Electronic hybridization detection in microarray format and DNA genotyping

Abstract

We describe an approach to substituting a fluorescence microarray with a surface made of an arrangement of electrolyte-gated field effect transistors. This was achieved using a dedicated blocking of non-specific interactions and comparing threshold voltage shifts of transistors exhibiting probe molecules of different base sequence. We apply the approach to detection of the 35delG mutation, which is related to non-syndromic deafness and is one of the most frequent mutations in humans. The process involves barcode sequences that are generated by Tas-PCR, a newly developed replication reaction using polymerase blocking. The barcodes are recognized by hybridization to surface attached probes and are directly detected by the semiconductor device.

DNA Hybridization Measured with Graphene Transistor Arrays

“…The surface in contact with the electrolyte is SiO 2 , as for the silicon arrays used in previous electronic measurements of DNA hybridization. [3,4,31] Moreover, the salt compositions of the electrolyte solutions used herein are similar to studies with silicon arrays. As expected, the signs of the threshold voltage shifts observed (upon PLL adsorption, DNA adsorption, and DNA hybridization) coincide with the ones described for silicon devices.…”

“…In addition, the amplitudes of the electronic signals of DNA hybridization are about 100 mV for our GFET arrays, strongly exceeding the typical 3-10 mV amplitudes of silicon FET arrays (see refs. [3,4,31]). The combination of small drift and high signal amplitude greatly facilitates real-time DNA hybridization detection when compared to silicon devices, as illustrated in Figure 6.…”

“…Indeed, efficient blocking is required for DNA detection in the microarray format. Following earlier work, [3] we combined a chemical and physical blocking procedure: the chip is first incubated in acetic anhydride and subsequently in a solution containing 21-mer oligonucleotides (Lprime). Lprime sequence differs in sequence to other molecules under study to avoid cross-hybridization.…”

“…For instance, a DNA molecule immobilized on an electrolyte-gated FET surface in contact with an aqueous electrolyte solution, can be detected by the electric field associated with the intrinsic charge of the molecule. Field-effect sensing of biomolecules has been achieved with planar silicon devices, [3][4][5] silicon nanowire FETs, [6][7][8][9][10][11] carbon nanotubes, [12,13] and graphene structures. [14,15] Among these materials, graphene is particularly promising for biosensing applications, [16][17][18] because it combines high room-temperature mobility of charge carriers, the possibility of a short (nanometer scale) distance between the graphene monolayer and the molecules to be detected, and the possibility of fabricating transistor arrays with surface areas of tens of square millimeters at moderate cost.…”

Novel Signal-Enhancing Approaches for Optical Detection of Nucleic Acids—Going beyond Target Amplification

“…As these fluorescent ultra-bright probes for PCR-independent nucleic acid detection develop, they might benefit from new chemical substances, nanotechnology and straightforward biotechnological approaches to enhance the signal [68][69][70]. Among other methods, fluorescence microscopy and SPR are two very promising techniques with a high potential for future biomolecular science and diagnostics.…”