A Practical Tool for Selecting Reliable PCR Primers

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Bioengineers at the University of California San Diego have developed an online tool that helps biomedical researchers solve a well-known and persistent laboratory challenge: successfully measuring gene expression within a cell by way of reverse-transcription quantitative polymerase chain reaction, or RT-qPCR.

The Primer PICKR tool is a literature-mining platform designed to help scientists identify reliable primer pairs for RT–qPCR. The team introduced their platform in a paper in Nature Communications entitled “Primer PICKR: literature-mined scoring platform for robust RT-qPCR primers”.

Primer PICKR was created in the lab of UC San Diego bioengineering Professor Adam Engler. It is available for researchers to use via Creative Commons (CC BY-NC-ND 4.0). Commercial licensing is available through UC San Diego's Office of Innovation and Commercialization.

Gene Expression and Picking Primers

RT–qPCR is one of the most widely used methods for measuring gene expression within cells. Measuring gene expression is useful because it reveals how cells respond to changes in their environment, disease state, or experimental treatment. It can identify which biological pathways are activated or suppressed and help researchers understand the molecular mechanisms underlying a phenotype.

While RT-qPCR is heavily used for measuring gene expression, selecting primers that amplify the correct target efficiently remains a common source of failed experiments, inconsistent results, and grant-funded expenditures that do not yield results.

Primer PICKR addresses this problem by mining more than 7,000,000 oligonucleotide sequences from approximately 400,000 scientific papers from PubMed and ranking primer pairs using literature evidence, biophysical properties and predicted compatibility between the forward and reverse primers. The site automatically updates monthly to stay current with the latest scientific findings and now includes data from 40 species and almost 18,000 genes for humans and 15,000 genes for mice. The tool, the researchers note, is not for clinical use.

“Researchers have collectively tested an enormous number of primers, but that knowledge has remained scattered across decades of publications,” said Thomas G. Molley, a co-lead author of the study and postdoctoral researcher in bioengineering at UC San Diego. “The most common gene, GAPDH, has over 10,000 unique sequences alone across the literature. Primer PICKR now brings that information together so scientists can begin with primers that already have strong evidence behind them rather than repeatedly starting from scratch.”

In experimental testing of 154 human primer pairs, primers receiving a PICKR score above 80 achieved approximately 99% amplification success. The freely accessible Primer PICKR platform also provides citation histories, predicted off-target information and relevant primer characteristics, enabling researchers to compare and select primer pairs in seconds.

The study’s experimental validation was led by Alis Balayan, a rising third-year medical student in the Medical Scientist Training Program at UC San Diego School of Medicine who just completed her PhD in Biomedical Sciences in the UC San Diego labs of both Adam Engler and Samuel Ward. “The validation showed a clear relationship between the PICKR score and experimental performance,” said Balayan, a co-lead author on the new paper. “By reducing the number of primer pairs that researchers need to purchase and test, the platform can conserve reagents, protect limited biological samples and make RT-qPCR studies more reproducible.”

Beyond improving experimental reliability, Primer PICKR could also deliver substantial time and financial savings for research laboratories. Investigators often purchase and test multiple primer pairs before identifying one that performs adequately, consuming reagents, valuable biological samples and personnel time. By directing researchers toward primer pairs with strong literature support and favorable predicted performance, Primer PICKR can reduce trial-and-error testing, shorten experimental timelines and limit spending on unsuccessful assays — savings that may be especially valuable for laboratories working with constrained budgets or rare clinical specimens.

With the tool, researchers can make better informed decisions about which primers to use in their qPCR experiments. “Our goal was to convert published experience into a transparent and quantitative recommendation,” said Abhinaba Banerjee, a co-lead author and a bioengineering PhD candidate in the Engler lab at UC San Diego. “The score does not rely on a single feature. It combines evidence that a primer has been used successfully by other laboratories with the physical properties that influence how well the primer pair should perform.”

The site launched in May 2026, and in little more than two months, the UC San Diego bioengineers report more than 1,400 unique visitors and over 4,000 primers searched, including more than 100 searches for GAPDH.

This project is an example of how research teams at the Jacobs School with deep domain knowledge in their fields are leveraging AI tools to help make the real-world benefits of research advances more accessible to more people. In this case, the team used LLMs as a development accelerator for Primer PICKR, enabling the entire team to prototype, troubleshoot, and build the software that powers the site more quickly.

“In my lab, we are using AI tools to help lower the barrier to programming projects built around scientific ideas," said Engler. "This is a particularly interesting effort at this moment because I see the growing awareness of how much more insight can be gleaned from the existing biomedical literature. As a community, we need to find ways to extract those insights in structured and reproducible ways. I am really proud of our Primer PICKR team. We have created a powerful tool that is poised to accelerate biomedical research around the nation. At the same time, we are offering yet another example of how AI tools, used carefully by subject-matter experts, can serve as a force amplifier for deep domain expertise in the biomedical space.” Engler is the Kenneth Bowles Endowed Chair, and Professor and Chair in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

Paper: “Primer PICKR: literature-mined scoring platform for robust RT-qPCR primers” in Nature Communications

To support further development and potential commercialization of the technology, the researchers filed a U.S. provisional patent application.

Authors: Thomas G. Molley, Abhinaba Banerjee, Alis Balayan, Jun K. Robbins and Adam J. Engler from UC San Diego.

Funding support for development of this tool came from the US National Institutes of Health.