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Volumn 273, Issue 3, 1997, Pages 668-680

Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)

Author keywords

Base pair parameters; Base stacking diagrams; DNA conformation; Global helical parameters; Step parameters

Indexed keywords

DINUCLEOTIDE; DNA A; DNA B; DNA Z; NUCLEOSIDE; PHOSPHATE; SUGAR;

EID: 0031592942     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1346     Document Type: Article
Times cited : (73)

References (49)
  • 1
    • 0015511563 scopus 로고
    • Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation
    • Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:1972;8205-8212.
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 8205-8212
    • Altona, C.1    Sundaralingam, M.2
  • 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 nucleic acid structures
    • Bansal M., Bhattacharyya D., Ravi B. NUPARM and NUCGEN: software for analysis and generation of sequence 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
  • 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
    • 0001705236 scopus 로고
    • To fit a plane to a set of points by least squares
    • Blow D. M. To fit a plane to a set of points by least squares. Acta Crystallog. 13:1960;168.
    • (1960) Acta Crystallog. , vol.13 , pp. 168
    • Blow, D.M.1
  • 10
    • 0021770861 scopus 로고
    • A base centered explanation of theBA
    • Calladine C. R., Drew H. R. A base centered explanation of theBA. J. Mol. Biol. 178:1984;773-781.
    • (1984) J. Mol. Biol. , vol.178 , pp. 773-781
    • Calladine, C.R.1    Drew, H.R.2
  • 13
    • 0003860639 scopus 로고
    • Usual and unusual DNA structure: A summing up
    • R.D. Wells, & S.C. Harvey. New York: Springer-Verlag
    • Dickerson R. E. Usual and unusual DNA structure: a summing up. Wells R. D., Harvey S. C. Unusual DNA Structures. 1988;Springer-Verlag, New York.
    • (1988) Unusual DNA Structures
    • Dickerson, R.E.1
  • 14
    • 0026702486 scopus 로고
    • DNA structure fromAZ
    • Dickerson R. E. DNA structure fromAZ. Methods Enzymol. 211:1992;67-111.
    • (1992) Methods Enzymol. , vol.211 , pp. 67-111
    • Dickerson, R.E.1
  • 15
    • 0024974308 scopus 로고
    • Definitions and nomenclature of nucleic acid structure parameters
    • Diekmann S. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205:1989;787-791.
    • (1989) J. Mol. Biol. , vol.205 , pp. 787-791
    • Diekmann, S.1
  • 17
    • 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
  • 18
    • 0030003963 scopus 로고    scopus 로고
    • Propeller-twisting of case-pairs and conformational mobility of dinucleotide steps in DNA
    • El Hassan M. A., Calladine C. R. Propeller-twisting of case-pairs and conformational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259:1996;95-103.
    • (1996) J. Mol. Biol. , vol.259 , pp. 95-103
    • El Hassan, M.A.1    Calladine, C.R.2
  • 22
    • 0019522154 scopus 로고
    • Deoxyribonucleic acid structure: A new model
    • Hopkins R. C. Deoxyribonucleic acid structure: a new model. Science. 211:1981;289-291.
    • (1981) Science , vol.211 , pp. 289-291
    • Hopkins, R.C.1
  • 23
    • 0020640597 scopus 로고
    • Transitions betweenBZ
    • Hopkins R. C. Transitions betweenBZ. J. Theoret. Biol. 101:1983;327-333.
    • (1983) J. Theoret. Biol. , vol.101 , pp. 327-333
    • Hopkins, R.C.1
  • 24
    • 0024595890 scopus 로고
    • Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions
    • Hunter W. N., Destaintot B. L., Kennard O. Structural variation in d(CTCTAGAG). implications for protein-DNA interactions. Biochemistry. 28:1989;2444-2451.
    • (1989) Biochemistry , vol.28 , pp. 2444-2451
    • Hunter, W.N.1    Destaintot, B.L.2    Kennard, O.3
  • 25
    • 0028085105 scopus 로고
    • DNA modeler: An interactive program for modeling stacks of DNA base pairs on a microcomputer
    • Jursa J. DNA modeler: an interactive program for modeling stacks of DNA base pairs on a microcomputer. Comput. Appl. Biosci. 10:1994;61-65.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 61-65
