3PD: Rapid design of optimal primers for chromosome conformation capture assays

BACKGROUND: Higher eukaryotes control the expression of their genes by mechanisms that we are just beginning to understand. A complex layer of control is the dynamic spatial organization of the nucleus. RESULTS: We present a bioinformatics solution (3PD) to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays. 3C assays take a snapshot of chromosomal contacts by a fixation step and quantify them by PCR. Our contribution is to rapidly design an optimal primer set for the crucial PCR step. Our primer design reduces the level of experimental error as primers are highly similar in terms of physical properties and amplicon length. All 3C primers are compatible with multiplex PCR reactions. Primer uniqueness is checked genome-wide with a suitable index structure. CONCLUSIONS: In summary, our software 3PD facilitates genome-wide primer design for 3C experiments in a matter of seconds. Our software is available as a web server at: http://www.pristionchus.org/3CPrimerDesign/.