title: Overcoming a barrier for DNA polymerization in triplex-forming sequences.
abstract: Folded structures in the DNA template, such as hairpins and multi-stranded structures, often serve as pause and arrest sites for DNA polymerases. DNA polymerization is particularly difficult on mirror-repeated homopurine.homopyrimidine templates where triple-stranded (triplex) structures may form between the nascent and folded template strands. In order to use a linear PCR amplification approach for the structural analysis of DNA in mirror-repeated sequences we modified a conventional protocol. The barrier for DNA synthesis can be eliminated using an oligonucleotide that hybridizes with the template to prevent its folding and is subsequently displaced by the progressing polymerase. The described approach is potentially useful for sequencing and analysis of chemical adducts and point mutations in a variety of sequences prone to the formation of folded structures, such as long hairpins and quadruplexes.
authors.affiliation: Institute of Biosciences and Technology, The Texas A&M University System Health Science Center, 2121 West Holcombe Boulevard, Houston, TX 77030, USA. vpotaman@ibt.tamu.edu
authors.forename: V N
authors.initials: VN
authors.lastname: Potaman
authors.forename: J J
authors.initials: JJ
authors.lastname: Bissler
mesh_terms: D000818:Animals; D001704:Biopolymers; D002417:Cattle; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000378:metabolism; D010957:Plasmids; D016133:Polymerase Chain Reaction / Q000379:methods*; D013698:Templates, Genetic
chemical_list: D001704:Biopolymers; D009841:Oligonucleotides; D004247:DNA; D004259:DNA-Directed DNA Polymerase