Engineering Smarter DNA for Sharper Detection
DNA is more than a genetic blueprint. In the right configuration, it can function as a catalytic tool for detecting disease-related molecules with high precision. This project focuses on designing and optimizing hemin-binding DNA aptamers to improve the sensitivity and specificity of biosensing platforms.
The research was presented at the Graduate Poster Exhibition during the 2025 SPARK! (Showcase of Projects, Art, Research, and Knowledge). Developed within the Ph.D. program in Computational and Integrative Biology, the project was completed by Nishat Jahan. Her work advances the development of split DNA aptamers capable of selectively binding hemin and detecting target DNA sequences through enhanced catalytic activity.
Abstract: Development and Optimization of Hemin-binding Aptamers for Biosensing
Hemin DNA aptamers can catalyze the hydrogen peroxide mediated oxidation of various chemical compounds. For instance, hemin G-quadruplexes convert Amplex Red into the fluorescent product resorufin, enabling fluorescence based detection. Due to their high catalytic efficiency, hemin binding DNA aptamers have been widely explored for biosensing applications for the detection of various targets.
In this study, we investigated a special non G-quadruplex hemin binding aptamer, Hem1, reported in the literature to enhance the peroxidase like activity of hemin. Hem1 features highly conserved repeating binding loops, cannot form a G-quadruplex, and shows selective binding for hemin. Because stacking based binding in G-quadruplex structures may lead to non specific interactions with other porphyrins and planar molecules, non G4 aptamers such as Hem1 provide greater discrimination, forming more robust hemin aptamer complexes with improved specificity.
For this study, we selected the hemin binding aptamer mutant Hem1-2T, which has a dissociation constant of 43 nM for hemin, to investigate the catalytic reaction with hydrogen peroxide using Amplex Red as the dye substrate for biosensor development. By splitting Hem1-2T into two fragments and optimizing their sequences, we aimed to develop split aptamer pairs that bind to hemin in the presence of target DNA, specifically COVID-19 DNA, with high affinity and enhanced catalytic activity toward hydrogen peroxide.
Different split aptamers were designed and evaluated under varying conditions, including pH, temperature, and magnesium ion concentrations, to improve sensitivity and specificity. Hybridization predictions were conducted using NUPACK analysis, and fluorescence spectroscopy was used for experimental characterization.
Our findings demonstrate the feasibility of using split aptamers for sensitive and selective target DNA detection, highlighting their potential for biosensing platforms with promising applications in diagnostics and molecular detection.
Graduate Poster Exhibition at SPARK!
The Graduate Poster Exhibition celebrates the research and creative work of the graduate community, showcasing everything from prose and code to original research and artistic expression. As part of SPARK! (Showcase of Projects, Art, Research, and Knowledge), a reimagining of Research Week, the exhibition highlights the depth, range, and impact of graduate scholarship and invites the campus community to engage with ideas taking shape across disciplines.
Bridging Disciplines: The Center for Computational and Integrative Biology
The Center for Computational and Integrative Biology (CCIB) at Rutgers–Camden combines experimental and computational methods to address complex biological questions. CCIB offers graduate programs leading to M.S. and Ph.D. degrees, emphasizing a holistic understanding of biological systems from molecular to population levels. The curriculum equips students like Basirat with the skills to conduct innovative research at the intersection of biology, chemistry, computer science, mathematics, and physics.
Spotlights & Stories
Want more stories like this? Spotlights and Stories highlights alumni, faculty, staff, and student experiences through stories, video, and voice. Learn more
Explore Graduate School Programs
Rutgers Graduate School-Camden offers 20+ graduate certificates, master’s, and doctoral programs across various disciplines, including biology, data science, creative writing, and psychology. We take pride in our academic diversity. Learn more
Former Students, Get Involved
Stay connected with Rutgers-Camden! Engage with former students, attend events, and support current students. Your involvement strengthens our community and helps shape future success. Learn more