Analysis of intermolecular base pair formation of prohead RNA of the phage ø29 DNA packaging motor using NMR spectroscopy
| Autor: | Aya Kitamura, Shelley Grimes, Paul J. Jardine, Dwight L. Anderson, Hiroshi Matsuo |
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| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Base pair
Stereochemistry Molecular Sequence Data Bacillus Phages Biology 010402 general chemistry 01 natural sciences Bacteriophage 03 medical and health sciences chemistry.chemical_compound DNA Packaging Genetics Base Pairing Nuclear Magnetic Resonance Biomolecular 030304 developmental biology 0303 health sciences Base Sequence Hydrogen bond Intermolecular force Prohead RNA Nuclear magnetic resonance spectroscopy biology.organism_classification 0104 chemical sciences Biochemistry chemistry Nucleic Acid Conformation RNA Viral Electrophoresis Polyacrylamide Gel Dimerization DNA |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | The bacteriophage o29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the CE-loop or the D-loop, respectively, were produced and shown to form a heterodimer in a Mg 2+ -dependent manner, similar to that with full-length pRNA. It has been hypothesized that four intermolecular base pairs are formed between pRNA molecules. Our NMR study of the heterodimer, for the first time, proved directly the existence of two intermolecular Watson–Crick G–C base pairs. The two potential intermolecular A–U base pairs were not observed. In addition, flexibility of the D-loop was found to be important since a Watson–Crick base pair introduced at the base of the D-loop disrupted the formation of the intermolecular G–C hydrogen bonds, and therefore affected heterodimerization. Introduction of this mutation into the biologically active 120-nt pRNA (U80C mutant) resulted in no detectable dimerization at ambient temperature as shown by native gel and sedimentation velocity analyses. Interestingly, this pRNA bound to prohead and packaged DNA as well as the wild-type 120-nt pRNA. |
| Databáze: | OpenAIRE |
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