Programmable DNA Interstrand Crosslinking by Alkene–Alkyne [2 + 2] Photocycloaddition

Abstract

Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2′-deoxyuridine ( Phe dU). The crosslinking ability of Phe dU was programmed by base pairing and by metal ion interaction at the Watson–Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene–alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a Phe dU dimer after short irradiation times of a few seconds. A Phe dU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.