The Influence of Nearest Neighbours on the Efficiency of Coaxial Stacking at Contiguous Stacking Hybridization of Oligodeoxyribonucleotides

Abstract

Contiguous stacking hybridization of oligodeoxyribonucleotides with a stem of preformed minihairpin structure of a DNA template was studied with the use of UV‐melting technique. It was shown that the free‐energy of the coaxial stacking interaction (ΔG°_ST at 37°C, 1 M NaCl, pH 7.4) at the complementary interface XA^*pTY/ZATV (an asterisk stands for a nick) strongly depends on the type of nearest neighbor bases X and Y flanking the nicked dinucleotide step. The maximum efficiency of the coaxial stacking was observed for the PuA^*pTPy/PuATPy interface, whereas the minimum efficiency was obtained for the PyA^*pTPu/PyATPu interface. A 5′‐phosphate residue in the nick enhances the coaxial stacking. In dependence on duplex structure the observed efficiency of A^*T/AT coaxial stacking varied from (− 0.97 kcal/mol) for unphosphorylated TA^*TA/TATA interface to three‐fold higher value (− 2.78 kcal/mol) for GA^*pTT/AATC interface.

Keywords:

• Coaxial stacking
• Contiguous hybridization
• Thermodynamic
• DNA duplex
• Tandem complex

Acknowledgments

This work was supported by grant of the program for young scientists of Siberian Division of RAS (#50), grant of MCB Program of RAS (#10.6) and integration grant of SD RAS (#126).