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. 1983 May 11;11(9):2893–2905. doi: 10.1093/nar/11.9.2893

A double helix B-type geometry based on high-resolution proton NMR of single-helical DNA fragments: d(TA)5 x d(TA)5.

J R Mellema, P N van Kampen, C N Carlson, H E Bosshard, C Altona
PMCID: PMC325931  PMID: 6856480

Abstract

A single-helical B-type geometry is presented based on 1H NMR observations on d(TATA) and several other small single-helical DNA fragments. The structure is extended to one complete turn of double-helical DNA and its characteristics are compared with other known B-type structures.

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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. Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J Am Chem Soc. 1973 Apr 4;95(7):2333–2344. doi: 10.1021/ja00788a038. [DOI] [PubMed] [Google Scholar]
  3. Arnott S., Chandrasekaran R., Hukins D. W., Smith P. J., Watts L. Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J Mol Biol. 1974 Sep 15;88(2):523–533. doi: 10.1016/0022-2836(74)90499-9. [DOI] [PubMed] [Google Scholar]
  4. Arnott S., Hukins D. W., Dover S. D. Optimised parameters for RNA double-helices. Biochem Biophys Res Commun. 1972 Sep 26;48(6):1392–1399. doi: 10.1016/0006-291x(72)90867-4. [DOI] [PubMed] [Google Scholar]
  5. Arnott S., Hukins D. W. Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J Mol Biol. 1973 Dec 5;81(2):93–105. doi: 10.1016/0022-2836(73)90182-4. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Hartel A. J., Lankhorst P. P., Altona C. Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method. Eur J Biochem. 1982 Dec 15;129(2):343–357. doi: 10.1111/j.1432-1033.1982.tb07057.x. [DOI] [PubMed] [Google Scholar]
  8. Kollman P. A., Weiner P. K., Dearing A. Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers. Biopolymers. 1981 Dec;20(12):2583–2621. doi: 10.1002/bip.1981.360201208. [DOI] [PubMed] [Google Scholar]
  9. Leslie A. G., Arnott S., Chandrasekaran R., Ratliff R. L. Polymorphism of DNA double helices. J Mol Biol. 1980 Oct 15;143(1):49–72. doi: 10.1016/0022-2836(80)90124-2. [DOI] [PubMed] [Google Scholar]
  10. Mellema J. R., Haasnoot C. A., Van Boom J. H., Altona C. Complete assignment and conformational analysis of a deoxyribotetranucleotide. d(TAAT). A 360 and 500 Mhz NMR study. Biochim Biophys Acta. 1981 Sep 28;655(2):256–264. doi: 10.1016/0005-2787(81)90016-2. [DOI] [PubMed] [Google Scholar]
  11. Olsthoorn C. S., Bostelaar L. J., Van Boom J. H., Altona C. Conformational characteristics of the trinucleoside diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies. Extrapolation to the stacked conformers. Eur J Biochem. 1980 Nov;112(1):95–110. doi: 10.1111/j.1432-1033.1980.tb04991.x. [DOI] [PubMed] [Google Scholar]
  12. Olsthoorn C. S., Doornbos J., de Leeuw H. P., Altona C. Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study. Eur J Biochem. 1982 Jul;125(2):367–382. doi: 10.1111/j.1432-1033.1982.tb06693.x. [DOI] [PubMed] [Google Scholar]
  13. Viswamitra M. A., Shakked Z., Jones P. G., Sheldrick G. M., Salisbury S. A., Kennard O. Structure of the deoxytetranucleotide d-pApTpApT and a sequence-dependent model for poly(dA-dT). Biopolymers. 1982 Mar;21(3):513–533. doi: 10.1002/bip.360210304. [DOI] [PubMed] [Google Scholar]
  14. Wang A. H., Fujii S., van Boom J. H., Rich A. Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA. Proc Natl Acad Sci U S A. 1982 Jul;79(13):3968–3972. doi: 10.1073/pnas.79.13.3968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wang A. H., Fujii S., van Boom J. H., van der Marel G. A., van Boeckel S. A., Rich A. Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA. Nature. 1982 Oct 14;299(5884):601–604. doi: 10.1038/299601a0. [DOI] [PubMed] [Google Scholar]
  16. 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]

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