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

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

Parallel DNA double helices incorporating isoG or m⁵ isoC bases studied by FTIR, CD and molecular modeling

FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m⁵isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A–T and isoG–C or m⁵isoC–G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson–Crick (WC) base pairs) reflect the formation of transWatson–Crick A–T base pairs. All carbonyl groups of cytosines, m⁵isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG–C and m⁵isoC–G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B->A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type->N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG–A)/d(C–T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water / trifluoroethanol solutions and its free energy at 0°C was estimated to be 6.6±0.3 kcal mol ⁻¹