Influence of N6-isopentenyladenosine (i6A) on thermal stability of RNA duplexes Original Research Article

The thermodynamic stability of self-complementary oligoribonucleotides containing N6-isopentenyladenosine (i6A) or N6-isopentanyladenosine (p6A) was determined. The base pairs i6A·U and p6A·U were placed in either an internal (separated and tandem) and a terminal position within the duplex, or unpaired i6A and p6A as a 3′-dangling ends. The thermal unfolding of the oligomers was determined by means of UV melting profiles and the thermodynamic parameters: enthalpy (ΔH°), entropy (ΔS°) and free energy (ΔG°37) as well as the melting temperature (Tm) were calculated. Both modified nucleosides destabilized the duplexes, however, the effect depended on the position of the modified adenosine within the duplex. The similarity of the behavior of oligomers containing i6A and p6A suggests a negligible effect of the double bond on the thermal stability. The largest destabilization was observed when derivatives of adenosine were placed in an internal position. The effect of 3′-dangling ends suggests that the presence of the N6-isopentenyl- or N6-isopentanyl substitutent affects hydrogen bonding rather than stacking within duplex.