Modified purine nucleosides as dangling ends of DNA duplexes: the effect of the nucleobase polarizability on stacking interactions

Base-modified nucleotide residues have been appended to the 5′-terminus of the self-complementary oligo-2′-deoxynucleotide duplex [5′-d(CGCGCG)]2 as dangling ends. Temperature-dependent UV measurements on the resulting oligomers indicate generally higher thermal stabilities (Tm) compared to that without an overhanging end. The duplex stabilization (ΔTm) was correlated with the molecular polarizability (αm) of the base of the pendant nucleoside showing that: the higher the molecular polarizability αm of a dangling nucleobase, the higher the thermal stability of the DNA duplex.