Single‐Molecule Classification of Aspartic Acid and Leucine by Molecular Recognition through Hydrogen Bonding and Time‐Series Analysis

Abstract

Amino acid detection/identification methods are important for understanding biological systems. In this study, we developed single-molecule measurements for investigating quantum tunneling enhancement by chemical modification and carried out machine learning-based time series analysis for developing accurate amino acid discrimination. We performed single-molecule measurement of L-aspartic acid (Asp) and L-leucine (Leu) with a mercaptoacetic acid (MAA) chemical modified nano-gap. The measured current was investigated by a machine learning-based time series analysis method for accurate amino acid discrimination. Compared to measurements using a bare nano-gap, it is found that MAA modification improves the difference in the conductance-time profiles between Asp and Leu through the hydrogen bonding facilitated tunneling phenomena. It is also found that this method enables determination of relative concentration. even in the mixture of Asp and Leu. It improves selective analysis for amino acids and therefore would be applicable in medicine, diagnosis, and singlemolecule peptide sequencing.

Machine learning and analytical methods for single-molecule conductance measurements

“…We previously demonstrated that modifying nanogap electrodes improves identification accuracy, even for molecules that cannot be distinguished using conventional machine learning methods alone. 36 Further progress in both statistical analysis method and novel and precise measurement technique development will be necessary to achieve these goals.…”

“…[22][23][24] The research of single-molecule measurements has developed to successfully measure the conductance of nucleotides in DNA and RNA [25][26][27][28][29][30] and amino acids. [31][32][33][34][35][36][37] As the nature of single-molecule measurements allows for the measurement of the direct conductance of a single molecule, they are expected to flourish as a new analytical method that is highly sensitive, rapid, and requires no pre-treatment steps. Furthermore, singlemolecule measurements play a crucial role in the investigating of novel physical and chemical properties in the nanoscale.…”

Engineering Biological Nanopore Approaches toward Protein Sequencing

“…To address the above challenges, some highly parallel, single-molecule techniques have been envisioned in the past decade for next-generation protein analysis and sequencing. 17,18 These emerging methods use tunneling currents, 19,20 fluorescence, 21 resistive-pulse nanopores, 3,22,23 and other nanotechnologies to sequence or identify individual proteins, down to the single-molecule level or in single cells. 24,25 The precision of these advanced measurement tools have the capacity to create many opportunities in biomedical research, with applications ranging from proteomics of single cells and bodily fluids to sensing and classifying low-abundance protein biomarkers for disease screening and precision diagnostics.…”

“…To address the above challenges, some highly parallel, single-molecule techniques have been envisioned in the past decade for next-generation protein analysis and sequencing. , These emerging methods use tunneling currents, , fluorescence, resistive-pulse nanopores, ,, and other nanotechnologies to sequence or identify individual proteins, down to the single-molecule level or in single cells. , The precision of these advanced measurement tools have the capacity to create many opportunities in biomedical research, with applications ranging from proteomics of single cells and bodily fluids to sensing and classifying low-abundance protein biomarkers for disease screening and precision diagnostics . Among the methods driving this era of advanced nanodevices for single-molecule recognition was the tunneling current method, as reported by Zwolak and Di Ventra for DNA sequencing. − This method was expanded to detect AAs using two metal electrodes separated by a nanogap (0.7–2 nm), comparable to the size of typical AA molecules.…”

Tunnel junction sensing of TATP explosive at the single-molecule level

“…In that approach, a probed molecule, positioned between two nanoelectrodes, could be detected by measuring the electric tunneling current. [22][23][24][25][26][27][28][29] There are two distinct approaches: (i) a molecule has no covalent bonds with electrodes (employed in DNA 22,23,30,31 or protein sequencing 24,25 ), and (ii) a molecule is covalently bound to one 26 or both electrodes (similar to molecular diodes [27][28][29] ). Although covalent bonds between the molecule and the electrodes are convenient for stable electronic transport, such sensors would need frequent chemical or thermal treatment for trapped TATP molecules cleaning.…”