Solution structure of a HNA-RNA hybrid

Background: Synthetic nucleic acid analogues with a conformationally restri cted sugar-phosphate backbone are widely used in antisense strategies for b iomedical and biochemical applications. The modified backbone protects the oligonucleotides against degradation within the living cell, which allows t hem to form stable duplexes with sequences in target mRNAs with the aim of arresting their translation. The biologically most active antisense oligonu cleotides also trigger cleavage of the target RNA through activation of end ogenous RNase H. Systematic studies of synthetic oligonucleotides have also been conducted to delineate the origin of the chirality of DNA and RNA tha t are both composed of D-nucleosides. Results: Hexitol nucleic acids (HNA) are the first example of oligonucleoti des with a six-membered carbohydrate moiety that can bind strongly and sele ctively to complementary RNA oligomers. We present the first high resolutio n nuclear magnetic resonance structure of a HNA oligomer bound to a complem entary RNA strand. The HNA-RNA complex forms an anti-parallel heteroduplex and adopts a helical conformation that belongs to the A-type family, Possib ly, due to the rigidity of the rigid chair conformation of the six-membered ring both the HNA and RNA strand in the duplex are well defined. The obser ved absence of end-fraying effects also indicate a reduced conformational f lexibility of the RNA-RNA duplex compared to canonical dsRNA or an RNA-DNA duplex. Conclusions: The P-P distance across the minor groove, which is close to A- form, and the rigid conformation of the HNA-RNA complex, explain its resist ance towards degradation by Rnase H. The A-form character of the HNA-RNA du plex and the reduced flexibility of the HNA strand is possibly responsible for the stereoselectivity of HNA templates in non-enzymatic replication of oligonucleotides, supporting the theory that nucleosides with six-membered rings could have existed at some stage in molecular evolution.