RNA Methodologies

3rd Edition

A Laboratory Guide for Isolation and Characterization

Authors: Robert E. Farrell, Jr.
Hardcover ISBN: 9780122496967
eBook ISBN: 9780080454764
Imprint: Academic Press
Published Date: 1st April 2005
Page Count: 688
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This laboratory guide represents a growing collection of tried, tested and optimized laboratory protocols for the isolation and characterization of eukaryotic RNA, with lesser emphasis on the characterization of prokaryotic transcripts. Collectively the chapters work together to embellish the RNA story, each presenting clear take-home lessons, liberally incorporating flow charts, tables and graphs to facilitate learning and assist in the planning and implementation phases of a project.

RNA Methodologies, 3rd edition includes approximately 30% new material, including chapters on the more recent technologies of RNA interference including: RNAi; Microarrays; Bioinformatics. It also includes new sections on: new and improved RT-PCR techniques; innovative 5’ and 3’ RACE techniques; subtractive PCR methods; methods for improving cDNA synthesis.

Key Features

  • Author is a well-recognized expert in the field of RNA experimentation and founded Exon-Intron, a well-known biotechnology educational workshop center
  • Includes classic and contemporary techniques
  • Incorporates flow charts, tables, and graphs to facilitate learning and assist in the planning phases of projects


Researchers, graduate students and lab technicians in the fields of molecular biology, cell biology, and biochemical genetics.

Table of Contents



Chapter 1: RNA and the Cellular Biochemistry Revisited

Why Study RNA?

What Is RNA?

Assembly of Polynucleotides

Types of RNA

Stringency: Conditions That Influence Nucleic Acid Structure

Types of Double-Stranded Molecules

Chapter 2: Transcription and the Organization of Eukaryotic Genes

Transcription and the Central Dogma

Gene Organization

RNA Polymerases and the Products of Transcription

Chapter 3: Messenger RNA

Topology of a Typical mRNA Molecule

Stability in the Cytoplasm

Levels of Regulation

Chapter 4: Resilient Ribonucleases


Elimination of Ribonuclease Activity

Types of Ribonuclease Inhibitors

Preparation of Equipment and Reagents

Other Reagents Used to Control Nuclease Activity

Protocol: Synthesis of Vanadyl Ribonucleoside Complexes

Chapter 5: RNA Isolation Strategies


Goals in the Purification of RNA

Lysis Buffer Formulations

Isolation of RNA with Guanidinium Buffers

Guanidinium-Acid-Phenol Extraction Techniques

Density Gradient Centrifugation

Simultaneous Isolation of RNA and DNA

The Word on Kits

Other Methods

Short- and Long-Term Storage of Purified RNA

Chapter 6: The Truth About Tissues


Tissue Culture or Tissue?

Homogenization Methods

RNA Isolation Strategies for Various Organs and Tissues

Protocol: LiCl–Urea Method for RNA Isolation from Tissue

Protocol: RNA Isolation from Lipid-Enriched Tissue

Purification of Polysome-Engaged mRNA

Collecting Samples in the Field

RNA “Clean-Up” Methods

Chapter 7: Isolation of Polyadenylated RNA



The Poly(A) Caveat

Selection of Polyadenylated Molecules



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About the Author

Robert E. Farrell, Jr.

Dr. Robert Farrell is a bench-current scientist who has 35 years of experience working with RNA in the study of transcriptional and posttranscriptional regulation of gene expression in a variety of model systems. He is also experienced in animal cell culture methods. Prior to joining the faculty at Penn State University, he operated a biotech education and service firm, winning the 1998 Small Business Contractor of the Year award from the U.S. Department of Agriculture. He is the recipient of campus- and college-wide awards for excellence in teaching, and has extensive experience running RNA and specialized biotechnology hands-on laboratory training programs all over the world. He often serves as a consultant within the pharmaceutical and biotech industries. Dr. Farrell received his Ph.D. and M.S. degrees from The Catholic University of America and his B.S. in Biology from Providence College. Dr. Farrell currently serves as the campus academic officer at Penn State York.

Affiliations and Expertise

Penn State University, York, PA, USA


Praise for the third edition @qu:"This third edition of RNA Methodologies is an updated version of a laboratory guide edited for the first time in 1993; it represents an exhaustive collection of tried, tested, and optimized protocols for isolation and chracterization of RNA. The third edition of RNA Methodologies is a well-documented guide for any researcher who has to manage RNA studies. Each chapter of this book provides a rationale to help in the decision-making process...The inclusion of troubleshooting hints and annotations based on personal experience are provided to improve the method(s). This laboratory guide offers protocols on traditional and new technologies, with a focus on how to use the expedient technique for achieving an experimental goal in the study of gene expression." @source:--Dr. Patrick Pagesy at INSERM for HEMOGLOBIN