Determination of Enthalpy and Entropy Changes upon NA Melting: Raman Study of Modified Thymidine Pentadecamers Complexes with Poly(rA)

Abstract

Hybridization properties of a novel type of internucleotide linkage modification have been studied by using multivariate analysis of concentration and temperature dependent Raman spectra. The linkage consists in an insertion of CH2 group into the phosphodiester bond.

Four phosphonate oligothymidylates differing in number and distribution of modified linkages were investigated in mixed solutions with poly(rA). The developed method allows simultaneous characterization of structural and thermodynamic properties of complexes.

Except the 3'-side all-phosphonate oligothymidylate, all pentadecamers as well as natural (dT)15 form stable Watson-Crick duplexes. Duplex stability increases in the order alternating (3'-type) ~ all-phosphonate (5'-type) < (dT)15 < alternating (5'-type).

Raman spectra revealed unusual conformation of both strands in the duplexes. The increased stability of the DNA:RNA hybrid duplex correlates with its more regular structure.