Decoding Both DNA and Methylated DNA Using a MXene-Based Nanochannel Device: Supervised Machine-Learning-Assisted Exploration

Abstract

An important pursuit in medical research is to develop a fast and low-cost technique capable of sequencing the entire human genome (DNA) and epigenome (methylated DNA) de novo. Such a method would enable the advancement of personalized medicines and a universal cancer screening test. In this regard, we introduce a novel supervised machine learning (ML) approach for ultrarapid prediction of transmission function of DNA and methylated DNA nucleobases using a MXene-based nanochannel device. The proposed device can detect the targeted nucleobases with good transmission sensitivity. The random forest regression (RFR) model can predict the transmission function of each unknown nucleobase with root-mean-square error (RMSE) values as low as 0.16. Interestingly, if the machine is trained with the dataset of methylated DNA nucleobases, it can selectively identify all four DNA nucleobases with good accuracy. Therefore, our study demonstrates an effective approach for quick and accurate whole-genome and epigenome sequencing applications.

Machine learning empowered next generation DNA sequencing: perspective and prospectus

“…MXene nanochannels are demonstrated to be promising for both genome and epigenome sequencing. 35 Using Ti 2 NS 2 MXene nanochannel, the transmission of both DNA and methylated DNA nucleobases is predicted with low root mean square error (∼0.16) (Fig. 7a and b).…”

Using Graphdiyne Nanoribbons for Molecular Electronics Spectroscopy and Nucleobase Identification: A Theoretical Investigation

“…2D materials have been a substantial focus of interest due to their remarkable structural, electrical, chemical, thermal, and optical characteristics. − In the domain of layered materials, wonder material graphene and its one-dimensional (1D) form, graphene nanoribbon, have exhibited diverse applications across multiple sectors, ranging from electronics to energy, health, and the environment. − Following the discovery of graphene, plenty of new carbon-based 2D materials such as graphyne, graphdiyne, graphone, and graphane have also been proposed and unveiled. , The exceptional and distinctive characteristics of these novel materials position them as highly promising candidates for utilization across various nanotechnology domains . In particular, the significance of broadening the utilization of these materials in molecular sensing and DNA/RNA sequencing for the advancement of new techniques and devices − makes the investigation of the interaction between biological molecules such as DNA and RNA and these carbon-based nanostructures particularly intriguing.…”

“…2D materials have been a substantial focus of interest due to their remarkable structural, electrical, chemical, thermal, and optical characteristics. 1 − 8 In the domain of layered materials, wonder material graphene and its one-dimensional (1D) form, graphene nanoribbon, have exhibited diverse applications across multiple sectors, ranging from electronics to energy, health, and the environment. 9 − 21 Following the discovery of graphene, plenty of new carbon-based 2D materials such as graphyne, graphdiyne, graphone, and graphane have also been proposed and unveiled.…”

Adsorption of DNA nucleobases on single-layer Ti3C2 MXene and graphene: vdW-corrected DFT and NEGF studies

“…Furthermore, combining DFT, NEGF, and supervised machine learning techniques, Mittal et al. 20 demonstrated the possibility of detecting both DNA and methylated DNA nucleobases using a Ti 2 NS 2 MXene nanochannel device.…”

“…So far, most of the studies for DNA sequencing using 2D MXenes have been based on the nanopore 18,19 or nanochannel 20 method. Another useful detection mechanism for DNA nucleobases is the physisorption mechanism, where the changes in sheet current due to physisorption of DNA nucleobases can be measured.…”