Skip to main content
SpringerLink
Log in

Effect of loop on the stability of intramolecular triplex DNA

  • Published:
Science in China Series B: Chemistry Aims and scope Submit manuscript

Abstract

Conformation stabilities of intramolecular triple-helical DNAs (intra-triplex DNAs: 5′-d(TC)6- d(T)m-d(CT)6-d(C)n-d(AG)6-3′, wherem andn are chosen to be 4 and 3) have been examined by molecular mechanics. The four intra-triplexes (H-DNAs) are compared with the intermolecular triplexes d(TC)6 * d(AG)6 · d(CT)6. The results revealed that loops do not significantly influence the intratriplex conformations, loop conformations, however, depend partly on its length. Loop also makes strand II of every intra-triplex DNA longer than that of the inter-triplex DNA. Most of residue sugar conformations of triple-helical DNAs are S-type, there also exist, however, N-type conformation and the conformations between S-type and N-type. Possible models of the five triplex DNAs are presented.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Felsenfeld, G., Davis, D. R., Rich, A., Formation of a three-stranded polynucleotide molecule,J. Amer. Chem. Soc., 1957, 79: 2023.

    Article  CAS  Google Scholar 

  2. Morgan, A. R., Wells, R. D., Specificity of three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences,J. Mol. Biol., 1968, 37: 63.

    Article  CAS  Google Scholar 

  3. Arott, S., Selsing, E., Structures for the polynucleotide complexes poly(dA) ·poly(dT) and poly(dT) -pdly(dA). poly(dT),J. Mol. Biol., 1974, 88: 509.

    Article  Google Scholar 

  4. Hoogsteen, K., The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine,Acta Crystallogr., 1959, 12: 822.

    Article  CAS  Google Scholar 

  5. Volker, J., Botes, D. P., Lindsery, G. G., Energetics of a stable intramolecular DNA triple helix formation,J. Mol. Biol., 1993, 230: 1278.

    Article  CAS  Google Scholar 

  6. Robert, L. B., Experimental tests of the theory of deoxyribonucleic acid melting with d(T-A) oliomers,Accounts of Chemical Research, 1971, 4: 265.

    Article  Google Scholar 

  7. Dorothy, A., Asif, K. S., Kenneth, J. B.et al., Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data,Biochemistry, 1993, 32: 436.

    Article  Google Scholar 

  8. Dorothy, E., Navin, S., Wilma, O.et al., A dumbbell-shaped, double-hairpin structure of DNA: A thermodynamic investigation,Biochemistry, 1987, 26: 7150.

    Article  Google Scholar 

  9. Blomers, M. J. J., Walters, J. A. L. I., Hasnoot, C. A. G.etal., Effects of base sequence on the loop folding in DNA hairpins,Biochemistry, 1989, 28: 7491.

    Article  Google Scholar 

  10. Mary, M., Roger, A. J., Kenneth, J. B., Influence of loop residue on the relative stabilities of DNA hairpin structure,Proc. Natl. Acad. Sci. USA, 1988, 85: 6242.

    Article  Google Scholar 

  11. Daina, Z. A., David, R., Structural characterization of d(CAACCCGTTG) and d(CAACGGGTTG) mini-hairpin loops by heteronuclear NMR: the effects of purines versus pyrimidines in DNA hairpins,Nucleic Acids Research, 1995, 23: 1260.

    Article  Google Scholar 

  12. Cheng Yuen-Ktt, Pettitt, M. B., Stability of double-and triple-strand helical nucleic acids,Prog. Biophys. Molec. Biol., 1992, 58: 225.

    Article  Google Scholar 

  13. Stephen, C. H., Jia Luo, Richard, L., DNA stem-loop structures in oligopurine-oligopyrimidine triplexes,Nucleic Acids Research, 1988, 16: 11795.

    Article  Google Scholar 

  14. Fang, Y., Bai, C., Wei, Y.etal., Determination of the conformations of intramolecular DNA triple helices by FT-IR spectroscopy: effect of loop length,J. Mol. Str., 1995, 372: 241.

    Article  CAS  Google Scholar 

  15. Michel, D., Chatelain, G., Herault, Y.et al., The long repetitive polypurinelpolyprimidine sequence (TTCCC)48 forms DNA triplex with Pu-Pu-Py base tripletsin vivo, Nucleic Acids Research, 1992, 20: 439.

    CAS  Google Scholar 

  16. Weiner, S. J., Kollman, P. A., Nguyen, D. T.etal., An all atom forcefield for simulations of proteins and nucleic acid,J. Comp. Chem., 1986, 7: 765.

    Google Scholar 

  17. Lee Imshik, Bai Chunli, Wang Chenet al., Computational analysis of triplex formation of oligonucleotides: protonated and 5′-methylated Py-Pu-Py motif,Science in China, Ser. B, 1997, 40: 113.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Chemistry, Chinese Academy of Sciences, 100080, Beijing, China

    Yang Linjing, Bai Chunli, Lee Imshik, Wang Xinwen & Wang Chen

Authors
  1. Yang Linjing
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bai Chunli
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lee Imshik
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Wang Xinwen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Project supported by the Chinese Academy of Sciences.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yang, L., Bai, C., Lee, I. et al. Effect of loop on the stability of intramolecular triplex DNA. Sc. China Ser. B-Chem. 40, 650–656 (1997). https://doi.org/10.1007/BF02875484

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02875484

Keywords

Search

Navigation