1g1n
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(New page: 200px<br /><applet load="1g1n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g1n" /> '''NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30...)
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Revision as of 22:33, 24 November 2007
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NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30 STRUCTURES
Overview
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.
About this Structure
1G1N is a Protein complex structure of sequences from [1] with PE6 as ligand. Full crystallographic information is available from OCA.
Reference
A nicked duplex decamer DNA with a PEG(6) tether., Kozerski L, Mazurek AP, Kawecki R, Bocian W, Krajewski P, Bednarek E, Sitkowski J, Williamson MP, Moir AJ, Hansen PE, Nucleic Acids Res. 2001 Mar 1;29(5):1132-43. PMID:11222763
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