High‐Fidelity Recognition of RNA: Solution Structure of a DNA:RNA Hybrid Duplex with a Molecular Cap

Abstract

Binding RNA targets, such as microRNAs, with high fidelity is challenging, particularly when the nucleobases to be bound are located at the terminus of the duplex between probe and target. Recently, a peptidyl chain terminating in a quinolone, called ogOA, was shown to act as a cap that enhances affinity and fidelity for RNAs, stabilizing duplexes with Watson-Crick pairing at their termini. Here we report the three-dimensional structure of an intramolecular complex between a DNA strand featuring the ogOA cap and an RNA segment, solved by NMR and restrained torsion angle molecular dynamics. The quinolone stacks on the terminal base pair of the hybrid duplex, positioned by the peptidyl chain, whose prolinol residue induces a sharp bend between the 5' terminus of the DNA chain and the glycine linked to the oxolinic acid residue. The structure explains why canonical base pairing is favored over hard-to-suppress mismatched base combinations, such as T:G and A:A, and helps to design improved high-fidelity probes for RNA.

Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid‐Phase and Template‐Directed Chain Assembly

“…The former are expected for an uninterrupted, continuously stacked double helix, whereas the latter point to a partially unwound helix. Further, attempts to generate a three-dimensional structure by restrained torsion angle molecular dynamics, using the available NOE constraints and previously applied to similar short helices, [32][33][34] did not give any violation-free structures despite numerous computational runs. Therefore, we suspected that 1 was disordered or incompletely folded in its terminal region at 25 °C. This hypothesis was corroborated by the results of a UVmelting study.…”