Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 Mar 11;14(5):2241–2249. doi: 10.1093/nar/14.5.2241

On the structure of poly d(A-S4T).

W Bökemeier, A G Lezius
PMCID: PMC339655  PMID: 3960720

Abstract

The helical twist of poly d(A-s4T) was determined from the periodicity of the cleavage patterns of the double stranded polydeoxynucleotide adsorbed on calcium phosphate and found to be 14 bp per turn. Both cleavage patterns and 31P NMR spectra indicate a mononucleotide structure rather than an alternating B DNA like poly d(A-T). The failure of nucleosome formation excludes a B type structure. The discrepancy of the mononucleotide structure found in 31P NMR spectra and the dinucleotide structure given by X ray fiber diffraction is explained by an alternating tilt of the planes of the base pairs (base roll) as a consequence of a strong propeller twist. The importance of interstrand stacking interactions of adjacent 4-thiothymidines for the helical stability is discussed.

Full text

PDF
2241

Selected References

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

  1. Ansorge W., Barker R. System for DNA sequencing with resolution of up to 600 base pairs. J Biochem Biophys Methods. 1984 Mar;9(1):33–47. doi: 10.1016/0165-022x(84)90064-2. [DOI] [PubMed] [Google Scholar]
  2. Behe M., Zimmerman S., Felsenfeld G. Changes in the helical repeat of poly(dG-m5dC) . poly(dG-m5dC) and poly(dG-dC) . poly(dG-dC) associated with the B-Z transition. Nature. 1981 Sep 17;293(5829):233–235. doi: 10.1038/293233a0. [DOI] [PubMed] [Google Scholar]
  3. Bugg C. E., Thewalt U. The crystal and molecular structure of 6-thioguanine. J Am Chem Soc. 1970 Dec 16;92(25):7441–7445. doi: 10.1021/ja00728a031. [DOI] [PubMed] [Google Scholar]
  4. Calladine C. R. Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol. 1982 Oct 25;161(2):343–352. doi: 10.1016/0022-2836(82)90157-7. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Germond J. E., Bellard M., Oudet P., Chambon P. Stability of nucleosomes in native and reconstituted chromatins. Nucleic Acids Res. 1976 Nov;3(11):3173–3192. doi: 10.1093/nar/3.11.3173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gottschalk E. M., Kopp E., Lezius A. G. A synthetic DNA with unusual base-pairing. Eur J Biochem. 1971 Dec 22;24(1):168–182. doi: 10.1111/j.1432-1033.1971.tb19668.x. [DOI] [PubMed] [Google Scholar]
  8. Jovin T. M., McIntosh L. P., Arndt-Jovin D. J., Zarling D. A., Robert-Nicoud M., van de Sande J. H., Jorgenson K. F., Eckstein F. Left-handed DNA: from synthetic polymers to chromosomes. J Biomol Struct Dyn. 1983 Oct;1(1):21–57. doi: 10.1080/07391102.1983.10507425. [DOI] [PubMed] [Google Scholar]
  9. Morgan R. S., Tatsch C. E., Gushard R. H., McAdon J., Warme P. K. Chains of alternating sulfur and pi-bonded atoms in eight small proteins. Int J Pept Protein Res. 1978 Mar;11(3):209–217. doi: 10.1111/j.1399-3011.1978.tb02841.x. [DOI] [PubMed] [Google Scholar]
  10. Patel D. J., Kozlowski S. A., Nordheim A., Rich A. Right-handed and left-handed DNA: studies of B- and Z-DNA by using proton nuclear Overhauser effect and P NMR. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1413–1417. doi: 10.1073/pnas.79.5.1413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Rhodes D., Klug A. Helical periodicity of DNA determined by enzyme digestion. Nature. 1980 Aug 7;286(5773):573–578. doi: 10.1038/286573a0. [DOI] [PubMed] [Google Scholar]
  13. Ruiz-Carrillo A., Jorcano J. L., Eder G., Lurz R. In vitro core particle and nucleosome assembly at physiological ionic strength. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3284–3288. doi: 10.1073/pnas.76.7.3284. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Saenger W., Suck D. The relationship between hydrogen bonding and base stacking in crystalline 4-thiouridine derivatives. Eur J Biochem. 1973 Feb 1;32(3):473–478. doi: 10.1111/j.1432-1033.1973.tb02630.x. [DOI] [PubMed] [Google Scholar]
  15. Scheffler I. E., Elson E. L., Baldwin R. L. Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J Mol Biol. 1968 Sep 28;36(3):291–304. doi: 10.1016/0022-2836(68)90156-3. [DOI] [PubMed] [Google Scholar]
  16. Shindo H., Simpson R. T., Cohen J. S. An alternating conformation characterizes the phosphodiester backbone of poly(dA-dT) in solution. J Biol Chem. 1979 Sep 10;254(17):8125–8128. [PubMed] [Google Scholar]
  17. Zipper P. A small-angle- x-ray scattering study on poly (d(A-t)-d(A-T)), poly(d(A-s4T)-d(A-s4T)) and poly (d(A-s4U)-d(A-s4U)). Eur J Biochem. 1973 Nov 15;39(2):493–498. doi: 10.1111/j.1432-1033.1973.tb03148.x. [DOI] [PubMed] [Google Scholar]

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

RESOURCES