Chemical probing studies of variants of the genomic hepatitis delta virus ribozyme by primer extension analysis
| Autor: | P.K.R. Kumar, Kazunari Taira, Satoshi Nishikawa |
|---|---|
| Rok vydání: | 1994 |
| Předmět: |
Stereochemistry
viruses Molecular Sequence Data Borohydrides Sulfuric Acid Esters Biology Nucleic Acid Denaturation Biochemistry Primer extension Dimethyl sulfate chemistry.chemical_compound Magnesium RNA Catalytic Protein secondary structure Base Composition Aniline Compounds Base Sequence Ribozyme RNA Molecular biology Reverse transcriptase Carbodiimides chemistry biology.protein Nucleic Acid Conformation RNA Viral Hepatitis Delta Virus Pseudoknot VS ribozyme |
| Zdroj: | Scopus-Elsevier |
| ISSN: | 1520-4995 0006-2960 |
| DOI: | 10.1021/bi00168a025 |
| Popis: | We have investigated in detail the higher order structure of the genomic hepatitis delta virus (HDV) ribozyme using various base-specific chemical probes under native, semi-denaturing, and denaturing conditions. The bases of the HDV ribozyme were probed by treatment with dimethyl sulfate [which reacts with A (at N1) and C (at N3)] and a carbodiimide [which reacts with U (at N3) and G (at N1)]. In addition, for probing G residues (at N7), RNA samples were treated with NaBH4 and aniline after modification by treatment with dimethyl sulfate. The sites of modified positions were identified by primer extension analysis with reverse transcriptase. In general, our results are consistent with the proposed pseudoknot model of secondary structure, a model that is based on data from ribonucleolytic cleavage experiments. Our results provide clues to the identification of interacting bases in the HDV ribozyme. Furthermore, using this method we identified local conformational changes in several stem variants. |
| Databáze: | OpenAIRE |
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