Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 May 11;18(9):2759–2767. doi: 10.1093/nar/18.9.2759

Molecular structure of deoxycytidyl-3'-methylphosphonate (RP) 5'-deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist.

F Han 1, W Watt 1, D J Duchamp 1, L Callahan 1, F J Kézdy 1, K Agarwal 1
PMCID: PMC330761  PMID: 2339061

Abstract

The crystal structure of d[Cp(CH3)G] has been determined as part of a project to study the mechanism of the B----Z transition in DNA. The asymmetric unit contains two dinucleotides and the equivalent of 7.5 water molecules, partially disordered over 12 definable positions. The two symmetry-independent dinucleotides form a duplex with Watson-Crick base-pairing and a right-handed helical sense. Comparison with previously determined structures of the B and A conformation showed that this duplex is closer to B than to A but significantly different from B. It corresponds to a stretched out helix with a 4 A rise per base pair and a helical twist of 32 degrees. This structure may serve as a model for the bending of DNA in certain situations. The configuration at the methyl phosphonate is RP, and a mechanism, based on this assignment, is presented for the B----Z transition in DNA.

Full text

PDF

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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. 1972 Nov 15;94(23):8205–8212. doi: 10.1021/ja00778a043. [DOI] [PubMed] [Google Scholar]
  2. Callahan L., Han F. S., Watt W., Duchamp D., Kézdy F. J., Agarwal K. B- to Z-DNA transition probed by oligonucleotides containing methylphosphonates. Proc Natl Acad Sci U S A. 1986 Mar;83(6):1617–1621. doi: 10.1073/pnas.83.6.1617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chacko K. K., Lindner K., Saenger W., Miller P. S. Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study. Nucleic Acids Res. 1983 May 11;11(9):2801–2814. doi: 10.1093/nar/11.9.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cosstick R., Eckstein F. Synthesis of d(GC) and d(CG) octamers containing alternating phosphorothioate linkages: effect of the phosphorothioate group on the B-Z transition. Biochemistry. 1985 Jul 2;24(14):3630–3638. doi: 10.1021/bi00335a035. [DOI] [PubMed] [Google Scholar]
  5. Crick F. H., Klug A. Kinky helix. Nature. 1975 Jun 12;255(5509):530–533. doi: 10.1038/255530a0. [DOI] [PubMed] [Google Scholar]
  6. Cruse W. B., Egert E., Kennard O., Sala G. B., Salisbury S. A., Viswamitra M. A. Self base pairing in a complementary deoxydinucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3'-5')-deoxyguanosine. Biochemistry. 1983 Apr 12;22(8):1833–1839. doi: 10.1021/bi00277a014. [DOI] [PubMed] [Google Scholar]
  7. Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
  8. Dickerson R. E., Drew H. R. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. doi: 10.1016/0022-2836(81)90357-0. [DOI] [PubMed] [Google Scholar]
  9. Gaffney B. L., Marky L. A., Jones R. A. The influence of the purine 2-amino group on DNA conformation and stability. Synthesis and conformational analysis of d[T(2-aminoA)]3. Nucleic Acids Res. 1982 Jul 24;10(14):4351–4361. doi: 10.1093/nar/10.14.4351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kopka M. L., Fratini A. V., Drew H. R., Dickerson R. E. Ordered water structure around a B-DNA dodecamer. A quantitative study. J Mol Biol. 1983 Jan 5;163(1):129–146. doi: 10.1016/0022-2836(83)90033-5. [DOI] [PubMed] [Google Scholar]
  11. Mirzabekov A. D., Shick V. V., Belyavsky A. V., Bavykin S. G. Primary organization of nucleosome core particle of chromatin: sequence of histone arrangement along DNA. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4184–4188. doi: 10.1073/pnas.75.9.4184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  13. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  14. Rosenberg J. M., Seeman N. C., Day R. O., Rich A. RNA double-helical fragments at atomic resolution. II. The crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. J Mol Biol. 1976 Jun 14;104(1):145–167. doi: 10.1016/0022-2836(76)90006-1. [DOI] [PubMed] [Google Scholar]
  15. Seeman N. C., Rosenberg J. M., Suddath F. L., Kim J. J., Rich A. RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate. J Mol Biol. 1976 Jun 14;104(1):109–144. doi: 10.1016/0022-2836(76)90005-x. [DOI] [PubMed] [Google Scholar]
  16. Shakked Z., Rabinovich D., Kennard O., Cruse W. B., Salisbury S. A., Viswamitra M. A. Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C). J Mol Biol. 1983 May 15;166(2):183–201. doi: 10.1016/s0022-2836(83)80005-9. [DOI] [PubMed] [Google Scholar]
  17. Vorlíckovă M., Kypr J., Stokrová S., Sponar J. A Z-like form of poly(dA-dC).poly(dG-dT) in solution? Nucleic Acids Res. 1982 Feb 11;10(3):1071–1080. doi: 10.1093/nar/10.3.1071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES