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. 1976 Mar;3(3):729–747. doi: 10.1093/nar/3.3.729

Analysis of the possible helical structures of nucleic acids and polynucleotides. Application of (n-h) plots.

N Yathindra, M Sundaralingam
PMCID: PMC342937  PMID: 1272796

Abstract

The two helical parameters n and h where n is the number of nucleotide residues per turn and h is the height per nucleotide residue have been evaluated for single stranded helical polynucleotide chains comprising C(3') -endo and C(2') endo class of nucleotides. The helical parameters are found to be especially sensitive to the C(4')-C(3') (sugar pucker) and the C(4')-C(5') torsions. The (n-h) plots display only one important helix forming domain for each class of nucleotides characterized by the sugar pucker and the C(4')-C(5') torsion. A correlation between the (n-h) plots and the known RNA (A,A') and DNA (A,B,C) helical forms has been established. It is found that all forms of helices except the C-DNA possess a favorable combination of P-O torsions. The analysis of the (n-h) plots suggests that C-DNA can have a conformation very similar to B-DNA. Although the (n-h) plots predict the stereochemical possibility of both right-handed and left-handed helices, nucleic acids apparently prefer right-handed conformation because of the energetics associated with the sugar-phosphate backbone and the base.

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Selected References

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

  1. 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]
  2. Arnott S., Chandrasekaran R., Marttila C. M. Structures for polyinosinic acid and polyguanylic acid. Biochem J. 1974 Aug;141(2):537–543. doi: 10.1042/bj1410537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. 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]
  4. Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504–1509. doi: 10.1016/0006-291X(72)90243-4. [DOI] [PubMed] [Google Scholar]
  5. Arnott S., Selsing E. The conformation of C-DNA. J Mol Biol. 1975 Oct 15;98(1):265–269. doi: 10.1016/s0022-2836(75)80115-x. [DOI] [PubMed] [Google Scholar]
  6. Arnott S. The geometry of nucleic acids. Prog Biophys Mol Biol. 1970;21:265–319. doi: 10.1016/0079-6107(70)90027-1. [DOI] [PubMed] [Google Scholar]
  7. Brahms J., Pilet J., Phuong Lan T. T., Hill L. R. Direct evidence of the C-like form of sodium deoxyribonucleate. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3352–3355. doi: 10.1073/pnas.70.12.3352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fuller W., Hutchinson F., Spencer M., Wilkins M. H. Molecular and crystal structures of double-helical RNA. I. An x-ray diffraction study of fragmented yeast RNA and a preliminary double-helical RNA model. J Mol Biol. 1967 Aug 14;27(3):507–524. doi: 10.1016/0022-2836(67)90055-1. [DOI] [PubMed] [Google Scholar]
  9. Ivanov V. I., Minchenkova L. E., Schyolkina A. K., Poletayev A. I. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 1973;12(1):89–110. doi: 10.1002/bip.1973.360120109. [DOI] [PubMed] [Google Scholar]
  10. MARVIN D. A., SPENCER M., WILKINS M. H., HAMILTON L. D. The molecular configuration of deoxyribonucleic acid. III. X-ray diffraction study of the C form of the lithium salt. J Mol Biol. 1961 Oct;3:547–565. doi: 10.1016/s0022-2836(61)80021-1. [DOI] [PubMed] [Google Scholar]
  11. RICH A., DAVIES D. R., CRICK F. H., WATSON J. D. The molecular structure of polyadenylic acid. J Mol Biol. 1961 Feb;3:71–86. doi: 10.1016/s0022-2836(61)80009-0. [DOI] [PubMed] [Google Scholar]
  12. Ramachandran G. N., Venkatachalam C. M., Krimm S. Stereochemical criteria for polypeptide and protein chain conformations. 3. Helical and hydrogen-bonded polypeptide chains. Biophys J. 1966 Nov;6(6):849–872. doi: 10.1016/s0006-3495(66)86699-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Saenger W., Riecke J., Suck D. A structural model for the polyadenylic acid single helix. J Mol Biol. 1975 Apr 25;93(4):529–534. doi: 10.1016/0022-2836(75)90244-2. [DOI] [PubMed] [Google Scholar]
  14. Yathindra N., Sundaralingam M. Backbone conformations in secondary and tertiary structural units of nucleic acids. Constraint in the phosphodiester conformation. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3325–3328. doi: 10.1073/pnas.71.9.3325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Zimmerman S. B., Cohen G. H., Davies D. R. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J Mol Biol. 1975 Feb 25;92(2):181–192. doi: 10.1016/0022-2836(75)90222-3. [DOI] [PubMed] [Google Scholar]

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