Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Oct 11;20(19):5011–5016. doi: 10.1093/nar/20.19.5011

A comprehensive classification of nucleic acid structural families based on strand direction and base pairing.

R Lavery 1, K Zakrzewska 1, J S Sun 1, S C Harvey 1
PMCID: PMC334277  PMID: 1383936

Abstract

We propose a classification of DNA structures formed from 1 to 4 strands, based only on relative strand directions, base to strand orientation and base pairing geometries. This classification and its associated notation enable all nucleic acids to be grouped into structural families and bring to light possible structures which have not yet been observed experimentally. It also helps in understanding transitions between families and can assist in the design of multistrand structures.

Full text

PDF
5011

Selected References

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

  1. Arnott S., Chandrasekaran R., Leslie A. G. Structure of the single-stranded polyribonucleotide polycytidylic acid. J Mol Biol. 1976 Sep 25;106(3):735–748. doi: 10.1016/0022-2836(76)90262-x. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  3. Borisova O. F., Golova YuB, Gottikh B. P., Zibrov A. S., Il'icheva I. A., Lysov YuP, Mamayeva O. K., Chernov B. K., Chernyi A. A., Shchyolkina A. K. Parallel double stranded helices and the tertiary structure of nucleic acids. J Biomol Struct Dyn. 1991 Jun;8(6):1187–1210. doi: 10.1080/07391102.1991.10507878. [DOI] [PubMed] [Google Scholar]
  4. Broitman S. L., Im D. D., Fresco J. R. Formation of the triple-stranded polynucleotide helix, poly(A.A.U). Proc Natl Acad Sci U S A. 1987 Aug;84(15):5120–5124. doi: 10.1073/pnas.84.15.5120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fukui T., Ikehara M. Polynucleotides XLVII. Synthesis and properties of poly(2-methylthio- and 2-ethylthioadenylic acid). Formation of non-Watson-Crick type complexes. Biochim Biophys Acta. 1979 May 24;562(3):527–533. doi: 10.1016/0005-2787(79)90115-1. [DOI] [PubMed] [Google Scholar]
  6. Hanvey J. C., Shimizu M., Wells R. D. Intramolecular DNA triplexes in supercoiled plasmids. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6292–6296. doi: 10.1073/pnas.85.17.6292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Harvey S. C. DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition. Nucleic Acids Res. 1983 Jul 25;11(14):4867–4878. doi: 10.1093/nar/11.14.4867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Htun H., Dahlberg J. E. Topology and formation of triple-stranded H-DNA. Science. 1989 Mar 24;243(4898):1571–1576. doi: 10.1126/science.2648571. [DOI] [PubMed] [Google Scholar]
  9. Hélène C., Toulmé J. J. Specific regulation of gene expression by antisense, sense and antigene nucleic acids. Biochim Biophys Acta. 1990 Jun 21;1049(2):99–125. doi: 10.1016/0167-4781(90)90031-v. [DOI] [PubMed] [Google Scholar]
  10. Kim S. H., Sussman J. L., Suddath F. L., Quigley G. J., McPherson A., Wang A. H., Seeman N. C., RICH A. The general structure of transfer RNA molecules. Proc Natl Acad Sci U S A. 1974 Dec;71(12):4970–4974. doi: 10.1073/pnas.71.12.4970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Klysik J., Rippe K., Jovin T. M. Parallel-stranded DNA under topological stress: rearrangement of (dA)15.(dT)15 to a d(A.A.T)n triplex. Nucleic Acids Res. 1991 Dec;19(25):7145–7154. doi: 10.1093/nar/19.25.7145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Morvan F., Rayner B., Imbach J. L., Chang D. K., Lown J. W. alpha-DNA-III. Characterization by high field 1H-NMR, anti-parallel self-recognition and conformation of the unnatural hexadeoxyribonucleotides alpha-[d(CpApTpGpCpG)] and alpha-[d(CpGpCpApTpG)]. Alpha-oligodeoxynucleotides as potential cellular probes for gene control. Nucleic Acids Res. 1987 May 26;15(10):4241–4255. doi: 10.1093/nar/15.10.4241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Pattabiraman N. Can the double helix be parallel? Biopolymers. 1986 Sep;25(9):1603–1606. doi: 10.1002/bip.360250903. [DOI] [PubMed] [Google Scholar]
  14. Pilch D. S., Levenson C., Shafer R. H. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry. 1991 Jun 25;30(25):6081–6088. doi: 10.1021/bi00239a001. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Ramsing N. B., Jovin T. M. Parallel stranded duplex DNA. Nucleic Acids Res. 1988 Jul 25;16(14A):6659–6676. doi: 10.1093/nar/16.14.6659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rose I. A., Hanson K. R., Wilkinson K. D., Wimmer M. J. A suggestion for naming faces of ring compounds. Proc Natl Acad Sci U S A. 1980 May;77(5):2439–2441. doi: 10.1073/pnas.77.5.2439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sun J. S., François J. C., Lavery R., Saison-Behmoaras T., Montenay-Garestier T., Thuong N. T., Hélène C. Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline conjugates: parallel and antiparallel double helices are formed with DNA and RNA, respectively. Biochemistry. 1988 Aug 9;27(16):6039–6045. doi: 10.1021/bi00416a032. [DOI] [PubMed] [Google Scholar]
  19. Sun J. S., Giovannangeli C., François J. C., Kurfurst R., Montenay-Garestier T., Asseline U., Saison-Behmoaras T., Thuong N. T., Hélène C. Triple-helix formation by alpha oligodeoxynucleotides and alpha oligodeoxynucleotide-intercalator conjugates. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6023–6027. doi: 10.1073/pnas.88.14.6023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sussman J. L., Holbrook S. R., Warrant R. W., Church G. M., Kim S. H. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol. 1978 Aug 25;123(4):607–630. doi: 10.1016/0022-2836(78)90209-7. [DOI] [PubMed] [Google Scholar]
  21. Thiele D., Guschlbauer W. The structures of polyinosinic acid. Biophysik. 1973 May 30;9(3):261–277. doi: 10.1007/BF01184691. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Westhof E. Westhof's rule. Nature. 1992 Aug 6;358(6386):459–460. doi: 10.1038/358459b0. [DOI] [PubMed] [Google Scholar]
  24. 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]

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

RESOURCES