Intrinsic conformational properties of deoxyribonucleosides: Implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

Biophysical Journal

Volumn 76, Issue 6, 1999, Pages 3206-3218

  Foloppe, Nicolas ^a,b   MacKerell Jr , Alexander D ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DEOXYCYTIDINE; DEOXYRIBONUCLEOSIDE; DNA A; DNA B; DNA Z; GUANINE; IMIDAZOLE; PURINE; PYRIMIDINE; THYMIDINE; URACIL;

ARTICLE; CHEMICAL BOND; CONFORMATION; CONTROLLED STUDY; DNA BASE COMPOSITION; THERMODYNAMICS;

EID: 0033032014     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77472-2     Document Type: Article

References (76)

1. Arnott, S., R. Chandrasekaran, D. W. L. Hukins, P. J. C. Smith, and L. Watts. 1974. Structural details of a double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J. Mol. Biol. 88:523-533.
2. Arnott, S., and E. Selsing. 1974a. The structure of polydeoxyguanilic acid · polydeoxycytidylic acid. J. Mol. Biol. 88:551-552.
3. Arnott, S., and E. Selsing. 1974b. Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dA) · poly(dT) · poly(dT). J. Mol. Biol. 88:509-521.
4. 13C]2′-deoxyribonucleosides: correlations with molecular structure. J. Am. Chem. Soc. 119:1737-1744.
5. Behe, M., and G. Felsenfeld. 1981. Effects of methylation on a synthetic polynucleotide: the B-Z transition in poly(dG-m5dC) · poly(dG-m5dC). Proc. Natl. Acad. Sci. U.S.A. 78:1619-1623.
6. Berman, H. M., W. K. Olson, D. L. Beveridge, J. Westbrook, A. Gelbin, T. Demeny, S.-H. Hsieh, A. R. Srinivasan, and B. Schneider. 1992. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:751-759.
7. Berthod, H., and B. Pullman. 1971a. Molecular orbital calculations of the conformation of nucleic acids and their constituents. I. Conformational energies of β-nucleosides with C(3′)- and C(2′)-endo sugars. Biochim. Biophys. Acta. 232:595-606.
8. Berthod, H., and B. Pullman. 1971b. Molecular orbital calculations of the conformation of nucleic acids and their constituents. II. Conformational energies of β-nucleosides with C(3′)- and C(2′)-exo sugars. Biochim. Biophys. Acta. 246:359-364.
9. Bram, S. 1971. Secondary structure of DNA depends on base composition. Nat. New Biol. 232:174-176.
10. Bram, S., and P. Tougard. 1972. Polymorphism of natural DNA. Nat. New Biol. 239:128-131.
11. Calladine, C. R., and H. R. Drew. 1984. A base-centered explanation of the B-to-A transition in DNA. J. Mol. Biol. 178:773-782.
12. Chuprina, V. P. 1985. Regularities in formation of the spine of hydration in the DNA minor groove and its influence on the DNA structure. FEBS Lett. 186:98-102.
13. Chuprina, V. P. 1987. Anomalous structure and properties of poly(dA) · poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove. Nucleic Acids Res. 15:293-311.
14. Clowney, L., S. C. Jain, A. R. Srinivasan, J. Westbrook, W. K. Olson, and H. M. Berman. 1996. Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118:509-518.
15. Davies, D. B. 1978. Conformations of nucleosides and nucleotides. Prog. Nucl. Magn. Reson. Spectrosc. 12:135-226.
16. Davies, D. R., and R. L. Baldwin. 1963. X-ray studies of two synthetic DNA copolymers. J. Mol. Biol. 6:251-255.
17. Dickerson, R. E. 1992. DNA structure from A to Z. Methods Enzymol. 211:67-111.
18. Dickerson, R. E., H. R. Drew, B. N. Conner, R. M. Wing, A. V. Fratini, and M. L. Kopka. 1982. The anatomy of A-, B-, and Z-DNA. Science. 216:475-485.
19. Dickerson, R. E., D. S. Goodsell, and S. Neidle. 1994. ". . . the tyranny of the lattice. . . ". Proc. Natl. Acad. Sci. USA. 91:3579-3583.
20. Drew, H. R., and R. E. Dickerson. 1981. Structure of a B-DNA dodecamer III. Geometry of hydration. J. Mol. Biol. 151:535-556.
21. Drew, H., T. Takano, S. Tanaka, K. Itakura, and R. E. Dickerson. 1980. High-salt d(CpGpCpG), a left-handed Z′-DNA double helix. Nature. 286:567-573.
22. Drew, H. R., R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, and R. S. Dickerson. 1981. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA. 78:2179-2183.
23. Feig, M., and B. M. Pettitt. 1998. Structural equilibrium of DNA represented with different force fields. Biophys. J. 75:134-149.
