Adeno-associated viral (AAV) vectors show great promise for gene therapy because of their excellent safety profile; however, development of robust dose-determining assays for AAV has presented a significant challenge. With the ultimate goal of future harmonization and standardization of AAV dose determination assays, we systematically analyzed the influence of key variables, including sample pr...

Design of primers for efficient DNA amplification using polymerase chain reaction is critical. Therefore, evaluation of hairpin structures while designing position dependent primers needs special attention. Here, we present the data on the effect of hairpins on DNA amplification using polymerase chain reaction. X-antigen of Hepatitis B Virus has been used as a model. Studies showed that hairpin...

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...

MOTIVATION DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in ...

Several primer prediction and analysis programs have been developed for diverse applications. However, none of these existing programs can be directly used for the design of primers in protein interaction experiments, since proteins may have transmembrane domains (TMDs) and/or a signal peptide that must be excluded from experiments. Furthermore, it is frequently the case that a short restrictio...

Reproducible and target-specific polymerase chain reaction (PCR) amplification relies on several interrelated factors of which primer design is central. Here, we describe new free bioinformatics software, the FastPCR which was developed, and continues to be updated, based on detailed experimental studies of PCR efficiency for the optimal design of primers and probe sequences and for repeat sear...