The success of the polymerase chain reaction (PCR) is highly dependent on primer design. Commonly used primer design programs rely upon a core set of parameters such as melting temperature, primer length, GC content, and complementarity to optimize the PCR product, but weight those parameters to differing degrees, as well as include other parameters for PCR specific tasks. An analysis of these ...

We have developed a locus-specific DNA target preparation method for highly multiplexed single nucleotide polymorphism (SNP) genotyping called MARA (Multiplexed Anchored Runoff Amplification). The approach uses a single primer per SNP in conjunction with restriction enzyme digested, adapter-ligated human genomic DNA. Each primer is composed of common sequence at the 5' end followed by locus-spe...

Three touchdown enzyme time release (TETR)-PCR assays were used to amplify different DNA sequences in the variable regions of the 16S and 16S-23S spacer rRNA genes specific for Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci as improved tests for sensitive diagnosis and rapid species differentiation. The TETR-PCR protocol used 60 cycles of amplification, which provided impro...

Certain species of Penicillium have been reported to produce the mycotoxin patulin, and research was undertaken to identify these with the use of oligonucleotide primer pairs. Species examined were found in food, plants, and soil and were reported to produce patulin. Penicillium expansum is the most commonly detected species linked to the presence of patulin in apple juice. At least 10 differen...

Mycoplasma gallinarum colonizes poultry as well as mammals, but is considered to have a commensal relationship with its hosts. Though unable to cause poultry disease by its self, reports have been published suggesting a synergism during mixed infections between M. gallinarum and respiratory viruses or their vaccine strains that can precipitate airsacculitis. Currently, little research is being ...

The occurrence of Actinobacteria in water-damaged building materials as well as the clinical relevance of some Actinobacteria (e.g. Saccharopolyspora spp., Mycobacterium spp., Nocardia spp., etc.), led us to develop a detection system to examine the actinobacterial community. A new primer system, Com2xf/Ac1186r (16S rRNA gene based) specific for Actinobacteria was designed. The adequacy for the...

Retroviruses and long terminal repeat-containing retroelements use host-encoded tRNAs as primers for the synthesis of minus strong-stop DNA, the first intermediate in reverse transcription of the retroelement RNA. Usually, one or more specific tRNAs, including the primer, are selected and packaged within the virion. The reverse transcriptase (RT) interacts with the primer tRNA and initiates DNA...

The evaluation of specific endogenous transcript levels is important for understanding transcriptional regulation. More specifically, it is useful for independent confirmation of results obtained by the use of microarray analysis or RNA-seq and for evaluating RNA interference (RNAi)-mediated gene knockdown. Designing specific and effective primers for high-quality, moderate-throughput evaluatio...