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UNE chemistry researcher John Stubbs receives NSF grant to study DNA interactions

August 27, 2013

John Stubbs, Ph.D., University of New England associate professor of chemistry, was recently awarded a $150,000 grant from the National Science Foundation to continue his research on DNA modeling.  

Stubbs' research project, entitled "RUI: Molecular Simulation of DNA Interactions in Oligonucleotide Microarrays," has extensive biomedical, forensic and environmental applications because it easily enables mutation detection, genetic sequencing (both having impacts on genetic disorder disease screening), species identification, and RNA expression to be carried out.

The three-year award includes support for six UNE undergraduate students to participate in the research, including the presentation of results at American Chemical Society national meetings.

Stubbs' research looks at DNA sensor microarrays, which consist of a single strand of DNA bound to a surface that ideally will only form a double helix with its complement.  This allows one to rapidly test for the presence of a given sequence of DNA in a sample for analysis.  Stubbs explains, "Our research will model these microarrays with computer simulations, which is an extremely useful approach because it provides molecular-level insight into experimental results that are otherwise difficult to interpret in a lab environment."

The results will describe how DNA interactions change when DNA is bound to a surface; this information can then be used to develop more robust DNA sensor microarrays in the future. This could improve both the sensitivity and specificity of applications and speed development of new applications in mutation detection, genetic sequencing, species identification, and RNA expression.

UNE students will be actively engaged in Stubbs' research, including analyzing the data and presenting it at national conferences and local symposia. Stubbs says, "This NSF funding enables me to build on my previous research successes while also providing important opportunities for UNE students.  From performing calculations to interpreting data and presenting results at national meetings, they will experience first-hand how innovative research is conducted, and how it can be used to benefit science and society."

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