Professor Peter Allen, one of Chai's early customers, and Tulsi Ram Damase (Professor Allen's Ph.D. student) along with their biochemistry research group at the University of Idaho, recently published a paper citing their use of Open qPCR with American Chemical Society's Combinatorial Science Journal. Professor Allen’s group is doing pioneering work within DNA nanotechnology (aptamers and designed DNA circuits) for engineering useful materials and sensors.

This paper highlights their unique work in the field: measuring the target-aptamer binding through aptamer binding curve analysis with thermofluorimetry. The use of thermofluorimetry to measure aptamer- virus binding is a wholly novel result; one that only one other group has accomplished. This process simplifies and reduces the expense and improves the efficiency of aptamer selection and characterization (e.g., relative to P-32 detection).

The article showcases the Open qPCR instrument's performance and versatility as well as its open API feature that easily enables its users to perform custom analysis. The title of the publication is "Application of the Open qPCR instrument for the in vitro selection of DNA aptamers against Epidermal Growth Factor Receptor and Drosophila C virus."

The Idaho researchers state in their ACS paper, "The unified use of a single instrument (the Open qPCR) to optimize amplification, screen candidates, and characterize binding is a unique result."

Further, they assert "The instrument is economically priced (∼$3000) and can be used to rapidly optimize a PCR reaction in place of a cycle course. It can also quantify DNA obtained after single strand generation, and screen and characterize aptamer candidates."

Article Abstract

The low-cost Open qPCR instrument can be used for different tasks in the aptamer selection process: Quantification of DNA, cycle course optimization, screening, and final binding characterization. We have selected aptamers against whole Drosophila C virus (DCV) particles and recombinant epidermal growth factor receptor (EGFR).

Aptamere selection flowchart

Flowchart highlighting the use of Open qPCR in the Aptamer selection process

We performed systematic evolution of ligands by exponential Enrichment (SELEX) using the Open qPCR to optimize each amplification step. The Open qPCR instrument identified the best aptamer candidate. The Open qPCR can perform melt curves, and we used this function to perform thermofluorimetric analysis (TFA) to quantify target-aptamer binding. We confirmed target-aptamer binding using flow cytometry. A sandwich type luminescence bioassay based on our anti-DCV aptamer was sensitive to DCV and did not respond to a related virus, demonstrating that our selected anti-DCV aptamer can be used to specifically detect DCV. If you’re an ACS member you can read the entire article here.

"When I first moved to the University of Idaho, even though there was a Real-time PCR instrument in a user facility on campus, I preferred having one in our lab. I find that my students and I procrastinate when we need to schedule a time and walk to another building to perform an experiment. I wanted a new machine that could perform DNA quantification, cycle course optimization and melt curve analysis and data that could be exported easily for our custom analyses.

I started looking at low-cost new and used qPCRs from commonly known brands (our budget was rather limited). But none of these instruments were attractive to us because either they were too expensive or didn’t have the features or software that supported advanced capabilities needed for our work.

As evident from our ACS paper, I am glad that we acquired Chai’s Open qPCR. Because not only it is 90% cheaper than ones from mainstream brands, but also it produces reliable and accurate results and has allowed us to reduce the time needed to complete a project drastically."

-- Professor Peter Allen, University of Idaho, Chemistry department

Read more on ResearchGate