Programmable nano-reactors for stochastic sensing

Abstract

Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, “programmable nano-reactors for stochastic sensing” (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.

Identification of Single-Molecule Catecholamine Enantiomers Using a Programmable Nanopore

“…All nanopore measurements in this study were carried out as previously reported. 33 A self-assembled lipid bilayer consisting of DPhPC separated the measurement device into two chambers. Each chamber contained 500 μL of buffer of 1.5 M KCl, 10 mM HEPES, pH 8.0.…”

“…However, owing to the technical complexity associated with the chemical engineering of the pore lumen, direct discrimination of enantiomers has been only rarely reported with nanopores. 29−32 Programmable nanoreactors for stochastic sensing (PNRSS) 33 is a versatile, recently developed strategy to probe single-molecule reactions.…”

“…The amount of sample required for a single measurement is 0.5 nmol, which is much less than is required for HPLC. 33 Assisted with a custom machine learning algorithm, a 98.2% accuracy has been achieved.…”

Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore

“…Phenylboronic acid (PBA) is known to form covalent bonds reversibly with 1,2 or 1,3-diols 39 . Previously, the introduction of PBA to the nanopore lumen was successfully applied to the detection of various cis-diol-containing analytes such as saccharides 40 , epinephrine and Remdesivir 41 . However, a hetero-octameric MspA nanopore containing a single PBA adaptor has not been reported previously and nanopore identification of a large variety of epigenetically modified nucleoside monophosphates (NMPs) has also never been reported.…”

Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

“…The proposed system would be potentially useful for medical applications if this system will integrate into a commercially available nanopore sequencer such as MinION (Oxford Nanopore Technologies). Moreover, several biological nanopores other than αHL have also been used for nanopore sensing. ,− The nanopore decoding will have the potential to apply to the different types of nanopores.…”