We have developed a new primer design method based on the QuickChange site-directed mutagenesis protocol, which significantly improves the PCR amplification efficiency. This design method minimizes primer dimerization and ensures the priority of primer-template annealing over primer self-pairing during the PCR. Several different multiple mutations (up to 7 bases) were successfully performed wit...

PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as fo...

MOTIVATION The optimization of the primer design is critical for the development of high-throughput SNP genotyping methods. Recently developed statistical models of the SNP-IT primer extension genotyping reaction allow further improvement of primer quality for the assay. RESULTS Here we describe how the statistical models can be used to improve primer design for the assay. We also show how to...

We have developed a new package of computer programs and algorithms for different PCR applications, including allele-specific PCR, multiplex PCR, and long PCR. The package is included in the upcoming VectorNTI suite software and attempts to incorporate most of the current knowledge about PCR primer design. A wide range of primer characteristics is available for user manipulation to provide impr...

To study functional diversity of proteins encoded from a single gene, it is important to distinguish the expression levels among the alternatively spliced variants. A variant-specific primer pair is required to amplify each alternatively spliced variant individually. For this purpose, we developed a new feature, homolog-specific primer design (HSPD), in our high-throughput primer and probe desi...

An essential pre-requisite to perform sound quantitative real-time polymerase chain reaction (qPCR) assays is to design outstanding primer pairs. This means they must have a good efficiency and be not prone to produce multiple amplicons or primer dimer products. To circumvent these issues, several softwares are available to help primer design. Although satisfactory computer-aided primer design ...

This service integrates primer designing code from the popular Primer3 1 software with a specificity check that uses a custom BLAST search. Primer-BLAST eliminates the need to design primers at another site and then perform a search with those primers using the main NCBI BLAST service to check specificity. Moreover, Primer-BLAST can design primers that amplify only a particular splice variant o...

Klebsiella granulomatis is gram-negative bacteria of the genus Klebsiella which causes sexually transmitted disease (STD) Donovanosis and urinary tract infection in older persons. In the present work, in silico approach for primer designing has been implemented; to gather more information about the bacterium. Primer plays an important role to initiate the process of Polymerase Chain Reaction (P...