Mechanistic analysis of the Hepatitis Delta Virus (HDV) ribozyme: Methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage

Durga M. Chadalavada, Andrea L. Cerrone-Szakal, Jennifer L. Wilcox, Nathan A. Siegfried, Philip C. Bevilacqua

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations

Abstract

Small ribozymes such as the hairpin, hammerhead, VS, glm S, and hepatitis delta virus (HDV) are self-cleaving RNAs that are typically characterized by kinetics and structural methods. Working with these RNAs requires attention to numerous experimental details. In this chapter we focus on four different experimental aspects of ribozyme studies: preparing the RNA, mapping its structure with reverse transcription and end-labeled techniques, solvent isotope experiments, and co-transcriptional cleavage assays. Although the focus of these methods is the HDV ribozyme, the methods should be applicable to other ribozymes.

Original languageEnglish (US)
Title of host publicationRibozymes
Subtitle of host publicationMethods and Protocols
EditorsJorg Hartig
Pages21-40
Number of pages20
DOIs
StatePublished - Mar 19 2012

Publication series

NameMethods in Molecular Biology
Volume848
ISSN (Print)1064-3745

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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    Chadalavada, D. M., Cerrone-Szakal, A. L., Wilcox, J. L., Siegfried, N. A., & Bevilacqua, P. C. (2012). Mechanistic analysis of the Hepatitis Delta Virus (HDV) ribozyme: Methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage. In J. Hartig (Ed.), Ribozymes: Methods and Protocols (pp. 21-40). (Methods in Molecular Biology; Vol. 848). https://doi.org/10.1007/978-1-61779-545-9_3