Biotechnology and Bioinformatics (1+1)

2.1.5.2. Probes

A probe is a piece of DNA or RNA used to detect specific nucleic acid sequence s by hybridization (binding of two nucleic acid chains by base pairing). They are radioactively labeled so that the hybridized nucleic acid can be identified by autoradiography . The size of probes ranges from a few nucleotide s to hundreds of kilobases. Long probes are usually made by cloning .

Originally they may be double-stranded, but the working probes must be single-stranded. Short probes ( oligonucleotide probes) can be made by chemical synthesis. They are single-stranded.

Suppose we have cloned a specific gene in yeast and want to find its homologous gene in human, then we may use the specific yeast gene as a probe to detect its homologous gene from the human genomic library.

On the other hand, if we know the conserved sequence in the specific gene between yeast and human, we may use oligonucleotide probes containing only the conserved sequence. Typically, an oligonucleotide about 20 nucleotides long is sufficient to screen a library.

In some cases, we have known the partial sequence of a protein and want to detect its gene in the library. Then we may synthesize oligonucleotide probes based on the known peptide sequence. Since an amino acid may be encoded by several DNA triplets, many different oligonucleotide probes are often needed.