What is an oligo- or oligonucleotide?
The term “oligonucleotide” or “oligo” usually refers to a synthetic laboratory-made DNA or RNA strand. Oligonucleotides are used in biochemistry, biology, molecular diagnostics, genomics, and other molecular biology experiments. Almost all applications using oligos involve synthesizing the complementary strand of a targeted, naturally occurring, strand of nucleic acid sequence.
In a hybridization experiment, the synthesized oligo will bind to the targeted sequence according to classic Watson-Crick base-pairing rules to form a double stranded nucleic acid molecule. The oligo base sequence is fully determined by the targeted sequence moiety of the duplex.
Since the length of an oligonucleotide is directly proportional to its synthesis cost, and inversely proportional to its efficacy, or the ability of the oligo to produce a desired or intended result, the desired oligo length is usually only a fraction of the targeted sequence’s length. Therefore, when designing primers or oligos selected as candidates for oligo binding regions, many subsequences will need to be considered. Determining the most effective oligo candidate can involve many metrics that can be calculated multiple ways. A good knowledge of oligo design principles definitely helps to achieve a good experimental design.
Experiments using oligonucleotides are usually divided into two types:
“Primers”; when oligos are used to start a chain reaction on the target, or
“Probes”; when oligos are used to bind and hold the target.
Applications that need a primer require a Polymerase Chain Reaction (PCR) product, such as DNA sequencing, end point PCR, and cDNA microarrays. Applications using a probe include Northern and Southern blotting, antisense gene expression inhibition and oligonucleotide microarrays.
There are multiple software tools available on the World Wide Web that offer help with the optimization and design of primers and probes.
Design of primers plus how to dilute them: http://www.biosyn.com/tew/primer-design-and-dilution.aspx
BNA Probes and Design: http://www.biosyn.com/bna-qpcr-snp-probes.aspx
Primer search NIH NCBI: http://www.ncbi.nlm.nih.gov/tools/primer-blast/