Interactions between avidin and graphene for development of a biosensing platform

Abstract

Fundamental understanding of interactions at the interface of biological molecules, such as proteins, and nanomaterials is crucial for developing various biocompatible hybrid materials and biosensing platforms. Biosensors comprising of graphene-based conductive nanomaterials offer the advantage of higher sensitivity and reliable diagnosis mainly due to their superior specific surface area and ballistic conductivity. Furthermore, conductive nanocomposite structures that immobilize proteins can synergize the properties of both transducers and molecular recognition elements improving the performance of the biosensing device. Here we report for the first time, using a combined molecular dynamics simulations and experimental approach, the interactions between avidin and graphene for the development of a sensing platform that can be used for the detection of biological macromolecules such as mismatch repair proteins through biotinylated DNA substrates. We find that the interactive forces between avidin and graphene are mainly hydrophobic, along with some van der Waals, electrostatic and hydrogen bonding interactions. Notably, the structure and function of the avidin molecule are largely preserved after its adsorption on the graphene surface. The MD results agree well with scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS) analysis of avidin immobilized on a graphenated polypyrrole (G-PPy) conductive nanocomposite confirming the adsorption of avidin on graphene nanoplatelets as observed from the Fourier-transform infrared spectroscopy (FTIR).

Surface Characteristics Control the Attachment and Functionality of (Chimeric) Avidin

“…For graphite, concerning the individual behavior, both experimental and theoretical work are in line with our results. In ref , simulation revealed that avidin and graphene can form stable complexes primarily via hydrophobic forces and suggested conformational rearrangement near the surface. However, this work uses only one monomer of avidin, while we have utilized the biologically more relevant tetrameric form.…”

Biolayer-Interferometry-Guided Functionalization of Screen-Printed Graphene for Label-Free Electrochemical Virus Detection

“…Because both electrodes were exposed to the same concentrations of biotin, the ΔR ct signal can be assumed to be limited primarily by the amount of avidin initially attached to the surface of the electrode. 48 In particular, the smoother surface of the SP compared to the AJP electrodes allows for a more densely packed avidin layer on the SP electrodes. Moreover, the rougher surface of the AJP electrodes leads to an inhomogeneous distribution of electrochemical properties (e.g., electrochemical current density, interfacial capacitance, and solution resistance) across the surface of the electrode, which induces further deviations from an ideal electrochemical response.…”

Quantum Dot Based Fluorescent Traffic Light Nanoprobe for Specific Imaging of Avidin-Type Biotin Receptor and Differentiation of Cancer Cells

“…For AV and SA, three polypeptide loops (L3-4, L5-6, and L7-8) cover their binding pockets, among which L3-4 (connect strands β3 to β4) is regarded to play a critical role in ligand binding. This critical loop contains nine residues in AV but only six residues in SA. − Therefore, L3-4 of AV is larger and more flexible than that of SA. The lidlike loop L3-4 of AV may adopt an openable conformation, whereas L3-4 of SA has a closed conformation upon ligand binding. , …”