexed keywords

ALGORITHM; ARTICLE; BASE PAIRING; COMPUTER PROGRAM; GEOMETRY; MATHEMATICS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL;

EID: 0033614014     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2390     Document Type: Article
Times cited : (90)

References (51)
  • 1
    • 84950267569 scopus 로고
    • Crystallographic databases: Search and retrieval of information from the Cambridge Structural Database
    • J. D. Dunitz, & H.-B. Bürgi. New York: VCH Publisher
    • Allen F. H., Kennard O., Watson D. G. Crystallographic databases: search and retrieval of information from the Cambridge Structural Database. Dunitz J. D., Bürgi H.-B. Structure Correlation. 1994;71-ü110 VCH Publisher, New York.
    • (1994) Structure Correlation , pp. 71-110
    • Allen, F.H.1    Kennard, O.2    Watson, D.G.3
  • 2
    • 0031776981 scopus 로고    scopus 로고
    • The structure of PurR mutant L54M shows an alternative route to DNA kinking
    • Arvidson D. N., Lu F., Faber C., Zalkin H., Brennan R. G. The structure of PurR mutant L54M shows an alternative route to DNA kinking. Nature Struct. Biol. 5:1998;436-441.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 436-441
    • Arvidson, D.N.1    Lu, F.2    Faber, C.3    Zalkin, H.4    Brennan, R.G.5
  • 3
    • 0028221654 scopus 로고
    • The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters
    • Babcock M. S., Olson W. K. The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. J. Mol. Biol. 237:1994;98-124.
    • (1994) J. Mol. Biol. , vol.237 , pp. 98-124
    • Babcock, M.S.1    Olson, W.K.2
  • 4
    • 0028230287 scopus 로고
    • Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures
    • Babcock M. S., Pednault E. P. D., Olson W. K. Nucleic acid structure analysis: mathematics for local cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237:1994;125-156.
    • (1994) J. Mol. Biol. , vol.237 , pp. 125-156
    • Babcock, M.S.1    Pednault, E.P.D.2    Olson, W.K.3
  • 5
    • 0029023343 scopus 로고
    • NUPARM and NUCGEN: Software for analysis and generation of sequence dependent nucleic acid structures
    • Bansal M., Bhattacharyya D., Ravi B. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci. 11:1995;281-287.
    • (1995) Comput. Appl. Biosci. , vol.11 , pp. 281-287
    • Bansal, M.1    Bhattacharyya, D.2    Ravi, B.3
  • 6
    • 0014413509 scopus 로고
    • The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye
    • Bauer W., Vinograd J. The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. J. Mol. Biol. 33:1968;141-171.
    • (1968) J. Mol. Biol. , vol.33 , pp. 141-171
    • Bauer, W.1    Vinograd, J.2
  • 8
    • 0024543897 scopus 로고
    • A self-consistent formulation for analysis and generation of non-uniform DNA structures
    • Bhattacharyya D., Bansal M. A self-consistent formulation for analysis and generation of non-uniform DNA structures. J. Biomol. Struct. Dynam. 6:1989;635-653.
    • (1989) J. Biomol. Struct. Dynam. , vol.6 , pp. 635-653
    • Bhattacharyya, D.1    Bansal, M.2
  • 9
    • 0025648066 scopus 로고
    • Local variability and base sequence effects in DNA crystal structure
    • Bhattacharyya D., Bansal M. Local variability and base sequence effects in DNA crystal structure. J. Biomol. Struct. Dynam. 8:1990;539-572.
    • (1990) J. Biomol. Struct. Dynam. , vol.8 , pp. 539-572
    • Bhattacharyya, D.1    Bansal, M.2
  • 11
    • 0342565151 scopus 로고
    • Helix comparison table
    • F. A. Jurnak, & A. McPherson. New York: Wiley-Interscience
    • Dickerson R. E. Helix comparison table. Jurnak F. A., McPherson A. Biological Macromolecules and Assemblies. 1985;471-494 Wiley-Interscience, New York.
    • (1985) Biological Macromolecules and Assemblies , pp. 471-494
    • Dickerson, R.E.1
  • 12
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • Dickerson R. E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucl. Acids Res. 26:1998;1906-1926.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 1906-1926
    • Dickerson, R.E.1
  • 15
    • 0029126044 scopus 로고
    • The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
    • El Hassan M. A., Calladine C. R. The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme. J. Mol. Biol. 251:1995;648-664.
    • (1995) J. Mol. Biol. , vol.251 , pp. 648-664
    • El Hassan, M.A.1    Calladine, C.R.2
  • 16
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
    • El Hassan M. A., Calladine C. R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. Roy. Soc. London. 355:1997;43-100.
    • (1997) Phil. Trans. Roy. Soc. London , vol.355 , pp. 43-100
    • El Hassan, M.A.1    Calladine, C.R.2
  • 19
    • 0020359857 scopus 로고
    • Reversible bending and helix geometry in a B-DNA dodecamer - CGCGAATTBrCGCG
    • Fratini A. V., Kopka M. L., Drew H. R., Dickerson R. E. Reversible bending and helix geometry in a B-DNA dodecamer - CGCGAATTBrCGCG. J. Biol. Chem. 257:1982;4686-4470.
