Conformational analysis of trinucleotides containing a single abasic residue; mimics of DNA damage

The conformations of three deoxytrinucleotide analogues [d(TpXpT), where X = T, tetrahydrofuran (THF) or propyl (Pr)] were investigated using 1H NMR spectroscopy as part of our studies of DNA-base damage. The phosphorus-decoupled 1H NMR spectrum of each compound was simulated and values for the vicinal proton–proton coupling constants of the sugar ring hydrogens were extracted at several different temperatures, for use in conformational analyses. It was found that the south-pucker preference of the sugar 3′ to the modification is increased whereas that of the 5′ is decreased relative to the puckers observed for the non-modified system. The conformational change is <25%. This subtle effect may be sufficient for recognition by DNA repair enzymes. Copyright © 2003 John Wiley & Sons, Ltd.