Conformational Aspects of Hairpin Loops in DNA Oligonucleotides

  • Cornelis A. G. Haasnoot
  • Marcel J. J. Blommers
  • Cornelis W. Hilbers
Part of the Springer Series in Biophysics book series (BIOPHYSICS, volume 1)


Our studies (2–5) towards the structure, kinetics and thermodynamics of DNA hairpins formed in solution by the homologous, (partly-) selfcomplementary DNA fragments d (ATCCTATnTAGGAT), n=0-7, showed that the inherent stability of DNA hairpins is at its maximum when the loop of the hairpin comprises four or five nucleotides. This finding is at variance with earlier experiments (6) which indicated that in RNA hairpins loop lengths of six to seven residues are the most favourable.


Lower Energy Structure Hairpin Loop Anticodon Loop Imino Proton Adenosine Residue 
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  1. 2.
    Haasnoot, C.A.G., den Hartog, J.H.J., de Rooij, J.F.M., van Boom, J.H. and Altona, C. (1980) Nucl. Acids Res. 8, 169.PubMedCrossRefGoogle Scholar
  2. 3.
    van Boom, J.H., van der Marel, G.A., Westerink, H.P., van Boeckel, C.A.A., Mellema, J.-R., Altona, C., Hilbers, C.W., Haasnoot, C.A.G., de Bruin, S.H. and Berendsen, R.G. (1983) Cold Spring Harbor Symp. Quant. Biol., Vol. XLVII, 403.Google Scholar
  3. 4.
    Haasnoot, C.A.G., de Bruin, S.H., Berendsen, R.G., Janssen, H.G. J.M., Binnendijk, T.J.J., Hilbers, C.W., van der Marel, G.A. and van Boom, J.H. (1983) J. Biomol. Struct. Dyns. 1, 115.Google Scholar
  4. 5.
    Hilbers, C.W., Haasnoot, C.A.G., de Bruin, S.H., Joordens, J.J.M., van der Marel, G.A. and van Boom, J.H. (1985) Biochimie 67, 685.PubMedCrossRefGoogle Scholar
  5. 6.
    Tinoco, I., Borer, P.N., Dengler, B., Levine, M.D., Uhlenbeck, O. C., Crothers, D.M. and Gralla, J. (19873) Nature New Biology 246, 40.Google Scholar
  6. 7.
    Haasnoot, C.A.G., de Bruin, S.H., Hilbers, C.W., van der Marel, G.A. and van Boom, J.H. (1985) Proc. Int. Symp. Biomol. Struct. Interactions, Suppl. J. Biosci. 8, 767.Google Scholar
  7. 8.
    Haasnoot, C.A.G., Hilbers, C.W., van der Marel, G.A., van Boom, J.H., Singh, U.C., Pattabiraman, N. and Kollman, P.A. (1986) J. Biomol. Struct. Dyns. 3, 843.Google Scholar
  8. 9.
    Weiner, S.J., Kollman, P.A., Case, D.A., Chandra Singh, U., Ghio, C., Alagona, G., Profeta, S. and Weiner, P. (1984) J. Amer. Chem. Soc. 106, 765.CrossRefGoogle Scholar
  9. 10.
    Singh, U.C., Weiner, S.J. and Kollman, P.A. (1985) Proc. Natl. Acad. Sci. USA 82, 755.PubMedCrossRefGoogle Scholar
  10. 11.
    Keepers, J.W. and James, T.L. (1984) J. Magn. Reson. 57, 404.Google Scholar
  11. 12.
    Blommers, M.J.J., Haasnoot, C.A.G. and Hilbers, C.W. (1986) to be published.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1987

Authors and Affiliations

  • Cornelis A. G. Haasnoot
    • 1
  • Marcel J. J. Blommers
    • 2
  • Cornelis W. Hilbers
    • 2
  1. 1.Unilever Research LaboratoryVlaardingenThe Netherlands
  2. 2.Laboratory of Biophysical ChemistryUniversity of NijmegenNijmegenThe Netherlands

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