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Sequence-Specific Recognition and Cleavage of Duplex DNA by Derivatized Oligonucleotides

  • Conference paper
Molecular Basis of Specificity in Nucleic Acid-Drug Interactions

Part of the book series: The Jerusalem Symposia on Quantum Chemistry and Biochemistry ((JSQC,volume 23))

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Abstract

A homopyrimidine 11-mer oligodeoxynucleotide selectively recognizes a 11-bp homopurine. homopyrimidine sequence in duplex DNA of simian virus 40 (SV40). Binding occurs in the major groove via Hoogsten base pairing of thymine and protonated cytosine to Watson-Crick A.T and G.C base pairs, respectively. The 11-mer oligonucleotide was covalently linked to 5-amino-1,10-phenanthroline via different linkers. Efficient cleavage of SV40 circular DNA was observed in the presence of Cu2+ and a reducing agent when a pentamethylene carboxamide linker was used to tether phenanthroline to a 5’-thiophosphate group of the 11-mer oligonucleotide. The distribution of the cleavage sites on the two strands was asymmetric. They were shifted towards the 3’-side indicating that cleavage occurred from the minor groove. Recognition of the major groove by the oligonucleotide and intercalation of phenanthroline at the triplex-duplex junction account for the observed sequence-specific cleavage reaction from within the minor groove. An ellipticine derivative was covalently attached to the 3’-end of the 11-mer oligonucleotide. Upon irradiation at wavelengths longer than 300 nm the DNA target was cleaved at the positions expected if the oligonucleotide binds in a parallel orientation to the homopurine sequence. In addition it was shown that triple helix formation by the unsubstituted 11-mer oligonucleotide targeted a photo-induced cleavage by free ellipticine derivatives at the triplex-duplex junctions. Molecular modeling and energy minimization studies revealed that the distortion at the triplex-duplex junctions could account for these results.

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Author information

Authors and Affiliations

  1. Laboratoire de Biophysique, INSERM U.201, CNRS UA.481, Muséum National d’Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France

    C. Helene, J. C. Francois, C. Giovannangeli & T. Saison-Behmoaras

  2. Centre de Biophysique Moléculaire, CNRS, 45071, Orleans Cedex 02, France

    U. Asseline & N. T. Thuong

Authors
  1. C. Helene
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  2. J. C. Francois
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  3. C. Giovannangeli
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  4. T. Saison-Behmoaras
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  5. U. Asseline
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  6. N. T. Thuong
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Editor information

Editors and Affiliations

  1. Institut de Biologie Physico-Chimique (Fondation Edmond de Rothschild), Paris, France

    Bernard Pullman

  2. Department of Chemistry, University of Tel-Aviv, Israel

    Joshua Jortner

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© 1990 Springer Science+Business Media Dordrecht

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Helene, C., Francois, J.C., Giovannangeli, C., Saison-Behmoaras, T., Asseline, U., Thuong, N.T. (1990). Sequence-Specific Recognition and Cleavage of Duplex DNA by Derivatized Oligonucleotides. In: Pullman, B., Jortner, J. (eds) Molecular Basis of Specificity in Nucleic Acid-Drug Interactions. The Jerusalem Symposia on Quantum Chemistry and Biochemistry, vol 23. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-3728-7_20

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  • DOI: https://doi.org/10.1007/978-94-011-3728-7_20

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5657-1

  • Online ISBN: 978-94-011-3728-7

  • eBook Packages: Springer Book Archive

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