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1al5

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{{STRUCTURE_1al5| PDB=1al5 | SCENE= }}
{{STRUCTURE_1al5| PDB=1al5 | SCENE= }}
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'''A-TRACT RNA DODECAMER, NMR, 12 STRUCTURES'''
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===A-TRACT RNA DODECAMER, NMR, 12 STRUCTURES===
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==Overview==
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The thermodynamic stability of nine dodecamers (four DNA and five RNA) of the same base composition has been compared by UV-melting. TheDeltaG of stabilisation were in the order: r(GACUGAUCAGUC)2&gt;r(CGCAAATTTGCG)2 approximately r(CGCAUAUAUGCG)2&gt;d(CGCAAATTTGCG)2 approximately r(CGCAAAUUUGCG)2&gt;d(CGCATATATGCG)2 approximately d(GACTGATCAGTC)2&gt;r(CGCUUUAAAGCG)2 approximately d(CGCTTTAAAGCG)2. Compared with the mixed sequences, both r(AAAUUU) and r(UUUAAA) are greatly destablising in RNA, whereas in DNA, d(TTTAAA) is destabilising but d(AAATTT) is stabilising, which has been attributed to the formation of a special B'structure involving large propeller twists of the A-T base pairs. The solution structure of the RNA dodecamer r(CGCAAAUUUGCG)2has been determined using NMR and restrained molecular dynamics calculations to assess the conformational reasons for its stability in comparison with d(CGCAAATTTGCG)2. The structures refined to a mean pairwise r.m.s.d. of 0.89+/-0.29 A. The nucleotide conformations are typical of the A family of structures. However, although the helix axis displacement is approximately 4.6 A into the major groove, the rise (3.0 A) and base inclination ( approximately 6 degrees ) are different from standard A form RNA. The extensive base-stacking found in the AAATTT tract of the DNA homologue that is largely responsible for the higher thermodynamic stability of the DNA duplex is reduced in the RNA structure, which may account for its low relative stability.
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(as it appears on PubMed at http://www.pubmed.gov), where 9185574 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9185574}}
==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=1AL5 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AL5 OCA].
==Reference==
==Reference==
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[[Category: Ribonucleic acid]]
[[Category: Ribonucleic acid]]
[[Category: Rna duplex]]
[[Category: Rna duplex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:04:51 2008''

Revision as of 14:04, 30 June 2008

Image:1al5.png

Template:STRUCTURE 1al5

A-TRACT RNA DODECAMER, NMR, 12 STRUCTURES

Template:ABSTRACT PUBMED 9185574

About this Structure

Full experimental information is available from OCA.

Reference

Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2., Conte MR, Conn GL, Brown T, Lane AN, Nucleic Acids Res. 1997 Jul 1;25(13):2627-34. PMID:9185574

Page seeded by OCA on Mon Jun 30 17:04:51 2008

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