title: 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 (deltaG degrees ST at 37 degrees 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.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SD RAS, Novosibirsk, Russia. pyshnyi@niboch.ncs.ru
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Pyshnyi
authors.forename: Eugenia M
authors.initials: EM
authors.lastname: Ivanova
mesh_terms: D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010766:Phosphorylation
chemical_list: D009838:Oligodeoxyribonucleotides