1XV0

Solution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG

Summary for 1XV0

• Entry DOI: 10.2210/pdb1xv0/pdb
• Descriptor: 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3', 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P)-3' (2 entities in total)
• Functional Keywords: thermodynamics and structure, base stacking and hydrogen bonding, 3-ga motif, rna
• Total number of polymer chains: 2
• Total formula weight: 6456.99

Authors

Chen, G.,Znosko, B.M.,Kennedy, S.D.,Krugh, T.R.,Turner, D.H. (deposition date: 2004-10-26, release date: 2004-11-09, Last modification date: 2024-05-22)

Primary citation

Chen, G.,Znosko, B.M.,Kennedy, S.D.,Krugh, T.R.,Turner, D.H.
Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs
Biochemistry, 44:2845-2856, 2005

PubMed Abstract: 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.

PubMed: 15723528
DOI: 10.1021/bi048079y

Experimental method

SOLUTION NMR