Nano-electrodes for ultrafast DNA/protein sequencing : Ab-initio quantum transport studies

Abstract

Recent advances in DNA/protein sequencing have paved their way in personalized medicine, which is the Next Frontier in our health care as it can be used to detect predisposition concerning several genetic illnesses and deliver proper treatments. To fully accomplish this, enhanced control and cost of the procedure are further needed to be improved. Modern DNA/protein sequencing techniques based on nanoscience and nanotechnology methods now concentrate on single-molecule resolution, amplification or label-free, and long read length sequencing. For this, several methods and techniques have recently been proposed to sequence nucleobases/amino acids using the unique properties of solid-state membrane nanomaterials. It includes sequencing of DNA/protein with solid-state nanopores, nanogaps, and nanochannels. Such solid-state nanomaterials based nanopores, nanogaps, and nanochannels devices, through which single-strand DNA and protein can be translocated, were identified as a possible technique of providing inexpensive and accurate human whole-genome sequencing by determining either ion-current as DNA/protein passes through the nanopore or by electronic transverse conductance and tunneling currents across the nanogap itself. Furthermore, it would also be useful to develop a nanochannel-based device that could hold each nucleobase/amino acid firmly while the nucleobase is being identified through current modulation sequencing. The field of two-dimensional (2D) and one-dimensional (1D) solid-state nanomaterials provides an entirely new avenue for studying DNA and protein sequencing techniques. Atomically thin 2D and 1D nanomaterials, with huge surface-to-volume-ratio, these materials are very attractive for biomolecule detection applications. Therefore, the theoretical prediction from atomically resolved computation modeling and simulations of 2D and 1D nanomaterials plays a vital role in nano-electrode designing and advancing DNA/protein sequencing techniques. The present thesis work describes several techniques employed to achieve single-molecule resolution for controlled and rapid sequencing of DNA and protein molecules. Part I includes the introduction, and a brief description of theoretical methods (DFT and NEGF formalism) and other computational approaches used in the numerical simulations are given in Chapter 1. We review the quantum transport phenomenon in nanoscale devices, which will help as the theoretical background of our studies. The basic Landauer and NEGF formalism are discussed. Part II includes the results and discussion of the nanoscale device application of 2D and 1D nanomaterials in Chapters 2-5. The ab-initio quantum transport and ionic current studies are discussed in Chapters 2-5 to investigate the electric readouts of DNA nucleotides and amino acids by using various solid-state nanomaterial-based nano-electrodes. In chapter 2, we have presented defected graphene nanogap and nanochannel-based DNA sequencing devices for the detection of DNA molecules. Transverse conductance and tunneling current-voltage characteristics have been used to detect each of the four DNA molecules. In Chapter 3, we have discussed the electric current patterns of all the four target nucleotides while placed inside the black phosphorene-based nanogap device. We have demonstrated that DNA sequencing is feasible to identify all four DNA nucleotides individually. In Chapter 4, we have demonstrated the most advanced and useful technique based on the measurements of ionic current signals when a ssDNA is translocated through a series of graphene nanogap-based devices. The ssDNA sequence is then decoded by the distinctive changes of ionic current such as magnitude and recorded ionic current time. Using different electric fields, we have shown that single nucleotide-specific identification is in principle possible when all the four ssDNA nucleotides [(dAMP)16, (dGMP)16, (dTMP)16, and (dCMP)16] translocate through the different nanogap sizes (i.e., 1.4 and 2.0 nm). In Chapter 5, we have investigated the newly synthesized 2D hydrogen boride sheet with a hexagonal boron network as a field-effect transistor (FET) for protein vii sequencing. In Chapter 6, the future prospects of the thesis has been discussed. It sheds light for researchers in the field of materials science, chemistry, nanoscience, nanotechnology, and biophysics to explore new avenues on the enhancement of DNA/protein sequencing applications.