Unwinding DNA and RNA with Synthetic Complexes: On the Way to Artificial Helicases

Abstract

Synthetic helicases can be designed on the basis of ligands that bind more strongly to single-stranded nucleic acids than to double-stranded nucleic acids. This can be achieved with ligands containing phenyl groups, which intercalate into single strands, but due to their small size not into double strands. Moreover, two phenyl rings are combined with a distance that allows bis-intercalation with only single strands and not double strands. In this respect, such ligands also mimic single-strand binding (SSB) proteins. Exploration with more than 23 ligands, mostly newly synthesised, shows that the distance between the phenyl rings and between those and the linker influence the DNA unwinding efficiency, which can reach a melting point decrease of almost ΔTm =50 °C at much lower concentrations than that with any other known artificial helicases. Conformational pre-organisation of the ligand plays a decisive role in optimal efficiency. Substituents at the phenyl rings have a large effect, and increase, for example, in the order of H<F<Cl<Br, which illustrates the strong role of dispersive interactions in intercalation. Studies with homopolymers revealed significant selectivity: for example, with a ligand concentration of 40 μM at 35 °C, only GC double strands melt (ΔTm =48 °C), whereas the AT strand remains untouched, and with poly(rA)-poly(rU) as an RNA model one observes unfolding at 29 °C with a concentration of only 30 μM.

Insights into the opening of DNA-like double-stranded helices in lamivudine duplex IV and the first polymorph of this drug

“…Therefore, D-tartrate counterions act as a helicase, [23][24] responsible for separating the strands of lamivudine duplex IV. The oxygen atoms O1T and O2T of the carboxylate group of the counterion are hydrogen bond acceptors by means of O5′A-H5′A⋯O1T and N4B-H4B1⋯O2T interactions from lamivudine units A and B, respectively.…”