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1my9

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{{STRUCTURE_1my9| PDB=1my9 | SCENE= }}
{{STRUCTURE_1my9| PDB=1my9 | SCENE= }}
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'''Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops'''
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===Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops===
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==Overview==
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Using CD and NMR, we determined the structure of an RNA oligomer, r(GGAGGUUUUGGAGG) (R14), comprising two GGAGG segments joined by a UUUU segment. A modified quadruplex structure was observed for r(GGAGGUUUUGGAGG) in solution even in the absence of K(+). An unusually stable dimeric RNA quadruplex architecture formed from two strands of r(GGAGGUUUUGGAGG) at low K(+) concentration is reported here. In each strand of r(GGAGGUUUUGGAGG), two sets of successive turns in the GGAGG segments and turns at both ends of the UUUU loops drive four G-G steps to align in a parallel manner, a core with two stacked G-tetrads being formed. Two adenine bases bind to two edges of one G:G:G:G tetrad through the sheared G:A mismatch augmenting the tetrad into a G:G(:A):G:G(:A) hexad. Thus, one molecule of r(GGAGGUUUUGGAGG) folds into a modified quadruplex comprising a G:G:G:G tetrad, a UUUU double-chain reversal loop and a G:G(:A):G:G(:A) hexad. Two such molecules further associate by stacking through the dimeric hexad-hexad interface with a rotational symmetry. The ribose rings of most nucleotides take S (close to C2'-endo) puckering, which is unusual for an RNA. K(+) can increase the stability of this quadruplex structure; the number of bound K(+) was estimated from the results of the titration experiment. Besides G:G and G:A mismatches, a network of hydrogen bonds including O4'-NH(2) and C-H..O hydrogen bonds, and the extensive base stacking contribute to the high thermodynamic stability of R14. Our results could provide the stereochemical and thermodynamic basis for elucidating the biological role of the GGAGG-containing RNA segments abundantly existing in various RNAs. Relevance to quadruplex-mediated mRNA-FMRP binding and HIV-1 genome RNA dimerization is discussed.
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(as it appears on PubMed at http://www.pubmed.gov), where 12367521 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12367521}}
==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=1MY9 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MY9 OCA].
==Reference==
==Reference==
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[[Category: Dimer of two quadruplex]]
[[Category: Dimer of two quadruplex]]
[[Category: Parallel rna quadruplex with a loop]]
[[Category: Parallel rna quadruplex with a loop]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 01:51:57 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:44:14 2008''

Revision as of 00:44, 29 July 2008

Image:1my9.png

Template:STRUCTURE 1my9

Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops

Template:ABSTRACT PUBMED 12367521

About this Structure

Full experimental information is available from OCA.

Reference

A dimeric RNA quadruplex architecture comprised of two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops., Liu H, Matsugami A, Katahira M, Uesugi S, J Mol Biol. 2002 Oct 4;322(5):955-70. PMID:12367521

Page seeded by OCA on Tue Jul 29 03:44:14 2008

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