Oligonucleotide, degenerated

Daigo Y, Chin S-F, Gorringe KL, et al. Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive Amplicon profiling of breast cancers. A new approach for the molecular analysis of paraffin-embedded cancer tissue. Am. J. Pathol. 2001 158 1623-1631. 

Stoecklein NH, Erbersdobler A, Schmidt-Kittler O, et al. SCOMP is superior to degenerated oligonucleotide primed-polymerase chain reaction for global amplification of minute amounts of DNA from microdissected archival tissue samples. Am. J. Pathol. 2002 161 43-51. 

Give the sequence of the least degenerate 20-resi-due-long oligonucleotide that hybridizes to the gene encoding this protein. 

Direct protein sequencing of the large proteins which constituted the channel was not possible both because of the very limited amount of material available and because of the not unexpected very hydrophobic nature of these membrane proteins. However short sequences from the amino terminal were obtained and these were sufficient to allow synthesis of degenerate oligonucleotide probes which were then used to probe a library of cDNA synthesized from a small quantity of mRNA extracted from the electric organ of the eel. The cDNA from the positive plasmids identified in this way was then sequenced and the primary amino acid sequence of all the subunits so obtained. 

Degenerate Oligonucleotide gene-shuffling (DOGS) easy to implement via PGR tunable levels of recombination reduced unshuffled background Gibbs, 2001... 

Aloe (Aloe arborescens) is a medicinal plant rich in aromatic polyketides such as pharmaceutically important aloenin (a hexaketide pyrone), aloesin (a heptaketide chromone), and barbaloin (an octaketide anthrone) (Fig. 4a). Pentaketide chromone synthase (PCS) and octaketide synthase (OKS) are novel plant-specific type III PKSs, which were obtained from the aloe plant by RT-PCR cloning using degenerate oligonucleotide primers based on the conserved sequences of known CHS enzymes [30-33]. The deduced amino acid sequences of PCS and OKS are 91% identical (368/403), and show 50-60% identity to those of other CHS superfamily type III PKSs of plant origin OKS shares 60% identity (240/403) with CHS from... 

Multiplex PCR of the muscular dystrophin gene was performed on-chip. The method of degenerate oligonucleotide-primed PCR (DOP-PCR) was first used to increase the number of DNA templates before multiplex PCR. Therefore, DOP-PCR can provide the template DNA from the whole human genome, but this procedure is feasible only when the amplicon size is less than 250 bp [931]. 

Cheng, J., Waters, L.C., Fortina, P., Hvichia, G., Jacobson, S.C., Ramsey, J.M., Kricka, L.J., Wilding, P., Degenerate oligonucleotide primed-polymerase chain reaction and capillary electrophoretic analysis of human DNA on microchip-based devices. Anal. Biochem. 1998, 257(2), 101-106. 

---