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A dumbbell double-stranded DNA decamer tethered with a hexaethylene glycol linker moiety (DDSDPEG), with a nick in the centre of one strand, has been synthesised. The standard NMR methods, E.COSY, TOCSY, NOESY and HMQC, were used to measure (1)H, (31)P and T:(1) spectral parameters. Molecular modelling using rMD-simulated annealing was used to compute the structure. Scalar couplings and dipolar contacts show that the molecule adopts a right-handed B-DNA helix in 38 mM phosphate buffer at pH 7. Its high melting temperature confirms the good base stacking and stability of the duplex. This is partly attributed to the presence of the PEG(6) linker at both ends of the duplex that restricts the dynamics of the stem pentamers and thus stabilises the oligonucleotide. The inspection of the global parameters shows that the linker does not distort the B-DNA geometry. The computed structure suggests that the presence of the nick is not disturbing the overall tertiary structure, base pair geometry or duplex base pairing to a substantial extent. The nick has, however, a noticeable impact on the local geometry at the nick site, indicated clearly by NMR analysis and reflected in the conformational parameters of the computed structure. The (1)H spectra also show much sharper resonances in the presence of K(+) indicating that conformational heterogeneity of DDSDPEG is reduced in the presence of potassium as compared to sodium or caesium ions. At the same time the (1)H resonances have longer T:(1) times. This parameter is suggested as a sensitive gauge of stabilisation.

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The infrared low-temperature Ar-matrix spectra of 5-halouracils and unsubstituted uracil were measured and interpreted in terms of the spectra calculated at the DFT/B3PW91/6-311G level followed by a potential energy distribution (PED) analysis. For the PED analysis, the sets of halouracil mode definitions were constructed so that dissimilarities in the interpretations of the different spectra were minimized. Anharmonic frequency calculations enabled more light to be shed on the Fermi resonance (FR) phenomena occurring in the nu(C=O) stretching vibrations region. For each halouracil vibrational spectrum, several FRs manifest themselves in the nu(C=O) stretching vibrations region. We show that the most frequent components participating in these resonances are the nu(C(4)=O(10)) frequency, a beta(N-H) mode frequency, and a beta(C=O) mode frequency. The experimental nu(N-H) frequencies are reproduced by the calculated anharmonic frequencies better than by the scaled harmonic ones, and the nu(C=O) frequencies respond in the opposite manner. The experimental frequencies located below 1500 cm(-1) are reproduced equally well by the two kinds of calculations.

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