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

We note that precautions are necessary when ligation-mediated PCR (LMPCR) i s applied to the detection of oligonucleotide-directed triple helix formati on in vitro and in vivo. Synthetic oligonucleotides applied to cell culture s can persist after chemical treatment and genomic DNA isolation and inhibi t a key step in LMPCR, causing an artifact that simulates a tripler footpri nt. Residual oligonucleotides apparently form triplexes during LMPCR, block ing ligation of the unidirectional linker in a site-specific manner. We sho w that careful removal of residual oligonucleotide prior to LMPCR alleviate s this problem.