1xv0
From Proteopedia
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'''Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG''' | '''Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV0 OCA]. | |
==Reference== | ==Reference== | ||
Solution structure of an RNA internal loop with three consecutive sheared GA pairs., Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH, Biochemistry. 2005 Mar 1;44(8):2845-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15723528 15723528] | Solution structure of an RNA internal loop with three consecutive sheared GA pairs., Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH, Biochemistry. 2005 Mar 1;44(8):2845-56. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15723528 15723528] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Chen, G.]] | [[Category: Chen, G.]] | ||
[[Category: Kennedy, S D.]] | [[Category: Kennedy, S D.]] | ||
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[[Category: Znosko, B M.]] | [[Category: Znosko, B M.]] | ||
[[Category: 3-ga motif]] | [[Category: 3-ga motif]] | ||
| - | [[Category: | + | [[Category: Base stacking and hydrogen bonding]] |
| - | [[Category: | + | [[Category: Thermodynamics and structure]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:32:31 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 12:32, 3 May 2008
Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG
Overview
Internal loops in RNA are important for folding and function. Many folding motifs are internal loops containing GA base pairs, which are usually thermodynamically stabilizing, i.e., contribute favorable free energy to folding. Understanding the sequence dependence of folding stability and structure in terms of molecular interactions, such as hydrogen bonding and base stacking, will provide a foundation for predicting stability and structure. Here, we report the NMR structure of the oligonucleotide duplex, 5'GGUGGAGGCU3'/3'PCCGAAGCCG5' (P = purine), containing an unusually stable and relatively abundant internal loop, 5'GGA3'/3'AAG5'. This loop contains three consecutive sheared GA pairs (trans Hoogsteen/Sugar edge AG) with separate stacks of three G's and three A's in a row. The thermodynamic consequences of various nucleotide substitutions are also reported. Significant destabilization of approximately 2 kcal/mol at 37 degrees C is found for substitution of the middle GA with AA to form 5'GAA3'/3'AAG5'. This destabilization correlates with a unique base stacking and hydrogen-bonding network within the 5'GGA3'/3'AAG5' loop. Interestingly, the motifs, 5'UG3'/3'GA5' and 5'UG3'/3'AA5', have stability similar to 5'CG3'/3'GA5' even though UG and UA pairs are usually less stable than CG pairs. Consecutive sheared GA pairs in the 5'GGA3'/3'AAG5' loop are preorganized for potential tertiary interactions and ligand binding.
About this Structure
Full crystallographic information is available from OCA.
Reference
Solution structure of an RNA internal loop with three consecutive sheared GA pairs., Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH, Biochemistry. 2005 Mar 1;44(8):2845-56. PMID:15723528 Page seeded by OCA on Sat May 3 15:32:31 2008
