Primer positions for 3C and 5C. (A) Primers used for PCR detection of 3C ligation product are designed so that they anneal to the same strand of genomic DNA and are able to prime amplification of a head-to-head 3C ligation product. (B) Primers used for 5C detection are designed so that they anneal to the opposite strands of genomic DNA and are able to detect a head-to-head 3C ligation product. Arrowheads on primers indicate the 3′ ends. The nonannealing gray sections of the 5C primers represent the universal tails (see the main text). Forward primers have a 5′ universal tail, whereas reverse primers carry a universal tail at their 3′ ends.