title: LMPCR for detection of oligonucleotide-directed triple helix formation: a cautionary note.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Foundation, Rochester, MN 55905, USA.
authors.forename: N A
authors.initials: NA
authors.lastname: Becker
authors.forename: L J
authors.initials: LJ
authors.lastname: Maher
mesh_terms: D016475:3T3 Cells; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000096:biosynthesis* / Q000235:genetics; D018983:DNA Footprinting; D051379:Mice; D016133:Polymerase Chain Reaction / Q000379:methods*
chemical_list: C051802:triplex DNA; D004247:DNA