메뉴 건너뛰기




Volumn 280, Issue 3, 1998, Pages 407-420

Sequence-dependent DNA structure: The role of the sugar-phosphate backbone

Author keywords

Base stacking interactions; DNA; Force field energy calculations; Sequence dependent structure; Virtual backbone model

Indexed keywords

DINUCLEOTIDE; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; SUGAR PHOSPHATE;

EID: 0032540859     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1865     Document Type: Article
Times cited : (90)

References (38)
  • 1
    • 0025648066 scopus 로고
    • Local variability and base sequence effects in DNA crystal-structures
    • Bhattacharyya D., Bansal M. Local variability and base sequence effects in DNA crystal-structures. J. Biomol. Struct. Dynam. 8:1990;539-572
    • (1990) J. Biomol. Struct. Dynam. , vol.8 , pp. 539-572
    • Bhattacharyya, D.1    Bansal, M.2
  • 2
    • 0020385863 scopus 로고
    • Mechanics of sequence-dependent stacking of bases in B-DNA
    • Calladine C.R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161:1982;343-352
    • (1982) J. Mol. Biol. , vol.161 , pp. 343-352
    • Calladine, C.R.1
  • 4
    • 0030953141 scopus 로고    scopus 로고
    • Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes
    • Cheatham T.E., Kollman P.A. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119:1997;4805-4825
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 4805-4825
    • Cheatham, T.E.1    Kollman, P.A.2
  • 6
    • 0020619672 scopus 로고
    • Base sequence and helix structure variation in B-DNA and A-DNA
    • Dickerson R.E. Base sequence and helix structure variation in B-DNA and A-DNA. J. Mol. Biol. 166:1983;419-441
    • (1983) J. Mol. Biol. , vol.166 , pp. 419-441
    • Dickerson, R.E.1
  • 7
    • 0026702486 scopus 로고
    • DNA structure from a to Z
    • Dickerson R.E. DNA structure from A to Z. Methods Enzymol. 211:1992;67-111
    • (1992) Methods Enzymol. , vol.211 , pp. 67-111
    • Dickerson, R.E.1
  • 9
    • 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
  • 12
    • 0029126044 scopus 로고
    • The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
    • Elhassan 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
    • Elhassan, M.A.1    Calladine, C.R.2
  • 13
    • 3142518260 scopus 로고    scopus 로고
    • Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
    • Elhassan 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. of London Ser. A, Math. Phys. Eng. Sci. 355:1997;43-100
    • (1997) Phil. Trans. Roy. Soc. of London Ser. A, Math. Phys. Eng. Sci. , vol.355 , pp. 43-100
    • Elhassan, M.A.1    Calladine, C.R.2
  • 14
    • 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;3686-4707
    • (1982) J. Biol. Chem. , vol.257 , pp. 3686-4707
    • Fratini, A.V.1    Kopka, M.L.2    Drew, H.R.3    Dickerson, R.E.4
  • 15
    • 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
  • 16
    • 0027318463 scopus 로고
    • Sequence dependent DNA structure: The role of base stacking interactions
    • Hunter C.A. Sequence dependent DNA structure the role of base stacking interactions. J. Mol. Biol. 230:1993;1025-1054
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 17
    • 0031556948 scopus 로고    scopus 로고
    • DNA base stacking interactions: A comparison of theoretical calculations with oligonucleotide crystal structures
    • Hunter C.A., Lu X.J. DNA base stacking interactions a comparison of theoretical calculations with oligonucleotide 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
  • 21
    • 0029757424 scopus 로고    scopus 로고
    • Constructing optimal backbone segments for joining fixed DNA base pairs
    • Mazur J., Jernigan R.L., Sarai A. Constructing optimal backbone segments for joining fixed DNA base pairs. Biophys. J. 71:1996;1493-1506
    • (1996) Biophys. J. , vol.71 , pp. 1493-1506
    • Mazur, J.1    Jernigan, R.L.2    Sarai, A.3
  • 22
    • 0016502853 scopus 로고
    • Configurational statistics of polynucleotide chains, a single virtual bond treatment
    • Olson W.K. Configurational statistics of polynucleotide chains, a single virtual bond treatment. Macromolecules. 8:1975;272-275
    • (1975) Macromolecules , vol.8 , pp. 272-275
    • Olson, W.K.1
  • 23
    • 0038359471 scopus 로고
    • Configurational statistics of polynucleotide chains, an updated virtual bond model to treat effects of base stacking
