Graphene field-effect transistor biosensors (GFETs) offer a promising platform to detect cancer DNA biomarkers at low concentration [1]. At their core, they have an electronic circuit containing a graphene sheet – a two-dimensional nanomaterial made of a single layer of carbon atoms – whose electronic properties are very sensitive to nearby electric charges. Leveraging that feature, the electrical current generated by a GFET can thus be made very sensitive to the concentration of a specific DNA sequence in a biological sample. To achieve this, the complementary DNA sequence is linked to the graphene to bind specifically the target DNA. In most GFETs, the link is done using 1-pyrenebutanoic acid succinimidyl ester (PBASE) because its pyrene group stacks on the graphene through pi-pi interactions, without disrupting the electronic properties of the graphene. However, recent experiments in the Bouilly group have shown variations in GFET sensitivity depending on the incubation time of graphene with PBASE.Here, we use a computational approach developed in our previous work [2] to investigate at the nanoscale the role of PBASE linker molecules on the sensitivity of the GFET. First, we use molecular dynamics simulations to characterize the conformational ensemble of a 10-nt single-stranded DNA sequence linked to a graphene sheet using PBASE. Second, we estimate the electrical response of the GFET from the electrostatic potential generated by these DNA conformations on the graphene, as determined using electrostatic Poisson-Boltzmann simulations. Our results show that the conformational ensemble of DNA is strongly affected by the presence of other PBASE adsorbed on the graphene, thus changing the electrostatic potential generated on the graphene. The predicted change of the electrostatic potential should impact measurably the detection signal of the GFET.We are now using these simulations to explain the experimental characterizations of a GFET designed to detect a genetic biomarker important in breast cancer profiling. Our simulations have the potential to support the development of GFETs with better sensitivity for DNA detection.[1] Béraud, A., Sauvage, M., Bazán, C. M., Tie, M., Bencherif, A., and Bouilly, D. (2021) Graphene field-effect transistors as bioanalytical sensors: design, operation and performance. Analyst. 146:403-428.[2] Côté, S., Mousseau, N., and Bouilly, D. (2022) The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations. Phys. Chem. Chem. Phys. 24:4174-4186.
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