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1uqb

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{{STRUCTURE_1uqb| PDB=1uqb | SCENE= }}
{{STRUCTURE_1uqb| PDB=1uqb | SCENE= }}
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'''SELF-COMPLEMENTARY DNA 5'-D(CAGCTG)2, NMR, MINIMIZED AVERAGE STRUCTURE'''
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===SELF-COMPLEMENTARY DNA 5'-D(CAGCTG)2, NMR, MINIMIZED AVERAGE STRUCTURE===
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==Overview==
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In this study, the solution structures of eight self-complementary deoxyribonucleic acid molecules, d(CGXX'CG)2 and d(CAXX'TG)2 (where X = C, G, T or A and X' is complementary to X), have been determined using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints. Based on the structural data obtained in solution, a novel sequence-specific local structure function, sigma LS, composed of the sum of the contributions from the helix twist omega, base roll rho, base-pair slide delta delta and propeller twist omega, is introduced to describe their sequence-specific local structures. Sigma LS is found to produce an acceptable correlation (r = 0.96) with the relative local stability (delta G0 10) of a base-pair-step. This result demonstrates that in addition to the inter-strand purine-purine clashes, the base morphology of nearest-neighbor base-pairs is also important in defining the local geometry of base-pairs. Thus, in analyzing the base-pair structural parameter blocks of trimers are used as the basic unit whereas for the base-pair-step structural parameters, the basic unit is composed of blocks of tetramers. The omega LS-delta G(zero) 10 correlation is the first experimental evidence demonstrating the relationship between the relative local stabilities and the sequence-specific local structures of DNA duplexes. It also forms the basis for using the trimer-tetramer model for the prediction of sequence-specific local structures of deoxyribonucleic acid molecules.
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The line below this paragraph, {{ABSTRACT_PUBMED_9102467}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 9102467 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9102467}}
==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=1UQB OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UQB OCA].
==Reference==
==Reference==
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[[Category: Deoxyribonucleic acid]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna]]
[[Category: Dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 11:33:28 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 20:52:52 2008''

Revision as of 17:52, 27 July 2008

Image:1uqb.png

Template:STRUCTURE 1uqb

SELF-COMPLEMENTARY DNA 5'-D(CAGCTG)2, NMR, MINIMIZED AVERAGE STRUCTURE

Template:ABSTRACT PUBMED 9102467

About this Structure

Full experimental information is available from OCA.

Reference

Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids., Lam SL, Au-Yeung SC, J Mol Biol. 1997 Mar 7;266(4):745-60. PMID:9102467

Page seeded by OCA on Sun Jul 27 20:52:52 2008

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