Conformational changes in the oligonucleotide duplex d(GCGTTGCG) x d(CGCAACGC) induced by formation of a cis-syn thymine dimer. A two-dimensional NMR study

J Kemmink, R Boelens, T M Koning, R Kaptein, G A van der Marel, J H van Boom

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

In order to obtain insight into the repair mechanism of DNA containing thymine photo-dimer, the conformation of the duplex d(GCGTTGCG) x d(CGCAACGC) with a thymine dimer incorporated has been studied by proton NMR and the results are compared with NMR data of the parent octamer. Two-dimensional nuclear Overhauser enhancement (2D NOE) spectroscopy and two-dimensional homonuclear Hartmann-Hahn spectroscopy have been applied to assign all the non-exchangeable base protons and most of the deoxyribose protons of both duplexes. From these experiments it is clear that indeed a cis-syn cyclobutane-type thymine photodimer is formed by the irradiation of this oligonucleotide with ultraviolet light. Comparison of 2D NOE spectra and the 1H chemical shifts of the damaged and the intact DNA duplexes reveals that formation of a thymine dimer induces small distortions of the B-DNA structure, the main conformational change occurring at the site of the thymine dimer.

Original languageEnglish
Pages (from-to)37-43
Number of pages7
JournalEuropean Journal of Biochemistry
Volume162
Issue number1
Publication statusPublished - 2 Jan 1987

Keywords

  • Binding Sites
  • DNA Repair
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides
  • Protons
  • Pyrimidine Dimers
  • Spectrum Analysis

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