Nucleic Acid Blotting Techniques for Virus Detection

This chapter focuses on the nucleic acid blotting techniques for virus detection. The Southern and Northern blotting procedures have evolved with some general alterations and numerous case-specific ones. The chapter discusses the techniques to prepare and process nucleic acids from cells and tissues for use in filter hybridization assays, along with a variety of techniques to separate nucleic acid pools to hybridization and the preparation of hybridization probes, and methods for detection and quantification of hybridization signals. Specific examples of these technologies show the detection of nucleic acids from human immunodeficiency virus type 1. The ability to identify specific nucleic acid sequences within the genome or as part of the pool of transcribed RNAs has proven to be an invaluable tool to all molecular biologists. Southern, Northern, and dot/slot blot procedures are currently widely used for detection of clinically relevant viral nucleic acids. The blotting-based procedures are highly sensitive, reproducible, and relatively inexpensive. In addition, Southern blotting of products of the polymerase chain reaction (PCR) is an important adjunct procedure used to increase the sensitivity of PCR and to confirm the identity of the amplified DNA.