What are they and how do they work?

I have looked online and only found journals and reviews which assume the reader already knowns about SSOP's and how they work. I am trying to find a simple explanation of what they are and how they function.

If you could point me in the right direction, I would greatly appreciate it.

Hi Jon,

From the Wikipedia page on oligonucleotides, this information may help:

Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary oligonucleotides, DNA, or RNA to form duplexes.

This basic property serves as a foundation for the use of oligonucleotides as probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarrays & Southern blots.

I hope this explains how strands of DNA or RNA can be used to bind and thus detect (probe) other such strands in a sample via a sequence specific manner.

Nick

To add, another popular use of sequence-specific oligos is PCR (either end-point or 'quantitative' as in qPCR). We often use various oligonucleotide-design programs and DNA databases to check oligo specificity for a single gene product; i.e., using these programs you can usually determine whether your oligo has the potential to 'cross-react' with genes other than the one you are interested in. This is aided by the fact that the sequencing of some genomes (e.g., human) has essentially been completed. We use the word 'stringency' to describe the conditions under which the oligo will bind to a specific DNA (or RNA) strand - a sequence-specific oligo can often be used at 'high stringency' (typically low salt concentration and/or high temperature used in your experiment) so that cross-reaction can be minimised, although on occasion you may want to detect a sequence that is common to a family of genes.