The 5-Me of thyminyl (T) interaction with the neighboring nucleobases dictate the relative stability of isosequential DNA–RNA hybrid duplexes†
Abstract
Relative energetic contributions from the base-pairing [ΔGobp] vis-a-vis stacking [ΔGostacking] to the total free-energy of stabilization [ΔGo37] for 14 pairs of isosequential hybrid DNA–RNA duplexes (taken from E. A. Lesnik and S. M. Freier, Biochemistry ,1995, 34, 10807) have been dissected in order to understand the differences in the intrinsic nature of the electrostatic forces that are responsible for the self-assembly of the heteroduplexes compared to homoduplexes. The pKa differences between the monomeric nucleotide 3′-ethylphosphates [(d/rN)pEt] as well as nucleotide 3′,5′-bis-ethylphosphates [Etp(d/rN)pEt] in both 2′-deoxy (dN) and ribo (rN) series (N = A/G/C/T/U), as the model donor and acceptor (in which stacking is completely eliminated) mimicking those of the internucleotide monomer building blocks of a duplex, can be qualitatively used (P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya and J. Chattopadhyaya, J. Am. Chem. Soc., 2004, 126, 2862) to understand the strength of base-pairing energies in different DNA–RNA (DR), RNA–DNA (RD), DNA–DNA (DD), and RNA–RNA (RR) duplexes. The study has led us to show the following. (1) As the number of excess %T in DR duplexes compared to the isosequential RD duplexes increase the differences in their thermal stabilization [ΔTm]DR–RD increase and vice-versa
(2) The total relative stabilizations, [ΔΔGo37]DR–RD among the 14 pairs of isosequential DR and RD duplexes (E. A. Lesnik and S. M. Freier, Biochemistry ,1995, 34, 10807) are wholly dependent on the differences in the number of 5-Me(T) stacking interactions with the nearest-neighbors in the D strands of DR duplexes compared to that of the RD duplexes (3) In the relative stabilization of the DR or RD duplexes differences in the free-energy of stackings [ΔΔGostacking]DR–RD play a more significant role than the differences in the free-energy of base-pairing, [ΔΔGobp]DR–RD. In contradistinction, our