    • (1982) J. Biol. Chem. , vol.257 , pp. 4686-4470
    • Fratini, A.V.1    Kopka, M.L.2    Drew, H.R.3    Dickerson, R.E.4
  • 20
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin A. A., Zhurkin V. B., Olson W. K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 21
    • 0030040722 scopus 로고    scopus 로고
    • A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein
    • Guzikevich-Guerstein G., Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol. 3:1996;32-37.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 32-37
    • Guzikevich-Guerstein, G.1    Shakked, Z.2
  • 22
    • 0031556948 scopus 로고    scopus 로고
    • DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures
    • Hunter C. A., Lu X. J. DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265:1997;603-619.
    • (1997) J. Mol. Biol. , vol.265 , pp. 603-619
    • Hunter, C.A.1    Lu, X.J.2
  • 24
    • 0025187081 scopus 로고
    • Refinement of Eco RI endonuclease crystal structure: A revised protein chain tracing
    • Kim Y., Grable J. C., Love R., Greene P. J., Rosenberg J. M. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science. 249:1990;1307-1309.
    • (1990) Science , vol.249 , pp. 1307-1309
    • Kim, Y.1    Grable, J.C.2    Love, R.3    Greene, P.J.4    Rosenberg, J.M.5
  • 25
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim Y., Geiger J. H., Halm S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Halm, S.3    Sigler, P.B.4
  • 26
    • 0028010888 scopus 로고
    • HhaI methyltransferase flips its target base out of the DNA helix
    • Klimasauskas S., Kumar S., Roberts R. J., Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
    • (1994) Cell , vol.76 , pp. 357-369
    • Klimasauskas, S.1    Kumar, S.2    Roberts, R.J.3    Cheng, X.4
  • 27
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6:1988;63-91.
    • (1988) J. Biomol. Struct. Dynam. , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 28
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery R., Sklenar H. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dynam. 6:1989;655-667.
    • (1989) J. Biomol. Struct. Dynam. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 30
    • 0021095856 scopus 로고
    • Protein folding by restrained energy minimization and molecular dynamics
    • Levitt M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170:1983;723-764.
    • (1983) J. Mol. Biol. , vol.170 , pp. 723-764
    • Levitt, M.1
  • 31
    • 0031592942 scopus 로고    scopus 로고
    • Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
    • Lu X. J., El Hassan M. A., Hunter C. A. Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). J. Mol. Biol. 273:1997a;668-680.
    • (1997) J. Mol. Biol. , vol.273 , pp. 668-680
    • Lu, X.J.1    El Hassan, M.A.2    Hunter, C.A.3
  • 32
    • 0031592938 scopus 로고    scopus 로고
    • Structure and conformation of helical nucleic acids: Rebuilding program (SCHNArP)
    • Lu X. J., El Hassan M. A., Hunter C. A. Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J. Mol. Biol. 273:1997b;681-691.
    • (1997) J. Mol. Biol. , vol.273 , pp. 681-691
    • Lu, X.J.1    El Hassan, M.A.2    Hunter, C.A.3
  • 34
    • 0028923794 scopus 로고
    • Comparison of rotation models for describing DNA conformations: Application to static and polymorphic forms
    • Mazur J., Jernigan R. L. Comparison of rotation models for describing DNA conformations: Application to static and polymorphic forms. Biophys. J. 68:1995;1472-1489.
    • (1995) Biophys. J. , vol.68 , pp. 1472-1489
    • Mazur, J.1    Jernigan, R.L.2
  • 35
    • 0022419269 scopus 로고
    • The crystal structure of d(G-G-G-G-C-C-C-C): A model for poly(dG)·poly(dC)
    • McCall M., Brown T., Kermard O. The crystal structure of d(G-G-G-G-C-C-C-C): a model for poly(dG)·poly(dC). J. Mol. Biol. 183:1985;385-396.
    • (1985) J. Mol. Biol. , vol.183 , pp. 385-396
    • McCall, M.1    Brown, T.2    Kermard, O.3
  • 36
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • Nelson H. C. M., Finch J. T., Luisi B. E., Klug A. The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature. 330:1987;221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.E.3    Klug, A.4
  • 37
    • 0030005131 scopus 로고    scopus 로고
    • Simulating DNA at low resolution
    • Olson W. K. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6:1996;242-256.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 242-256
    • Olson, W.K.1
  • 38
    • 0027317556 scopus 로고
    • Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA
    • Olson W. K., Marky N. L., Jernigan R. L., Zhurkin V. B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232:1993;530-554.
    • (1993) J. Mol. Biol. , vol.232 , pp. 530-554
    • Olson, W.K.1    Marky, N.L.2    Jernigan, R.L.3    Zhurkin, V.B.4
  • 39
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W. K., Gorin A. A., Lu X. J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 95:1998;11163-11168.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 40
    • 0031968248 scopus 로고    scopus 로고
    • Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond
    • Pardo L., Pastor N., Weinstein H. Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond. Biophys. J. 74:1998;2191-2198.
