High-affinity triplex-forming oligonucleotide target sequences in mammalian genomes.

Site-specific recognition of duplex DNA by triplex-forming oligonucleotides (TFOs) provides a promising approach to manipulate mammalian genomes. A prerequisite for successful gene targeting using this approach is that the targeted gene must contain specific, high-affinity TFO target sequences (TTS). To date, TTS have been identified and characterized in only approximately 37 human or rodent genes, limiting the application of triplex-directed gene targeting. We searched the complete human and mouse genomes using an algorithm designed to identify high-affinity TTS. The resulting data set contains 1.9 million potential TTS for each species. We found that 97.8% of known human and 95.2% of known mouse genes have at least one potential high-affinity TTS in the promoter and/or transcribed gene regions. Importantly, 86.5% of known human and 83% of the known mouse genes have at least one TTS that is unique to that gene. Thus, it is possible to target the majority of human and mouse genes with specific TFOs. We found substantially more potential TTS in the promoter sequences than in the transcribed gene sequences or intergenic sequences in both genomes. We selected 12 mouse genes and 2 human genes critical for cell signaling, proliferation, and/or carcinogenesis, identified potential TTS in each, and determined TFO binding affinities to these sites in vitro. We identified at least one high-affinity, specific TFO binding site within each of these genes. Using this information, many genes involved in mammalian cell proliferation and carcinogenesis can now be targeted.

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 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.

Effect of transport stress on respiratory disease, serum antioxidant status, and serum concentrations of lipid peroxidation biomarkers in beef cattle.

OBJECTIVE: To determine the effect of transportation stress on serum concentrations of oxidative stress biomarkers of calves. ANIMALS: 105 crossbred beef steer calves (mean [+/-SD] body weight, 207 +/- 21.2 kg). PROCEDURE: Calves were assembled at 1 location in Tennessee, and pretransit (day -3) blood samples were collected. Calves were allotted randomly by body weight into 2 groups. Calves were transported 1,930 miles to a feedlot in Texas, and 1 group received tilmicosin phosphate (33 microg/kg, s.c.) upon arrival. Calves were weighed and blood samples collected on the day of arrival (day 1) and on days 15, 22, and 28. Calves were scored daily for signs of bovine respiratory disease (BRD). Serum total antioxidant capacity (TACA) and serum malondialdehyde (MDA) concentrations were determined. RESULTS: Transportation stress significantly decreased mean serum TACA concentrations (from 147 +/- 31.2 U/mL to 133 +/- 20.1 U/mL) and significantly increased serum MDA concentrations (from 10.9 +/- 18.3 microg/mL to 30.2 +/- 50.5 microg/mL). Calves that died had a 43% increase in serum MDA concentration on day 1, compared with calves that lived (42.2 +/- 67.0 microg/mL vs 29.4 +/- 49.4 microg/mL, respectively). Calves that had > or =3 episodes of BRD had 2-fold higher serum MDA concentrations on day 1 than healthy calves. Tilmicosin-treated calves had a 20.8% significantly greater average daily gain and significantly greater serum TACA concentration than nontreated calves on day 28. CONCLUSIONS AND CLINICAL RELEVANCE: Transportation stress increases serum concentrations of oxidative stress biomarkers that are related to episodes of BRD and mortality in calves.

Exposure of mouse skin to organic peroxides: subchronic effects related to carcinogenic potential.

Screening of newly synthesized organic peroxides for tumor initiating/promoting activity would be greatly facilitated if predictive methodologies could be developed using topical exposures shorter than those required for definitive tumor assessment in mouse skin models. Nine organic peroxides [benzoyl peroxide (BZP), di-t-butyl peroxide (DTBP), t-butyl peroxybenzoate (TBPB), p-t-butyl isopropylbenzene hydroperoxide (TBIBHP), cumene hydroperoxide (CHP), dicetyl peroxydicarbonate (DPD), dicumyl peroxide (DCP), methyl ethyl ketone peroxide (MEKP) and O,O-t-butyl-O-(2-ethylhexyl) monoperoxycarbonate (TBEC)] were evaluated for their ability to increase biomarkers of tumor promotion in mouse skin, i.e. sustained epidermal hyperplasia, dermal inflammation and oxidative DNA damage. Evaluations were performed using SENCAR mice exposed topically for 4 weeks. The organic peroxides varied in their effects on these biomarkers. BZP, TBPB and TBIBHP exhibited significant increases in all three biomarkers associated with tumor promoting activity, CHP produced increases only in sustained epidermal hyperplasia and dermal inflammation, MEKP and DCP produced increases only in sustained epidermal hyperplasia and TBEC produced an increase only in dermal inflammation. DTBP and DPD had no effect on the three parameters studied. TBPB and TBIBHP were selected for further examination of their ability to produce mutations in codons 12, 13 and 61 of the c-Ha-ras protooncogene, i.e. those mutations known to be involved in the initiation of mouse skin tumors, because they were the only peroxides to exhibit significant positive results in all assays except the Ha-ras mutation following 4 weeks of exposure. Evaluations were performed using SENCAR mice dosed topically for 8 or 12 weeks in a complete carcinogenesis protocol or 16 weeks in an initiation/promotion protocol using 7,12-dimethylbenz[a]anthracene, urethane, benzo[a]pyrene and N-methyl-N'-nitro-N-nitrosoguanidine as positive controls. Neither TBPB nor TBIBHP produced detectable mutations in the c-Ha-ras protooncogene, indicating that they are not likely to possess tumor initiating or complete carcinogenic activity.