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Nucleic Acids Research, Vol 25, Issue 17 3440-3444, Copyright © 1997 by Oxford University Press

ARTICLES

Sequence-specific targeting and covalent modification of human genomic DNA

ES Belousov, IA Afonina, MA Podyminogin, HB Gamper, MW Reed, RM Wydro and RB Meyer
Epoch Pharmaceuticals, Inc., 1725 220th Street SE, #104, Bothell, WA 98021, USA.

We compare two techniques which enable selective, nucleotide-specific covalent modification of human genomic DNA, as assayed by quantitative ligation- mediated PCR. In the first, a purine motif triplex-forming oligonucleotide with a terminally appended chlorambucil was shown to label a target guanine residue adjacent to its binding site in 80% efficiency at 0.5 microM. Efficiency was higher in the presence of the triplex-stabilizing intercalator coralyne. In the second method, an oligonucleotide targeting a site containing all four bases and bearing chlorambucil on an interior base was shown to efficiently react with a specific nucleotide in the target sequence. The targeted sequence in these cases was in the DQbeta1*0302 allele of the MHC II locus.
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