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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: Methods. 2009 Mar 6;48(4):361–367. doi: 10.1016/j.ymeth.2009.02.018

Fig. 1. Schematic depiction of the outcome of 3C analysis using divergent, convergent and tandem primer pairs.

Fig. 1

Primers are denoted by lower case letters a – j. Restrictions sites are denoted by roman numerals I – VI. DNA fragments X and Y are either juxtaposed such that crosslinking occurs between the regions depicted as red and green circles (right side) or are not juxtaposed and do not become crosslinked (left side). PCR products from tandem primer pairs a &c or b & d are definitive for juxtaposition of fragments X and Y, whereas PCR products from divergent primer pairs a & d are definitive for X–Y juxtaposition only if PCR controls, e.g., using convergent primer pairs b & j, e & i, f & h or g &c, are included to established cutting of DNA between fragments X and Y. PCR products from convergent primer pairs b & c are definitive for looping, but should be avoided because of potential to yield multiple PCR products and to deplete PCR reactions of primers and dNTP substrates.