INTRODUCTION TO NUCLEASE PROTECTION ASSAY

The Nuclease Protection Assay, also known as the RNase Protection Assay or Ribonuclease Protection Assay, is a highly sensitive and specific technique used to detect, quantify, and analyze the structure and stability of RNA molecules. This method was developed in the 1980s and has since become an essential tool for researchers in the fields of molecular biology, genetics, and biochemistry.

Principles of Nuclease Protection Assay

The Nuclease Protection Assay is based on the selective digestion of RNA molecules by specific endonucleases, such as RNase A or RNase T1. These enzymes cleave RNA at specific sites, while hybridized DNA molecules are protected from digestion due to their double-stranded nature. By comparing the protected and digested RNA fractions, researchers can determine the structure and stability of the RNA molecules.

The assay involves the following steps:

1. Transcription of a DNA template containing the RNA of interest into a hybrid RNA-DNA molecule.
2. Hybridization of the RNA-DNA molecule with a radiolabeled RNA probe complementary to the target RNA sequence.
3. Incubation with specific endonucleases to digest single-stranded RNA.
4. Separation of the protected and digested RNA fractions on a denaturing polyacrylamide gel.
5. Exposure of the gel to an X-ray film or a phosphorimager to visualize the protected RNA bands.

Applications of Nuclease Protection Assay

The Nuclease Protection Assay has several applications in molecular biology research, including:

1. Detection and quantification of specific RNA molecules.
2. Analysis of RNA structure and stability.
3. Identification of RNA processing events, such as splicing and polyadenylation.
4. Detection of RNA-RNA or RNA-protein interactions.
5. Mapping of RNA secondary structures.