Applications of RNA Probes

In Northern blotting, the RNA under study is fractionated by gel electrophoresis. The molecules are then transferred to a membrane that is incubated with the labeled probe(s). Hybridization of complementary sequences allows visualization of target RNA sequences. (1)

RNase protection assays, like Northern blots, depend on the hybridization of probes to target RNAs. In RPA, however, the hybridization takes place in solution. Probes are designed to have non-hybridizing regions. Controlled RNase digestion of the hybrids followed by separation and detection of the remaining probes allows for quantitative analysis of the target RNA in a sample and can provide information on target RNA structure.

In situ hybridization experiments allow for the localization of RNA or DNA targets in cells and tissues. This technique uses cultured cells or tissue sections as the substrates for hybridization and detection. Cells or tissues are processed so that their endogenous nucleic acids are fixed in place, but available for hybridization to and detection by labeled probes.

Southern blotting involves the fractionation and transfer of DNA to membranes. Membranes are then are incubated with the labeled probe(s). Hybridization of complementary sequences allows visualization of target DNA sequences. (2)

1. Rio, D. C., et al. RNA: A Laboratory Manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 2011, 77-87.
2. Cooper, Geoffery M. The Cell: A Molecular Approach. 4th ed. Washington D.C.: ASM Press 2007. 131-2.