Interactions of cations with RNA loop-loop complexes
| Autor: | Latsavongsakda Sethaphong, Abhishek Singh, Yaroslava G. Yingling |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
chemistry.chemical_classification
Base Sequence Nucleic Acid Base pair Metal ions in aqueous solution Biophysics RNA Sequence (biology) Molecular Dynamics Simulation Molecular dynamics Crystallography Viral replication chemistry Metals Cations Solvents Nucleic Acid Conformation Nucleotide Counterion Base Pairing |
| Zdroj: | Biophysical journal. 101(3) |
| ISSN: | 1542-0086 |
| Popis: | RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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