24. Foloppe, N., and A. D. MacKerell, Jr. 1998. Conformational properties of the deoxyribose and ribose moieties of nucleic acids: a quantum mechanical study. J. Phys. Chem. B. 102:6669-6678.
25. Franklin, R. E., and R. G. Gosling. 1953. Molecular configuration in sodium thymonucleate. Nature. 171:740-741.
26. Frisch, M. J., G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. J. P. Stewart, M. Head-Gordon, C. Gonzalez, and J. A. Pople. 1996. Gaussian 94. Gaussian, Inc., Pittsburgh, PA.
27. Gelbin, A., B. Schneider, L. Clowney, S.-H. Hsieh, W. K. Olsen, and H. M. Berman. 1996. Geometric parameters in nucleic acids: sugar and phosphate constituents. J. Am. Chem. Soc. 118:519-529.
28. Grzeskowiak, K., K. Yanagi, G. G. Prive, and R. E. Dickerson. 1991. The structure of B-helical CGATCGATCG and comparison with CCAACGTTGG. The effect of basepair reversals. J. Biol. Chem. 266: 8861-8883.
29. Guschlbauer, W., and K. Jankowski. 1980. Nucleoside conformation as determined by the sugar substituent. Nucleic Acids Res. 8:1421-1433.
30. Guzikevich-Guerstein, G., and Z. Shakked. 1996. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nat. Struct. Biol. 3:32-37.
31. Hartmann, B., and R. Lavery. 1996. DNA structural forms. Q. Rev. Biophys. 29:309-368.
32. Heinemann, U., C. Alings, and M. Hahn. 1994. Crystallographic studies of DNA helix structure. Biophys. Chem. 50:157-167.
33. Herbert, A., and A. Rich. 1996. The biology of left-handed Z-DNA. J. Biol. Chem. 271:11595-11598.
34. Ho, P. S., M. J. Ellison, G. J. Quigley, and A. Rich. 1986. A computer-aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5:2737-2744.
35. Hunter, C. A. 1993. Sequence-dependent DNA structure. The role of base stacking interactions. J. Mol. Biol. 230:1025-1054.
36. Ivanov, V. I., and L. E. Minchenkova. 1995. The A-form of DNA: in search of biological role (a review). Mol. Biol. (Engl. ed.). 28:780-788.
37. Kopka, M. L., A. V. Fratini, H. R. Drew, and R. E. Dickerson. 1983. Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol. 163:129-146.
38. Lakshminarayanan, A. V., and V. Sasisekharan. 1969. Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base-sugar units. Biopolymers. 8:475-488.
39. Lakshminarayanan, A. V., and V. Sasisekharan. 1970. Stereochemistry of nucleic acids and polynucleotides. II. Allowed conformations of the monomer unit for different ribose puckerings. Biochim. Biophys. Acta. 204:49-59.
40. Langridge, R. 1969. Nucleic acids and polynucleotides. J. Cell Physiol. 74(Suppl. 1):1-20.
41. Lavery, R., and H. Sklenar. 1989. Defining the structure of irregular nucleic acids: convention and principles. J. Biomol. Struct. & Dyn. 6:655-667.
42. Leslie, A. G. W., S. Arnott, R. Chandrasekaran, and R. L. Ratliff. 1980. Polymorphism of DNA double helices. J. Mol. Biol. 143:49-72.
43. Liepinsh, E., G. Otting, and K. Wütrich. 1992. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 20:6549-6553.
44. MacKerell, A. D., Jr. 1998. Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA. In Molecular Modeling of Nucleic Acids. N. B. Leontis and J. SantaLucia, Jr., editors. American Chemical Society, Washington, DC. 304-311.
45. Mazur, J., A. Sarai, and R. L. Jemigan. 1989. Sequence dependence of the B-A conformational transition of DNA. Biopolymers. 28:1223-1233.
46. McCall, M., T. Brown, and O. Kennard. 1985. The crystal structure of d(GGGGCCCC). A Model for Poly(dG) · poly(dC). J. Mol. Biol. 183: 385-396.
47. Nelson, H. C. M., J. T. Finch, B. F. Luisi, and A. Klug. 1987. The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature. 330:221-226.
48. Olson, W. K. 1973. Syn-anti effects on the spatial configuration of polynucleotide chains. Biopolymers. 12:1787-1814.
49. Olson, W. K. 1982. How flexible is the furanose ring? 2. An updated potential energy estimate. J. Am. Chem. Soc. 104:278-286.
50. Olson, W. K., and P. J. Flory. 1972a. Spatial configuration of polynucleotide chains. I. Steric interactions in polyribonucleotides: a virtual bond model. Biopolymers. 11:1-23.
51. Olson, W. K., and P. J. Flory. 1972b. Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides. Biopolymers. 11:25-56.
52. Olson, W. K., and J. L. Sussman. 1982. How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies. J. Am. Chem. Soc. 104:270-278.
