A Step toward Amino Acid-Labeled DNA Sequencing: Boosting Transmission Sensitivity of Graphene Nanogap

Abstract

Existing obstacles in next-generation DNA sequencing techniques, for instance, high noise, high translocation speed, and configurational fluctuations, call for approaches capable of reaching the goal and accelerating the process of personalized medicine development. The labeling nucleotide approach has the potential to overcome these barriers and boost the recognition sensitivity of a solid-state nanodevice. In this theoretical report, the first-principles density functional theory calculations have been employed to study the role of three different labels, tyrosine (Tyr), aspartic acid (Asp), and arginine (Arg), for labeling DNA nucleotides and study their effect in rapid and controlled DNA sequencing at atomic resolution. Remarkable differences in interaction energy values are noticed in all three cases of differently labeled nucleotides. The zero-bias transmission spectra confirm that proposed labels have the ability to detect the individual nucleotide, amplifying the tunneling current sensitivity by several orders of magnitude. The current−voltage characteristics of Arglabeled nucleotides are found to be promising for single nucleotide recognition even at a very low bias voltage of 0.1 V.

Machine learning empowered next generation DNA sequencing: perspective and prospectus

“…For widespread adoption of ML in real DNA sequencing, a signicant number of challenges must be addressed, such as efficient training of machines, real-time efficient data, fast processing of electronic data, etc. So far, various alternatives have been proposed to achieve singlenucleotides resolution, such as two-dimensional molecular electronics spectroscopy, 25 different edge functionalization, 77,78 labeling of DNA nucleotides, 79,80 different device architecture, 81,82 nucleobase analogs, 82,83 heterostructure, 84,85 hybrid nanopore, 55,86 and so on. However, the potential of integrating ML with these methods to accelerate the DNA sequencing process has not yet been fully explored.…”

Uncovering an Emerging Group of Halogenated Nucleobase-Derived Disinfection Byproducts in Drinking Water: Prioritization of the Highly Cytotoxic 2-Chloroadenine

“…Halogenated nucleobases and nucleosides shared the characteristics of both biological molecules and chemical modification. Bioanalytical methods, such as quantitative PCR , and sequencing methods, , are unable to provide structural information. Liquid chromatography–mass spectrometry (LC–MS) can realize the specific detection of nucleic acid substances, but the sensitivity is limited.…”