Stabilization of DNA Hairpins by Stilbene Capping of the Terminal Base Pair

Abstract

Abstract The synthesis and properties of DNA mini‐hairpin conjugates possessing stilbene capping groups have been investigated for two hairpin base sequences with three stilbene capping groups. The two hairpin sequences 5′‐TTTCACCGAAA vs. 5′‐ATTCACCGAAT differ in the orientation of the terminal base pair, the latter forming the more stable hairpin. Conjugation of these hairpins with a 5′‐stilbenecarboxamide capping group significantly increases hairpin stability and reduces the difference in stability observed for the unmodified hairpins. Replacement of the stilbene phenyl by either a pentafluorophenyl or trimethoxy‐phenyl group results in enhanced stability for the first hairpin sequence but not for the second. These differences are attributed to structure‐specific interactions between the substituted stilbene rings with adenine. Quenching of the fluorescence of the pentafluorostilbene in the capped hairpins is attributed to an electron transfer processes. The enhanced fluorescence observed for the stilbene and methoxystilbene hairpin conjugates is indicative of both the absence of electron transfer quenching by adjacent bases and an increase in the barrier for stilbene nonradiative decay via double bond torsion.