Work

Mechanistic Analysis of the Hepatitis Delta Virus (HDV) Ribozyme: Methods for RNA Preparation, Structure Mapping, Solvent Isotope Effects, and Co-transcriptional Cleavage

Year: 2012

Type: book-chapter

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.

Source: Methods in molecular biology

DOI: 10.1007/978-1-61779-545-9_3

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

Institutions: Pennsylvania State University, National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of North Carolina at Chapel Hill

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funder: National Science Foundation

Award: The Influence of Secondary Structure on the Folding and Catalysis of Functional RNAs