Ottawa Scientists Create (free) Program that Automates Primer Design

Bruno Fonseca, PhD scientist at the Children’s Hospital of Eastern Ontario Research Institute and Riu Liu, PhD scientist at the University of Southampton (United Kingdom) collaborated over the past four years to develop a software tool that automates the design of primers for site-directed mutagenesis. Their new software program is called PrimerGenesis.

“We’ve automated a Nobel-prize winning research technique,” says Bruno Fonseca, co-creator of the software. “Genome sequencing yields vast amounts of data on disease-causing mutations in DNA. Investigating each mutation by a common practice called site-directed mutagenesis is a laborious and time-consuming task. There’s an appetite for automating this task in the field of molecular biology research, so it’s been rewarding to develop this software.”

Generating mutations in a gene typically requires a researcher to manually design a small strip of DNA called “primer”. Instead of counting individual nucleotides within a strip of DNA, this time-consuming task can be completed computationally in a matter of seconds by using this new software program.

“We’ve aimed to make it as user-friendly as possible,” said Rui Liu, co-creator of PrimerGenesis. “The software is extremely versatile and can be widely applied; yes, it can be used to generate mutations but it can also be used to introduce specific tags upstream or downstream of a gene.”

PrimerGenesis is free and available globally without registration or download requirements at: http://primergenesis.com or https://twitter.com/primergenesis

Thanks to CHEO for contributing this story.

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Precision Blue dye facilitates precise pipetting and accurate reaction tracking in multiwell microplates during qPCR setup

Bio-Rad Laboratories, announced the launch of its Precision Blue real-time PCR dye, making it easier for researchers to set up real-time PCR (qPCR) experiments.

The blue dye improves the visibility of qPCR reaction mixtures, enabling loading of small volume reactions with greater speed, accuracy, and precision. Applications such as single nucleotide polymorphism (SNP) genotyping and high-throughput gene expression analysis using 384-well plates will particularly benefit from use of this dye.

Precision Blue dye is compatible with Bio-Rad’s universal qPCR supermixes (iTaq™ universal and SsoAdvanced™ universal supermixes) and does not interfere with SYBR® Green- or probe-based detection. The dye can be used with all Bio-Rad CFX real-time PCR systems and all other vendors’ real-time PCR systems.

For convenience, Precision Blue can be added directly to the supermix or used as a component of a reaction master mix. The dye is concentrated 200x, and delivers 500 x 20 µl reactions.

For more information about Precision Blue dye, please visit www.bio-rad.com/PrecisionBlue.

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Summer Student Tutorial: How to Avoid a Leaky Gel

This week’s summer student tutorial is something that we have all experienced in the past. Leaky gels. While the best solution is probably to purchase a new pad, for the more resourceful scientists out there, here is a tip for you.

The video is courtesy of LabTricks which has no affiliation to Bio-Rad Laboratories.