1mv1
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(New page: 200px<br /><applet load="1mv1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mv1" /> '''The Tandem, Sheared PA Pairs in 5'(rGGCPAGCC...)
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Revision as of 19:56, 24 November 2007
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The Tandem, Sheared PA Pairs in 5'(rGGCPAGCCU)2
Overview
The contribution of amino groups to the thermodynamics, structure, and, dynamics of tandem A.A mismatches is investigated by substitution of, purine (P) for adenine (A) within the RNA duplex, 5'(rGGCAAGCCU)(2), to, give 5'(rGGCPAGCCU)(2), 5'(rGGCAPGCCU)(2), and 5'(rGGCPPGCCU)(2). The, 5'(rGGCAAGCCU)(2) duplex has sheared A(anti).A(anti) (A.A trans, Hoogsteen/Sugar-edge) pairs in which the A5 amino group is involved in, hydrogen bonds but the A4 amino group is not [Znosko, B. M., Burkard, M., E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) Biochemistry, 41, 14969-14977]. In comparison to 5'(rGGCAAGCCU)(2), replacing the amino, group of A4 with a hydrogen stabilizes the duplex by 1.3 kcal/mol, replacement of the A5 amino group destabilizes the duplex by 0.6 kcal/mol, and replacement of both A4 and A5 amino groups destabilizes the duplex by, 0.8 kcal/mol. In NMR structures, the P.A noncanonical pairs of the, 5'(rGGCPAGCCU)(2) duplex have a sheared anti-anti structure (P.A trans, Hoogsteen/Sugar-edge) with P4.A5 interstrand hydrogen bonding and A5 bases, that interstrand stack, similar to the structure of 5'(rGGCAAGCCU)(2). In, contrast, the A.P pairs of the 5'(rGGCAPGCCU)(2) duplex have a, face-to-face conformation (A.P trans Watson-Crick/Watson-Crick) with, intrastrand stacking resembling typical A-form geometry. Although the P5, bases in 5'(rGGCPPGCCU)(2) are involved in an interstrand stack, the loop, region is largely undefined. The results illustrate that both, hydrogen-bonded and non-hydrogen-bonded amino groups play important roles, in determining the thermodynamic, structural, and dynamic characteristics, of purine rich internal loops.
About this Structure
1MV1 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2., Znosko BM, Burkard ME, Krugh TR, Turner DH, Biochemistry. 2002 Dec 17;41(50):14978-87. PMID:12475247
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