    • Jursa, J.1
  • 26
    • 0025940363 scopus 로고
    • Single-crystal X-ray diffraction studies of oligonucleotides and oligonucleotide-drug complexes
    • Kennard O., Hunter W. N. Single-crystal X-ray diffraction studies of oligonucleotides and oligonucleotide-drug complexes. Agnew. Chem. Int. Ed. Engl. 30:1991;1254-1277.
    • (1991) Agnew. Chem. Int. Ed. Engl. , vol.30 , pp. 1254-1277
    • Kennard, O.1    Hunter, W.N.2
  • 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
    • 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. 273:1997;681-691.
    • (1997) J. Mol. Biol. , vol.273 , pp. 681-691
    • Lu, X.J.1    El Hassan, M.A.2    Hunter, C.A.3
  • 32
    • 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
  • 33
    • 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., Kennard 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    Kennard, O.3
  • 34
    • 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. F., 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.F.3    Klug, A.4
  • 35
    • 0029868524 scopus 로고    scopus 로고
    • The high resolution crystal structure of the DNA decamer d(AGGCATGCCT)
    • Nunn C. M., Neidle S. The high resolution crystal structure of the DNA decamer d(AGGCATGCCT). J. Mol. Biol. 256:1996;340-351.
    • (1996) J. Mol. Biol. , vol.256 , pp. 340-351
    • Nunn, C.M.1    Neidle, S.2
  • 36
    • 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
    • 0029051383 scopus 로고
    • The crystal structure of r(CCCCGGGG) in two distinct lattices
    • Portmann S., Usman N., Egli M. The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry. 34:1995;7569-7575.
    • (1995) Biochemistry , vol.34 , pp. 7569-7575
    • Portmann, S.1    Usman, N.2    Egli, M.3
  • 40
    • 0031052180 scopus 로고    scopus 로고
    • Making DNA do a U-turn: IHF and related proteins
    • Rice P. A. Making DNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol. 7:1997;86-93.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 86-93
    • Rice, P.A.1
  • 41
    • 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
  • 42
    • 0017098687 scopus 로고
    • RNA double helices generated from crystal structures of double helical dinucleotide phosphates
    • Rosenberg J. M., Seeman. N. C., Day R. O., Rich A. RNA double helices generated from crystal structures of double helical dinucleotide phosphates. Biochem. Biophys. Res. Commun. 69:1976;979-987.
    • (1976) Biochem. Biophys. Res. Commun. , vol.69 , pp. 979-987
    • Rosenberg, J.M.1    Seeman, N.C.2    Day, R.O.3    Rich, A.4
  • 44
    • 0000137136 scopus 로고
    • To fit a plane or a line to a set of points by least squares
    • Schomaker V., Waser J., Marsh R. E., Bergman G. To fit a plane or a line to a set of points by least squares. Acta Crystallog. 12:1959;600-604.
    • (1959) Acta Crystallog. , vol.12 , pp. 600-604
    • Schomaker, V.1    Waser, J.2    Marsh, R.E.3    Bergman, G.4
  • 46
    • 0028098726 scopus 로고
    • An extension of the rigorous base-unit oriented description of the nucleic-acid structures
    • Tung C. S., Soumpasis D. M., Hummer G. An extension of the rigorous base-unit oriented description of the 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
  • 48
    • 0000795223 scopus 로고
    • A structure for deoxyribose nucleic acid
    • Watson J. D., Crick F. H. C. A structure for deoxyribose nucleic acid. Nature. 1953;171-738.
    • (1953) Nature , pp. 171-738
    • Watson, J.D.1    Crick, F.H.C.2
  • 49
    • 0017885231 scopus 로고
    • Conformations of DNA as revealed by computer calculations
    • Zhurkin V. B., Lysov Y. P., Ivanov V. I. Conformations of DNA as revealed by computer calculations. Biopolymers, 17:1978;377-412.
    • (1978) Biopolymers , vol.17 , pp. 377-412
    • Zhurkin, V.B.1    Lysov, Y.P.2    Ivanov, V.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.