Influence of internucleotide phosphate linkage on relative base stacking in 3′–5′ and 2′–5′ RNA: A circular dichroic spectroscopic study of RNA hexamer AACCUU

The variations in base stacking interactions of two isomeric RNA hexamers, 3′–5′r(AACCUU) and 2′–5′r′(AACCUU), have been studied using temperature dependent CD spectroscopy. Both RNA hexamers, in single strand form, exhibited a right handed helical sense. Van't Hoff analysis of the CD spectral results, derived from a two state model, gave a higher enthalpy of stacking for 3′–5′ RNA than for 2′–5′RNA. The results suggest that 3′–5′ linkage in RNA facilitates formation of better helical stacks in relation to an isomeric 2′–5′ linkage.