A nicked duplex decamer DNA with a PEG(6) tether

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 H-1, P-31 and T-1 spectral parameters, Molecular modelling using rMD-simuiated annealing was used to compute the structure. Scalar cou plings 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 duple x that restricts the dynamics of the stem:pentamers and thus stabilises the oligonucleotide. The inspection of the global parameters shows that the li nker does not distort the B-DNA geometry. The computed structure suggests t hat the presence of the nick is not disturbing the overall tertiary structu re, 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 si te, indicated clearly by NMR analysis and reflected in the conformational p arameters of the computed structure. The H-1 spectra also show much sharper resonances in the presence of K+ indicating that conformational heterogene ity of DDSDPEG is reduced in the presence of potassium as compared to sodiu m or caesium ions, At the same time the H-1 resonances have longer T-1 time s, This parameter is suggested as a sensitive gauge of stabilisation.