1my9
From Proteopedia
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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
Overview
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.
About this Structure
1MY9 is a Protein complex structure of sequences from [1]. Full crystallographic 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
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