We investigate the problem of designing efficient multiplex PCR for medical applications. We show that the problem is NP-complete by transformation to the Multiple Choice Matching problem and give an efficient approximation algorithm. We developed this algorithm in a computer program that predicts which genomic regions may be simultaneously amplified by PCR. Practical use of the software shows ...

The incorporation of locked nucleic acids (LNAs) into oligonucleotide primers has been shown to increase template binding strength and specificity for DNA amplification. Real-time PCR and DNA sequencing have been shown to be significantly enhanced by the use of LNAs. Theoretically, increasing primers' binding strength may also increase the sensitivity of conventional PCR, reducing minimum templ...

The PCR-amplification of unknown homologous or paralogous genes generally relies on PCR primers predicted from multi sequence alignments. But increasing sequence divergence can induce the need to use degenerate primers which entails the problem of testing the characteristics, unwanted interactions and potential mispriming of degenerate primers. Here I introduce easyPAC, a new software for the p...

Each year, large volumes of ornamental and food plant propagative stock are imported into the North America; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 107 new R. solanacearum strains were collected over a 10-year period from imported propagative stock and compared with 32 previously characterized R. solanacearum strains using repeti...

Most short interspersed elements (SINEs) in eukaryotic genomes originate from tRNA and have internal promoters for RNA polymerase III. The promoter contains two boxes (A and B) spaced by approximately 33 bp. We used oligonucleotide primers specific to these boxes to detect SINEs in the genomic DNA by polymerase chain reaction (PCR). Appropriate DNA fragments were revealed by PCR in 30 out of 35...

BACKGROUND Distinguishing desired mutants from parental templates and undesired mutants is a problem not well solved in Quikchange™ mutagenesis. Although Dpn I digestion can eliminate methylated parental (WT) DNA, the efficiency is not satisfying due to the existence of hemi-methylated DNA in the PCR products, which is resistant to Dpn I. The present study designed a novel critical annealing te...

forty monoconidial isolates of magnaporthe grisea were examined, for an identification of vegetative compatibility group and a characterization of genetic diversity, using rep-pcr genomic fingerprinting. the isolates were collected from weeds digitaria sanguinalis (crabgrass), setaria italica (foxtail millet), echinochloa crus-galli (barnyard millet), and some other unknown ones during 2003 - 2...

We have evaluated a new set of primers (TRC(4)) in comparison with the IS6110 primers commonly used in PCR to detect tuberculous meningitis among children. The levels of concordance between the results of IS6110 PCR and TRC(4) PCR with cerebrospinal fluid specimens from patients with clinically confirmed tuberculous meningitis were 80 and 86%, respectively. Results with the two primer sets were...

1 Biological scientists often need to design primers. These are short pieces of DNA used for copying sections of a DNA sequence using the polymerase chain reaction (PCR). Primers have various properties that influence the likelihood of success and scientists wish to quickly and easily select the best primers for amplification of a target sequence. Current web-based primer design software (Prime...