A web-based search engine for triplex-forming oligonucleotide target sequences

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 bin...

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Bibliographic Details
Published inOligonucleotides Vol. 16; no. 2; p. 196
Main Authors Gaddis, Sara S, Wu, Qi, Thames, Howard D, DiGiovanni, John, Walborg, Earl F, MacLeod, Michael C, Vasquez, Karen M
Format Journal Article
LanguageEnglish
Published United States Mary Ann Liebert, Inc 01.01.2006
Subjects
Animals
Base Sequence
Binding sites
Databases, Genetic
Deoxyribonucleic acid
DNA
DNA - chemistry
Gene expression
Gene Targeting
Genetics
Genome - genetics
Genome, Human - genetics
Humans
Internet
Mice
Mutation
Oligonucleotides - chemistry
Search engines
Sequence Analysis, DNA - methods
Software
Websites
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Summary: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.
ISSN:1545-4576
2159-3337
2159-3345
DOI:10.1089/oli.2006.16.196