    • Olson W.K. Configurational statistics of polynucleotide chains, an updated virtual bond model to treat effects of base stacking. Macromolecules. 13:1980;721-728
    • (1980) Macromolecules , vol.13 , pp. 721-728
    • Olson, W.K.1
  • 25
    • 0015262029 scopus 로고
    • Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond model
    • Olson W.K., Flory P.J. Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides a virtual bond model. Biopolymers. 11:1972;1-23
    • (1972) Biopolymers , vol.11 , pp. 1-23
    • Olson, W.K.1    Flory, P.J.2
  • 27
    • 0026059567 scopus 로고
    • Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
    • Privé G.G., Yanagi K., Dickerson R.E. Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J. Mol. Biol. 217:1991;177-199
    • (1991) J. Mol. Biol. , vol.217 , pp. 177-199
    • Privé, G.G.1    Yanagi, K.2    Dickerson, R.E.3
  • 29
    • 0029763315 scopus 로고    scopus 로고
    • Interdependence of conformational variables in double-helical DNA
    • Sarai A., Jernigan R.L., Mazur J. Interdependence of conformational variables in double-helical DNA. Biophys. J. 71:1996;1507-1518
    • (1996) Biophys. J. , vol.71 , pp. 1507-1518
    • Sarai, A.1    Jernigan, R.L.2    Mazur, J.3
  • 30
    • 0031195002 scopus 로고    scopus 로고
    • Conformations of the sugar-phosphate backbone in helical DNA crystal structures
    • Schneider B., Neidle S., Berman H.M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers. 42:1997;113-124
    • (1997) Biopolymers , vol.42 , pp. 113-124
    • Schneider, B.1    Neidle, S.2    Berman, H.M.3
  • 31
    • 0029788346 scopus 로고    scopus 로고
    • Hydrogen-bonding and stacking of DNA bases: A review of quantum-chemical ab initio studies
    • Sponer J., Leszczynski J., Hobza P. Hydrogen-bonding and stacking of DNA bases a review of quantum-chemical ab initio studies. J. Biomol. Struct. Dynam. 14:1996;117-135
    • (1996) J. Biomol. Struct. Dynam. , vol.14 , pp. 117-135
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 32
    • 0023350241 scopus 로고
    • Nucleic acid model building: Multiple backbone solutions
    • Srinvasan A.R., Olson W.K. Nucleic acid model building Multiple backbone solutions. J. Biomol. Struct. Dynam. 4:1987;895
    • (1987) J. Biomol. Struct. Dynam. , vol.4 , pp. 895
    • Srinvasan, A.R.1    Olson, W.K.2
  • 33
    • 0031555483 scopus 로고    scopus 로고
    • Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA
    • Suzuki M., Amano N., Kakinuma J., Tateno M. Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. J. Mol. Biol. 274:1997;421-435
    • (1997) J. Mol. Biol. , vol.274 , pp. 421-435
    • Suzuki, M.1    Amano, N.2    Kakinuma, J.3    Tateno, M.4
  • 34
    • 0021760286 scopus 로고
    • A molecular mechanical model to predict the helix twist angles of B-DNA
    • Tung C.S., Harvey S.C. A molecular mechanical model to predict the helix twist angles of B-DNA. Nucl. Acids Res. 12:1984;3343-3356
    • (1984) Nucl. Acids Res. , vol.12 , pp. 3343-3356
    • Tung, C.S.1    Harvey, S.C.2
  • 35
    • 0023045698 scopus 로고
    • Computer-graphics program to reveal the dependence of the gross 3-D structure of the B-DNA double helix on primary structure
    • Tung C.S., Harvey S.C. Computer-graphics program to reveal the dependence of the gross 3-D structure of the B-DNA double helix on primary structure. Nucl. Acids Res. 14:1986;381-387
    • (1986) Nucl. Acids Res. , vol.14 , pp. 381-387
    • Tung, C.S.1    Harvey, S.C.2
  • 36
    • 0028695270 scopus 로고
    • Extended electron distributions applied to the molecular mechanics of some intermolecular interactions
    • Vinter J.G. Extended electron distributions applied to the molecular mechanics of some intermolecular interactions. J. Comp. Aided Mol. Design. 8:1994;653-668
    • (1994) J. Comp. Aided Mol. Design , vol.8 , pp. 653-668
    • Vinter, J.G.1
  • 37
    • 0025966606 scopus 로고
    • Analysis of local helix geometry in three B-DNA decamers and 8 dodecamers
    • Yanagi K., Privé G.G., Dickerson R.E. Analysis of local helix geometry in three B-DNA decamers and 8 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
  • 38
    • 0017885231 scopus 로고
    • Different families of double-stranded conformations of DNA as revealed by computer calculations
    • Zhurkin V.B., Lysov Y.P., Ivanov V.I. Different families of double-stranded 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.