LMPCR for detection of oligonucleotide-directed triple helix formation: a cautionary note.

We note that precautions are necessary when ligation-mediated PCR (LMPCR) is applied to the detection of oligonucleotide-directed triple helix formation in vitro and in vivo. Synthetic oligonucleotides applied to cell cultures can persist after chemical treatment and genomic DNA isolation and inhibit a key step in LMPCR, causing an artifact that simulates a triplex footprint. Residual oligonucleotides apparently form triplexes during LMPCR, blocking ligation of the unidirectional linker in a site-specific manner. We show that careful removal of residual oligonucleotide prior to LMPCR alleviates this problem.