Stabilization of hairpins and bulged secondary structures of nucleic acids by single incorporation of α,β-D-CNA featuring a gauche(+) alpha torsional angle

Abstract

A constrained dinucleotide unit featuring a gauche(+) alpha torsional angle configuration was used to stabilize DNA hairpin or bulged structures. Large five nucleotides having looped hairpin structures can be stabilized up to +5 °C. Depending on the nature of the closing base pair, the increased hairpin stability can be reached through loop moiety preorganization or stem rearrangement induced on the first two base pairs. With an alpha gauche(+) constraint either within or opposite to the bulge, the larger bulged structures had better stabilization.