Abstract—Biomarkers are molecules that indicate changes in a physiological state and are detected by biosensors. Aptamer based biosensors are highly efficient, with high specificity and reusability. The present paper focuses on Molecular Dynamics (MD) modeling to simulate, analyze, and subsequently visualize the aptamer binding combination of mucin 1(MUC1) peptide, a breast cancer biomarker, and Anti-MUC1 aptamer. Analysis indicated that the peptide associated twice with this aptamer. In particular, the peptide associated with the 12th tyrosine residue of the aptamer loop after 25ns before dissociating and binding with the 3’ and 5’ ends of the aptamer. Post simulation analysis of the radius of gyration, atomic distance to the wet lab surface plasma resonance imaging (SPRi) results corroborated with the observations of the simulation results. Computational molecular dynamics simulations can provide molecular level insight for aptamer-peptide binding process, which is difficult to probe directly in wet lab experiments.

Index Terms—Biosensors, biomarkers, peptide-aptamer binding, molecular dynamics modeling.

Kristen L. Rhinehardt, Ram V. Mohan, Goundla Srinivas, and Ajit D. Kelkar are with Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC 27401, USA (e-mail: rvmohan@ncat.edu).

 

Cite:Kristen L. Rhinehardt, Ram V. Mohan, Goundla Srinivas, and Ajit D. Kelkar, "Computational Modeling of Peptide – Aptamer Binding in Biosensor Applications," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 3, no. 6, pp. 639-642, 2013.