Low copy number (LCN) DNA evidence (≤100pg) can become difficult to analyze with traditional STR analysis due to allele drop-out and increased stochastic effects. To overcome these limitations, whole genome amplification (WGA) has been investigated. Degenerate oligonucleotide-primed PCR (DOP-PCR), one form of WGA, uses a partially degenerate primer and a low annealing temperature (30oC) to gene...

Using an enhancement of the polymerase chain reaction (PCR) technique, we have isolated a complementary DNA encoding SRP14 (14-kDa subunit), one of six proteins contained in the signal recognition particle (SRP). Several pools of degenerate oligonucleotides encoding different peptide sequences of SRP14 were used to generate amplified DNA by the PCR. A cross-hybridization procedure was developed...

The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomple...

The genome of beet yellows virus (BYV), the type representative of the closterovirus group, encodes a homologue of the cellular heat-shock protein (HSP) 70 family. A pair of degenerate primers targeted to motifs A and E, which are highly conserved in HSP70s, was synthesized. Genomes of several definite and possible members of the closterovirus group were screened for the presence of the HSP70 g...

A set of universal degenerate primers which amplified, by PCR, a 600-bp oligomer encoding a portion of the 60-kDa heat shock protein (HSP60) of both Staphylococcus aureus and Staphylococcus epidermidis were developed. However, when used as a DNA probe, the 600-bp PCR product generated from S. epidermidis failed to cross-hybridize under high-stringency conditions with the genomic DNA of S. aureu...

Integrons were detected in 59 of 120 (49%) urinary isolates of Enterobacteriaceae by PCR using degenerate primers targeted to conserved regions of class 1, 2, and 3 integrase genes. PCR sequencing analysis of the cassette arrays revealed a predominance of cassettes that confer resistance to the aminoglycosides and trimethoprim.

Incorporation of synthetic degenerate oligonucleotides into plasmids for building highly diverse genetic libraries requires efficient and quantitative DNA manipulation. We present a fast and seamless method for generating libraries of PCR-synthesized plasmids designed with a degenerate sequence and short overlapping ends. Our method called QuickLib should find many applications in synthetic bio...

It is well known that in operations research‎, ‎degeneracy can cause a cycle in a network‎ ‎simplex algorithm which can be prevented by maintaining strong‎ ‎feasible bases in each pivot‎. ‎Also‎, ‎in a network consists of n arcs‎ ‎and m nodes‎, ‎not considering any new conditions on the entering‎ ‎variable‎, ‎the upper bound of consecutive degenerate pivots is equal‎ $left( ‎begin{array}{c}‎ ‎n...

To detect anoxygenic bacteria containing either type 1 or type 2 photosynthetic reaction centers in a single PCR, we designed a degenerate primer set based on the bchY gene. The new primers were validated in silico using the GenBank nucleotide database as well as by PCR on pure strains and environmental DNA.