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1g1n

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{{STRUCTURE_1g1n| PDB=1g1n | SCENE= }}
{{STRUCTURE_1g1n| PDB=1g1n | SCENE= }}
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'''NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30 STRUCTURES'''
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===NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30 STRUCTURES===
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==Overview==
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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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(as it appears on PubMed at http://www.pubmed.gov), where 11222763 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11222763}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G1N OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G1N OCA].
==Reference==
==Reference==
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[[Category: Nicked duplex dna]]
[[Category: Nicked duplex dna]]
[[Category: Peg6 tether]]
[[Category: Peg6 tether]]
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Revision as of 01:16, 1 July 2008

Image:1g1n.png

Template:STRUCTURE 1g1n

NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30 STRUCTURES

Template:ABSTRACT PUBMED 11222763

About this Structure

Full experimental 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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