Duplex Stabilization by DNA-Hoechst 33258 Conjugates: Effects of Base Pair Mismatches

Abstract

Three types of DNA-Hoechst conjugates are examined for duplex stability in the presence of single-site base pair mismatches. Two of the complexes have the Hoechst ligand tethered to an internal phosphate residue, while the third complex employs terminally labeled conjugate. The presence of the mismatched base pair reduces the T_m values for the non-conjugate duplexes as is expected. Addition of the conjugated Hoechst ligand enhances the T_m values for the mismatched duplexes, but these values remain significantly below that obtained for the native conjugated duplex. While stabilization by the tethered ligand is observed for both cognate and non-cognate sequences, the differences suggest that significant sequence selectivity is still apparent for these conjugates.