FTIR and UV Spectroscopy of Parallel-Stranded DNAs with Mixed A•T/G•C Sequences and Their A•T/I•C Analogues

Abstract

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 studied in comparison with antiparallel-stranded (aps) duplexes and a corresponding set of molecules with hypoxanthine as a G base analogue 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 and 1668 cm-1. The latter band was superimposed on the stretching vibration of the free C6=O6 group of guanine. Substitution 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 duplexes. This result is in agreement with a model of trans-Watson-Crick G*C base pairs with two 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 A*T/G*C steps. Molecular modeling 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.

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Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

“…These results are consistent with experiments indicating a reduced stability of the W:W trans geometry for the G:C pair. For example, it has been shown that the introduction of G:C W:W trans base pairs in all A-T parallel strand DNA duplexes, characterized by W:W trans base pairs (31,32), significantly reduces the duplex thermodynamic stability, both for base stacking and hydrogen bonding contributions (33,34). …”

Mg2+ binding and archaeosine modification stabilize the G15–C48 Levitt base pair in tRNAs

“…Experimental studies on parallel strand DNA (psDNA) duplexes, characterized by RWC base pairs (Pattabiraman 1986;Mohammadi et al 1998), have shown that, whereas the all A-T psDNA duplexes are quite stable, the introduction of G-C base pairs significantly reduces the psDNA duplex thermodynamic stability, both for base stacking and hydrogen bonding contributions (Rippe et al 1990;Rentzeperis et al 1992). Moreover, theoretical studies have shown that repulsive amino-amino and carbonyl-carbonyl contacts make the RWC arrangement unfavorable for an isolated G-C pair in the gas phase (Zhanpeisov et al 1998).…”