title: A web-based search engine for triplex-forming oligonucleotide target sequences.
abstract: Triplex technology offers a useful approach for site-specific modification of gene structure and function both in vitro and in vivo. Triplex-forming oligonucleotides (TFOs) bind to their target sites in duplex DNA, thereby forming triple-helical DNA structures via Hoogsteen hydrogen bonding. TFO binding has been demonstrated to site-specifically inhibit gene expression, enhance homologous recombination, induce mutation, inhibit protein binding, and direct DNA damage, thus providing a tool for gene-specific manipulation of DNA. We have developed a flexible web-based search engine to find and annotate TFO target sequences within the human and mouse genomes. Descriptive information about each site, including sequence context and gene region (intron, exon, or promoter), is provided. The engine assists the user in finding highly specific TFO target sequences by eliminating or flagging known repeat sequences and flagging overlapping genes. A convenient way to check for the uniqueness of a potential TFO binding site is provided via NCBI BLAST. The search engine may be accessed at spi.mdanderson.org/tfo.
authors.affiliation: Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, TX 78957, USA.
authors.forename: Sara S
authors.initials: SS
authors.lastname: Gaddis
authors.forename: Qi
authors.initials: Q
authors.lastname: Wu
authors.forename: Howard D
authors.initials: HD
authors.lastname: Thames
authors.forename: John
authors.initials: J
authors.lastname: DiGiovanni
authors.forename: Earl F
authors.initials: EF
authors.lastname: Walborg
authors.forename: Michael C
authors.initials: MC
authors.lastname: MacLeod
authors.forename: Karen M
authors.initials: KM
authors.lastname: Vasquez
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D018390:Gene Targeting; D016678:Genome / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D020407:Internet; D051379:Mice; D009841:Oligonucleotides / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA