Binding of Hoechst 33258 and 4',6-diamidino-2-phenylindole to self-complementary decadeoxynucleotides with modified exocyclic base substituents

Fluorescence titrations have been carried out to determine the association constants (K{sub a}) for binding of the dyes Hoechst 33258 and DAPI to the self-complementary decamer d(CTGAATTCAG) and nine duplex derivatives with exocyclic substituent changes in the six central base pairs. Many K{sub a} values are in the range (2-5) {times} 10{sup 8} (duplex M){sup {minus}1} at 5.5 {degree}C. Replacement of the leftmost adenine by 2-aminopurine in the sequence decreases K{sub a} for Hoechst 33258 by a factor of 170. When the centermost adenine is replaced by 2-aminopurine, K{sub a} for Hoechst 33258 and DAPI is too small to be evaluated. When the centermost adenine is replaced by purine, K{sub a} for both dyes increases, but this very stable duplex-Hoechst 33258 complex is nonfluorescent. The measured affinities are compared to expectations derived from X-ray studies with dodecamer-dye complexes having an identical central binding sequence.