53. Peticolas, W. L., Y. Wang, and G. A. Thomas. 1988. Some rules for predicting the base-sequence dependence of DNA conformation. Proc. Natl. Acad. Sci. U.S.A. 85:2579-2583.
54. Pilet, J., and J. Brahms. 1972. Dependence of B-A conformational change in DNA on base composition. Nat. New Biol. 236:99-100.
55. Pohl, F. M., and T. M. Jovin. 1972. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol. 67:375-396.
56. Poncin, M., B. Hartmann, and R. Lavery. 1992. Conformational substates in B-DNA. J. Mol. Biol. 226:775-794.
57. Privé, G. G., K. Yanagi, and R. E. Dickerson. 1991. Structure of the B-DNA decamer CCAACGTTGG and comparison with isomorphous decamers CCAAGATTGG and CCAGGCCTGG. J. Mol. Biol 217: 177-199.
58. 13C nuclear-magnetic-resonance relaxation. Eur. J. Biochem. 53:517-524.
59. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer-Verlag, New York.
60. Saran, A., D. Perahia, and B. Pullman. 1973. Molecular orbital calculations of the conformation of nucleic acids and their constituents. VII. Conformation of the sugar ring in β-nucleosides: the pseudorotational representation. Theoret. Chim. Acta. 30:31-44.
61. Saran, A., B. Pullman, and D. Perahia. 1972. Molecular orbital calculations on the conformation of nucleic acids and their constituents. IV. Conformations about the exocyclic C(4′)-(C5′) bond. Biochim. Biophys. Acta. 287:211-231.
62. Son, T., W. Guschlbauer, and M. Guéron. 1972. Flexibility and conformations of guanosine monophosphates by the Overhauser effects. J. Am. Chem. Soc. 94:7903-7911.
63. Subirana, J. A., and T. Faria. 1997. Influence of sequence on the conformation of the B-DNA helix. Biophys. J. 73:333-338.
64. Sundaralingam, M. 1969. Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleosides mono-, di-, tetraphosphates, nucleic acids, and polynucleotides. Biopolymers. 7:821-860.
65. Uesugi, S., H. Miki, M. Ikehara, H. Iwahashi, and Y. Kyogoku. 1979. A linear relationship between electronegativity of 2′-substituents and conformation of adenine nucleosides. Tetrahedron Lett. 42:4073-4076.
66. Vorlickova, M., J. Kypr, S. Stokrova, and J. Sponar. 1982. A Z-like form of poly(dA-dC) · poly(dG-dT) in solution? Nucleic Acids Res. 10: 1071-1080.
67. Wang, A. H.-J., S. Fujii, J. H. van Boom, G. A. van der Marel, S. A. A. van Boeckel, and A. Rich. 1982. Molecular structure of r(GCG)d(TATACGC): a DNA-RNA hybrid helix joined to double helical DNA. Nature. 299:601-604.
68. Wang, A. H.-J., T. Hakoshima, G. van der Marel, v. B. J. H., and A. Rich. 1984. AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG). Cell. 37:321-331.
69. Wang, S., and E. T. Kool. 1995. Origins of the large differences in stability of DNA and RNA helices: C- 5 methyl and 2′-hydroxyl effects. Biochemistry. 34:4125-4132.
70. Wang, A. H.-J., G. J. Quigley, F. J. Kolpak, J. L. Crawford, J. H. van Boom, G. van der Marel, and A. Rich. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:680-686.
71. Wang, Y., G. A. Thomas, and W. L. Peticolas. 1987a. Sequence dependence of the B to Z transition in crystals and aqueous NaCl solutions for deoxyribonucleotides containing all four canonical DNA bases. Biochemistry. 26:5178-5186.
72. Wang, Y., G. A. Thomas, and W. L. Peticolas. 1987b. Sequence dependent conformations of oligomeric DNA's in aqueous solutions and in crystals. J. Biomol. Struct. & Dyn. 5:249-274.
73. Wang, Y., G. A. Thomas, and W. L. Peticolas. 1989. A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions. J. Biomol. Struct. & Dyn. 6:1177-1187.
74. Westhof, E., and M. Sundaralingam. 1980. Interrelationships between the pseudorotation parameters P and τm and the geometry of the furanose ring. J. Am. Chem. Soc. 102:1493-1500.
75. Yathindra, N., and M. Sundaralingam. 1973. Conformational studies on guanosine nucleotides and polynucleotides. The effect of the base on the glycosyl and backbone conformations. Biopolymers. 12:2075-2082.
76. Zimmer, C., S. Tymen, C. Marck, and W. Guschlbauer. 1982. Conformational transitions of poly(dA-dC)poly(dG-dT) induced by high salt or in ethanolic solution. Nucleic Acids Res. 3:1081-1091.