FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A·T/G·C sequences and their inosine analogs.

The infrared spectra of parallel-stranded (ps) hairpin duplexes with mixed AT/GC composition and either isolated or sequential G·C pairs were studied in comparison with antiparallel-stranded (aps) duplexes and a corresponding set of with molecules with inosine as a G base analog lacking the exocyclic amino group. The ps duplexes showed the characteristic bands for the C2=O2 and C4=O4 stretching vibrations of thymine residues in trans-Watson-Crick A·T pairing at 1683 cm-1 and 1668 cm-1. The latter band was superimposed on the stretching vibration of the free C6=O6 group of guanine. Substitution of guanines by inosines 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 duplexes with mixed AT/GC composition. This result is in agreement with a model of trans-Watson-Crick G·C base pairs with 2 H-bonds [N2H2(G)-N3(C)) and (N1H(G)-O2(C)]. However, trans-Watson-Crick A·T and G·C base pairs with two H-bonds are not isomorphous, which may explain the decreased stability of the ps, but not the aps, duplexes upon increasing the number of AT/GC junctions. Molecular modelling studies performed on two of the ps duplexes reveal the existence of propeller twist for avoiding a clash between the N2(G) and N4(C) amino groups, and favorable stacking of sequential G·C base pairs. The optimized hairpin ps duplexes invariably incorporated G·C base pairs with two H- bonds, regardless of the initial structures adopted for the force field calculations