期刊
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
卷 23, 期 6-7, 页码 1057-1064出版社
MARCEL DEKKER INC
DOI: 10.1081/NCN-200026071
关键词
coaxial stacking; contiguous hybridization; thermodynamic; DNA duplex; tandem complex
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 (DeltaGdegrees(ST) at 37degreesC, 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.
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