    • (1998) Biophys. J. , vol.74 , pp. 2191-2198
    • Pardo, L.1    Pastor, N.2    Weinstein, H.3
  • 41
    • 0027718102 scopus 로고
    • Nucleic acids structure analysis: A users guide to a collection of new analysis programs
    • Pednault E. P. D., Babcock M. S., Olson W. K. Nucleic acids structure analysis: a users guide to a collection of new analysis programs. J. Biomol. Struct. Dynam. 11:1993;597-628.
    • (1993) J. Biomol. Struct. Dynam. , vol.11 , pp. 597-628
    • Pednault, E.P.D.1    Babcock, M.S.2    Olson, W.K.3
  • 42
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
    • Rice P. A., Yang S. W., Mizuuchi K., Nash H. A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 87:1996;1295-1306.
    • (1996) Cell , vol.87 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.W.2    Mizuuchi, K.3    Nash, H.A.4
  • 44
    • 84946632750 scopus 로고
    • A rigorous basepair oriented description of DNA structures
    • Soumpasis D. M., Tung C. S. A rigorous basepair oriented description of DNA structures. J. Biomol. Struct. Dynam. 6:1988;397-420.
    • (1988) J. Biomol. Struct. Dynam. , vol.6 , pp. 397-420
    • Soumpasis, D.M.1    Tung, C.S.2
  • 45
    • 84947409428 scopus 로고
    • Relationships among rise, cup, roll and stagger in DNA suggested by empirical potential studies of base stacking
    • Sponer J., Kypr J. Relationships among rise, cup, roll and stagger in DNA suggested by empirical potential studies of base stacking. J. Biomol. Struct. Dynam. 11:1993a;27-41.
    • (1993) J. Biomol. Struct. Dynam. , vol.11 , pp. 27-41
    • Sponer, J.1    Kypr, J.2
  • 46
    • 0027370181 scopus 로고
    • Theoretical analysis of the base stacking in DNA: Choice of the force field and a comparison with the oligonucleotide crystal structures
    • Sponer J., Kypr J. Theoretical analysis of the base stacking in DNA: choice of the force field and a comparison with the oligonucleotide crystal structures. J. Biomol. Struct. Dynam. 11:1993b;277-292.
    • (1993) J. Biomol. Struct. Dynam. , vol.11 , pp. 277-292
    • Sponer, J.1    Kypr, J.2
  • 47
    • 0016670764 scopus 로고
    • X-ray crystallographic visualization of drug-nucleic acid intercalative binding: Structure of an ethidium- dinucleoside monophosphate crystalline complex ethidium: 5-iodouridylyl (3′-5′) adenosine
    • Tsai C. C., Jain S. C., Sobell H. M. X-ray crystallographic visualization of drug-nucleic acid intercalative binding: Structure of an ethidium- dinucleoside monophosphate crystalline complex ethidium: 5-iodouridylyl (3′-5′) adenosine. Proc. Natl Acad. Sci. USA. 72:1975;628-632.
    • (1975) Proc. Natl Acad. Sci. USA , vol.72 , pp. 628-632
    • Tsai, C.C.1    Jain, S.C.2    Sobell, H.M.3
  • 48
    • 0028098726 scopus 로고
    • An extension of the rigorous base-unit oriented description of nucleic-acid structures
    • Tung C. S., Soumpasis D. M., Hummer G. An extension of the rigorous base-unit oriented description of nucleic-acid structures. J. Biomol. Struct. Dynam. 11:1994;1327-1344.
    • (1994) J. Biomol. Struct. Dynam. , vol.11 , pp. 1327-1344
    • Tung, C.S.1    Soumpasis, D.M.2    Hummer, G.3
  • 49
    • 0030046809 scopus 로고    scopus 로고
    • Intercalation, DNA kinking, and the control of transcription
    • Werner M. E., Gronenborn A. M., Clore G. M. Intercalation, DNA kinking, and the control of transcription. Science. 271:1996;778-784.
    • (1996) Science , vol.271 , pp. 778-784
    • Werner, M.E.1    Gronenborn, A.M.2    Clore, G.M.3
  • 50
    • 0025966606 scopus 로고
    • Analysis of local helix geometry in three B -DNA decamers and eight dodecamers
    • Yanagi K., Privé G. G., Dickerson R. E. Analysis of local helix geometry in three B -DNA decamers and eight dodecamers. J. Mol. Biol. 217:1991;201-214.
    • (1991) J. Mol. Biol. , vol.217 , pp. 201-214
    • Yanagi, K.1    Privé, G.G.2    Dickerson, R.E.3
  • 51
    • 0018447932 scopus 로고
    • Anisotropic flexibility of DNA and the nucleosomal structure
    • Zhurkin V. B., Lysov Y. P., Ivanov V. I. Anisotropic flexibility of DNA and the nucleosomal structure. Nucl. Acids Res. 6:1979;1081-1096.
    • (1979) Nucl. Acids Res. , vol.6 , pp. 1081-1096
    • Zhurkin, V.B.1    Lysov, Y.P.2    Ivanov, V.I.3


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