Chromosome conformation capture primer design

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 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 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/.