Local areas of conserved amino acid sequence in the replicase and coat proteins of potyviruses were used to select nucleotide sequences for use in the construction of sets of degenerate oligonucleotide primers for amplification of DNA fragments on potyvirus-specific templates in a combined assay of reverse transcription and the polymerase chain reaction (RT-PCR). Sequences selected for the cons...

Intervertebral disc (IVD) cells derived from degenerate tissue respond aberrantly to mechanical stimuli, potentially due to altered mechanotransduction pathways. Elucidation of the altered, or alternative, mechanotransduction pathways operating with degeneration could yield novel targets for the treatment of IVD disease. Our aim here was to investigate the involvement of RGD-recognising integri...

Amplification of multiple DNA sequences in a single Polymerase Chain Reaction (PCR) experiment, called Multiplex PCR (MPPCR), is a widely known laboratory technique that requires efficient selection of a set of synthetic strings called Degenerate Primers to result in successful PCR products. The Multiple Degenerate Primer Selection Problem (MDPSP) is a fundamental problem in molecular biology a...

The multiplex polymerase chain reaction (MP-PCR) is a quick and an inexpensive technique in molecular biology for amplifying multiple DNA loci in a single Polymerase Chain Reaction (PCR). One of the criteria to achieve highly specific reaction products is to keep the concentration of the amplification primers low. In research, the dilemma associated with primer minimization for MP-PCR reactions...

Degenerate primers or probes have been widely used in molecular cloning, but the calculation of their melting temperatures could not simply be done using thermodynamic parameters because of degeneracy and the lack of a computer program. We present here a simple computer program named dPrimer for the calculation of melting temperature of degenerate oligonucleotides based on the nearest-neighbor ...

A conformational pairing analysis was used to devise nucleobase analogs capable of forming nonselective and energetically favorable base pairs opposite either the purine or the pyrimidine constituents of nucleic acids. 5-methylisocytosine and isoguanine were conceived as a degenerate pyrimidine and a degenerate purine, respectively. Data from previous DNA duplex melting experiments verified tha...