Theoretical Analysis of Transport and Diffusion of Mismatch Repair
Proteins using Graphene/PPY Biosensor
1
1Departmen
2Department
Mohammed Almadhi, 1Isaac Macwan, 1,2Prabir Patra
of Biomedical Engineering, University of Bridgeport, Bridgeport CT 06604
of Mechanical Engineering, University of Bridgeport, Bridgeport CT 06604
The primary function of DNA mismatch and repair protein(MMR protein) is to eliminate
the base pair mismatches and the insertion-deletion loops that occur during DNA
replication. Mutations or defects in human MMR genes affect the MMR mechanism
causing MMR deficiency. MMR deficiency is the cause of the majority of Lynch
syndrome cases, which is also known medically as hereditary nonpolyposis colorectal
cancer (HNPCC).
A proposed biosensor device is under development that can assist in the detection of
the deficiency of MMR proteins at an early stage by using a graphene/Polypyrrole
device. This device integrate graphene with PPY because of the unique properties of
graphene in electrochemical sensing applications. These properties include excellent
conductivity and high surface area to volume ratio, which enhance the analyte capture
capability and a good interaction with nano-sized biomolecules.
This research work focuses on the simulation of the mass transfer and the diffusion of
MMR proteins in the proposed lynch syndrome biosensor. The simulation is baesd on
finite element method by using COMSOL Multiphysics. In this work, we implemented a
computational model that includes the actucal size of biosensors' geometry (2D
geometry), the immobilized mismatched DNA probes and the analyte concentration. In
the simulation environment, the transport of diluted species interface is used in order to
simulate the MMR protein transport on the sensor by diffusion and convection based on
Fick’s law of diffusion. The simulation further investigates the diffusion of analyte in case
of using single dsDNA probe and number of similar DNA probes to understand how
analyte is diffused at nanoscale in such a device from the viewpoint of optimizing the
sensors' sensitivity and speed of operation.