Quantitative Ratio of Primer Pairs and Annealing Temperature Affecting PCR Products in Duplex Amplification

Quantitative ratio of primer pairs and annealing temperature affecting PCR products in duplex amplification.

The quantity of PCR products that are simultaneously amplified from two different loci in a duplex amplification (DA) are significantly lower for one of the loci, as compared to identical PCR amplification in separate single-band amplifications (SBA). This difference in amplification probably occurs already after the second cycle of amplification. To further analyze this phenomenon, we tested d...

Annealing control primer system for improving specificity of PCR amplification.

A novel primer designed to improve the specificity of PCR amplification, called the annealing control primer (ACP), comprises a tripartite structure with a polydeoxyinosine [poly(dI)] linker between the 3' end target core sequence and the 5' end nontarget universal sequence. We show that this ACP linker prevents annealing of the 5' end nontarget sequence to the template and facilitates primer h...

Analysis of primer-derived, nonspecific amplification products in RAPD-PCR.

Recently, we applied the randomamplified polymorphic DNA polymerase chain reaction (RAPD-PCR) (17), also known as arbitrarily primed PCR (AP-PCR) (16), procedure to fingerprint genomes of various varieties and wild relatives of sugarcane (Saccharum spp.) (4). Unlike restriction fragment length polymorphism (RFLP) (2), RAPD-PCR is a simpler, faster, less laborious and less expensive procedure. H...

Optimal ratio of degenerate primer pairs improves specificity and sensitivity of PCR.

PCRTiler: automated design of tiled and specific PCR primer pairs

Efficiency and specificity of PCR amplification is dependent on several parameters, such as amplicon length, as well as hybridization specificity and melting temperature of primer oligonucleotides. Primer design is thus of critical importance for the success of PCR experiments, but can be a time-consuming and repetitive task, for example when large genomic regions are to be scanned for the pres...