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Nucleic Acids Research, Vol 25, Issue 20 4123-4131, Copyright © 1997 by Oxford University Press

ARTICLES

Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides

JN Lampe, IV Kutyavin, R Rhinehart, MW Reed, RB Meyer and HB Gamper Jr
Epoch Pharmaceuticals, Inc., 1725 220th Street SE, #104, Bothell, WA 98021, USA.

G/A motif triplex-forming oligonucleotides (TFOs) complementary to a 21 base pair homopurine/homopyrimidine run were conjugated at one or both ends to chlorambucil. These TFOs were incubated with several synthetic duplexes containing the targeted homopurine run flanked by different sequences. The extent of mono and interstrand cross-linking was compared with the level of binding at equilibrium. Covalent modification took place within a triple-stranded complex and usually occurred at guanine residues in the flanking double-stranded DNA. The efficiency of alkylation was dependent upon the sequence of the flanking duplex, the solution conditions, and the rate of triplex formation relative to the rate of chlorambucil reaction. Self- association of the TFOs as parallel duplexes was demonstrated and this did not interfere with triple strand formation. With an optimal target, cross-linking of the triplex was very efficient when incubation was carried in a physiological buffer supplemented with the triplex selective intercalator coralyne.
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