Differential stability of 20F-ANARNA and ANARNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility

Hybrids of RNA with arabinonucleic acids 20F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other bio-physical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 20F-ANARNA and ANARNA hybrids indicates that the increased binding affinity of 20F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (20F–purine H8) which contrasts with unfavor-able 20-OH–nucleobase steric interactions in the case of ANA. While both 20F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 20F-ANA strand’s structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANARNA duplex showed lower uptake of counterions than its 20F-ANARNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 20F-ANA single strands may be more suit-ably preorganized for duplex formation. Thus the dramatically increased stability of 20F-ANARNA and ANARNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important