Therapeutic Applications of Ribozymes and Riboswitches: Methods and Protocols

ISBN-13: 9781493962969 / Angielski / Miękka / 2016 / 278 str.

Daniel A. LaFontaine; Audrey Dube

Opis

In Therapeutic Applications of Ribozymes and Riboswitches: Methods and Protocols, expert researchers in the field provide a complete overview of protocols used in the development of RNA molecule as drugs and drug target. These include methods and protocols on recent and precise RNA molecule approaches or studies in the development of an RNA therapeutic tool. We are convinced that these methods will help researchers from various domains of life sciences, including clinicians, biochemists and virologists. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.Authoritative and practical, Therapeutic Applications of Ribozymes and Riboswitches: Methods and Protocols seeks to aid scientists in the further development of new therapeutic applications implicating RNA molecules or directly targeting harmful RNA.

Spis treści

1. Identification of Regulatory RNA in Bacterial Genomes by Genome-Scale Mapping of Transcription Start Sites

Navjot Singh and Joseph T. Wade

 2. Screening Inhibitory potential of anti-HIV RT RNA Aptamers

Margaret J. Lange and Donald H. Burke

 3. Design and Evaluation of Clinically Relevant SOFA-HDV Ribozymes Targeting HIV RNA

Robert J. Scarborough, Michel V. Lévesque, Jean-Pierre Perreault, and Anne Gatignol

 4. Directing RNase P-mediated Cleavage of Target mRNAs by Engineered External Guide Sequences in Cultured Cells

Xiaohong Jiang, Naresh Sunkara, Sangwei Lu, and Fenyong Liu

 5. Design and Analysis of Hammerhead Ribozyme Activity Against an Artificial Gene Target

James Carter, Pruksa Nawtaisong, Velmurugan Balaraman, and Malcolm J. Fraser Jr.

 6. Knockdown Strategies for the Study of Proprotein Converstase and Proliferation in Prostate Cancer Cells

François D’Anjou, Frédéric Couture, Roxane Desjardins and Robert Day

 7. Use of Tumor-Targeting Trans-Splicing Ribozyme for Cancer Treatment

Seong-Wook Lee and Jin-Sook Jeong

 8. Characterization of Hairpin Ribozyme Reactions

Preeti Bajaj and Christian Hammann

 9. Finding Instances of Riboswitches and Ribozymes by Homology Search of Structured RNA with Infernal

Amell El Korbi, Jonathan Ouellet, Mohammad Reza Naghdi, and Jonathan Perreault

 10. Structure-based Virtual Screening for the Identification of RNA-binding Ligands

Peter Daldrop and Ruth Brenk

 11. Probing Riboswitch Binding Sites with Molecular Docking, Focused Libraries, and in-line Probing Assays

Francesco Colizzi, Anne-Marie Lamontagne, Daniel A. Lafontaine, and Giovanni Bussi

 12. Discovery of Small Molecule Modifiers of microRNAs for the Treatment of HCV Infection

Valerie T. Tripp and Douglas D. Young

 13. Bacterial Flavin Mononucleotide Riboswitches as Targets for Flavin Analogs

Danielle Biscardo Pedrolli and Matthias Mack

 14. Construction and Application of Riboswitch-based Sensors That Detect Metabolites Within Bacterial Cells

Casey C. Fowler and Yingfu Li

 15. Screening Assays to Identify Artificial glmS Ribozyme Activators

Christina E. Lünse and Günter Mayer

 16. Analysis of Riboswitch Structure and Ligand Binding using Small-angle X-ray Scattering (SAXS)

Nathan J. Baird and Adrian R. Ferré-D'Amaré

 17. Use of SHAPE to Select 2AP Substitution sites for RNA-ligand Interactions and Dynamics Studies

Marie F. Soulière and Ronald Micura

 18. Cell Internalization SELEX:  In Vitro Selection for Molecules that Internalize into Cells

Amy Yan and Matthew Levy

 19. DNA Electronic Switches Based on Analyte-Responsive Aptamers

Jason M. Thomas, Hua-Zhong Yu, and  Dipankar Sen