FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A center dotT/G center dot C sequences and their A center dot T/I center dot C analogues

The infrared spectra of parallel-stranded (ps) hairpin duplexes with mixed A.T/G.C composition and either isolated or sequential G.C pairs were studie d in comparison with antiparallel-stranded (aps) duplexes and a correspondi ng set of molecules with hypoxanthine as a G base analogue lacking the exoc yclic amino group. The ps duplexes showed the characteristic bands for the C2=O2 and C4=O4 stretching vibrations of thymine residues in trans-Watson-C rick A.T pairing at 1683 and 1668 cm(-1). The latter band was superimposed on the stretching vibration of the free C6=O6 group of guanine. Substitutio n of guanine by hypoxanthine inhibited the formation of ps hairpin duplexes whatever the sequence, demonstrating that in the H-bonding between G and C the 2-NH2 group is necessary for stabilizing all of the investigated ps du plexes. This result is in agreement with a model of trans-Watson-Crick G.C base pairs with two H-bonds [N2H(2)(G)-N3(C) and N1H(G)-O2(C)]. However, tr ans-Watson-Crick A.T and G.C base pairs with two H-bonds are not isomorphou s, which may explain the decreased stability of the ps, but not the aps, du plexes upon increasing the number of A.T/G.C steps. Molecular modeling stud ies performed on two of the ps duplexes reveal the existence of propeller t wist for avoiding a clash between the N2(G) and N4(C) amino groups, and fav orable stacking of sequential G.C base pairs. The optimized hairpin ps dupl exes invariably incorporated G.C base pairs with two H-bonds, regardless of the initial structures adopted for the force field calculations.