1xv0
From Proteopedia
(New page: 200px<br /><applet load="1xv0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xv0" /> '''Solution NMR structure of RNA internal loop ...) |
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'''Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG'''<br /> | '''Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Internal loops in RNA are important for folding and function. Many folding | + | 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== | ==About this Structure== | ||
| - | 1XV0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1XV0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV0 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Chen, G.]] | [[Category: Chen, G.]] | ||
| - | [[Category: Kennedy, S | + | [[Category: Kennedy, S D.]] |
| - | [[Category: Krugh, T | + | [[Category: Krugh, T R.]] |
| - | [[Category: Turner, D | + | [[Category: Turner, D H.]] |
| - | [[Category: Znosko, B | + | [[Category: Znosko, B M.]] |
[[Category: 3-ga motif]] | [[Category: 3-ga motif]] | ||
[[Category: base stacking and hydrogen bonding]] | [[Category: base stacking and hydrogen bonding]] | ||
[[Category: thermodynamics and structure]] | [[Category: thermodynamics and structure]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:58:54 2008'' |
Revision as of 13:58, 21 February 2008
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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
1XV0 is a Protein complex structure of sequences from [1]. 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
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