Logo of biophysjLink to Publisher's site
Biophys J. 1995 Sep; 69(3): 1068–1076.
PMCID: PMC1236334

Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations.


A first principles model for calculating hydrogen bonding interactions, previously applied to water, is here applied to the more difficult problem of interactions between DNA bases. We first consider the energetics and geometry for the A-T and the G-C basepairs, comparing our results to other calculated results as well as to experiment. Next, we study the interactions of isomorphic DNA base triplet structures, which are important because of their suggested role in the recombination process. We find that energetically the third base in the triplet tends to favor a position along the dyadic axis, where it is hydrogen bonded to both bases in the duplex.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.1M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Arnott S. The geometry of nucleic acids. Prog Biophys Mol Biol. 1970;21:265–319. [PubMed]
  • Camerini-Otero RD, Hsieh P. Parallel DNA triplexes, homologous recombination, and other homology-dependent DNA interactions. Cell. 1993 Apr 23;73(2):217–223. [PubMed]
  • Durland RH, Kessler DJ, Gunnell S, Duvic M, Pettitt BM, Hogan ME. Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry. 1991 Sep 24;30(38):9246–9255. [PubMed]
  • Hsieh P, Camerini-Otero CS, Camerini-Otero RD. Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev. 1990 Nov;4(11):1951–1963. [PubMed]
  • Jiang SP, Jernigan RL, Ting KL, Syi JL, Raghunathan G. Stability and cooperativity of nucleic acid base triplets. J Biomol Struct Dyn. 1994 Oct;12(2):383–399. [PubMed]
  • Kim Y, Prohofsky EW. Defect-mediated hydrogen-bond instability of poly(dG)-poly(dC). Phys Rev B Condens Matter. 1986 Apr 15;33(8):5676–5681. [PubMed]
  • Kowalczykowski SC, Eggleston AK. Homologous pairing and DNA strand-exchange proteins. Annu Rev Biochem. 1994;63:991–1043. [PubMed]
  • Lacks S. Integration efficiency and genetic recombination in pneumococcal transformation. Genetics. 1966 Jan;53(1):207–235. [PMC free article] [PubMed]
  • Meselson MS, Radding CM. A general model for genetic recombination. Proc Natl Acad Sci U S A. 1975 Jan;72(1):358–361. [PMC free article] [PubMed]
  • Pilch DS, Levenson C, Shafer RH. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry. 1991 Jun 25;30(25):6081–6088. [PubMed]
  • Poltev VI, Shulyupina NV. Simulation of interactions between nucleic acid bases by refined atom-atom potential functions. J Biomol Struct Dyn. 1986 Feb;3(4):739–765. [PubMed]
  • Powell JW, Edwards GS, Genzel L, Kremer F, Wittlin A, Kubasek W, Peticolas W. Investigation of far-infrared vibrational modes in polynucleotides. Phys Rev A. 1987 May 1;35(9):3929–3939. [PubMed]
  • Pullman B, Claverie P, Caillet J. Interaction energies in hydrogen-bonded purine-pyrimidine triplets. Proc Natl Acad Sci U S A. 1967 Jun;57(6):1663–1669. [PMC free article] [PubMed]
  • Rao BJ, Chiu SK, Radding CM. Homologous recognition and triplex formation promoted by RecA protein between duplex oligonucleotides and single-stranded DNA. J Mol Biol. 1993 Jan 20;229(2):328–343. [PubMed]
  • Stasiak A, Di Capua E, Koller T. Elongation of duplex DNA by recA protein. J Mol Biol. 1981 Sep 25;151(3):557–564. [PubMed]
  • Stasiak A. Three-stranded DNA structure; is this the secret of DNA homologous recognition? Mol Microbiol. 1992 Nov;6(22):3267–3276. [PubMed]
  • Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. [PubMed]
  • West SC, Cassuto E, Howard-Flanders P. Postreplication repair in E. coli: strand exchange reactions of gapped DNA by RecA protein. Mol Gen Genet. 1982;187(2):209–217. [PubMed]
  • West SC, Countryman JK, Howard-Flanders P. Enzymatic formation of biparental figure-eight molecules from plasmid DNA and their resolution in E. coli. Cell. 1983 Mar;32(3):817–829. [PubMed]
  • West SC. Three-stranded DNA helices as intermediates in genetic recombination. Bioessays. 1991 Jan;13(1):37–38. [PubMed]
  • Yanson IK, Teplitsky AB, Sukhodub LF. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers. 1979 May;18(5):1149–1170. [PubMed]
  • Zhurkin VB, Raghunathan G, Ulyanov NB, Camerini-Otero RD, Jernigan RL. A parallel DNA triplex as a model for the intermediate in homologous recombination. J Mol Biol. 1994 Jun 3;239(2):181–200. [PubMed]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...