Northeastern University

University of York

University of Illinois

The University of North Carolina at Charlotte

Meni Wanunu

Joseph Larkin

Alfred Antson

Sandra Greive

Benjamin Cressiot

Swastik Kar

Aleksei Aksimentiev

Hirohito Yamazaki

Pradeep Waduge

Ismail Bilgin

Robert Henley

Mohammadamin Alibakhshi

Kirill Andreevich Afonin

Andrey Ivankin

Moneesh Upmanyu

Zhuoyu Zhang

Xinqi Kang

Behzad Mehrafrooz

Luning Yu

Bedanga Sapkota

Alfred A Antson

Hybrid nanopores, comprising a protein pore supported within a solid-state membrane, which combine the robust nature of solid-state membranes with the easily tunable and precise engineering of protein nanopores. In an embodiment, a lipid-free hybrid nanopore comprises a water soluble and stable, modified portal protein of thebacteriophage G20c, electrokinetically inserted into a larger nanopore in a solid-state membrane. The hybrid pore is stable and easy to fabricate, and exhibits low peripheral leakage, allowing sensing and discrimination among different types of biomolecules.

Lipid-free anchoring of thermophilic bacteriophage G20c portal adapter into solid-state nanopores

A method and system for performing single molecule proteomics utilizing a nanopore sensor to measure an electronic signature of protein or peptide being transported through the nanopore from a first chamber to a second chamber. The protein's electronic signature is a function of ionic current over time. The method and system utilizing an agent, such as guanidinium chloride, to bind to the nanopore's interior and provide an electroosmotic force within the nanopore. The electroosmotic force, in some embodiments, enables stretching and unfolding of the protein during transport through the nanopore. The agent may also or alternatively induce the unfolding of the protein before transport through the nanopore and/or provide force moving the protein through the nanopore.

Method and system for linearization and translocation of single protein molecules through nanopores

Lipid-free anchoring of thermophilic bacteriophage G20C portal adapter into solid-state nanopores

An apparatus is provided for sensing a molecule in a sample. The apparatus utilizes an electric field to draw molecules from a first chamber through an aperture, defined by a chemical layer, into a second chamber. The apparatus can detect a DNA molecule with, for example, 4, 5, or 6 unique base pairs. As molecules pass through the aperture, a sensor detects or measures a change in an electric parameter used to generate the electric field, thereafter translating the change in the electric parameter into information about the molecule. A divider element separates the first and second chambers and supports a chemical layer defining the aperture. The apparatus enables detection or measurement of molecules over prolonged time at a higher electric field strength than other nanopores, due to a combination of the shape of the divider, structural elements thereon, and thickness of the chemical layer at the aperture.

Method and apparatus for sensing a molecule

A porous membrane comprising stacked layers of nanosheets, each nanosheet comprising one to three atomic layers of a 2D material comprising or consisting of one or more transition metal dichalcogenides is provided. The nanosheets have pores and the membrane comprises a network of water permeation pathways including through-pathways formed by the pores, horizontal pathways formed by gaps between the layers, and vertical pathways formed by gaps between adjacent nanosheets and stacking defects between the layers. Also provided is a method for making the membrane.

Porous membranes comprising nanosheets and fabrication thereof

A multiplexed digital detection platform embodiment for molecular species in solution is based on a single-molecule immunochemistry, and/or aptamer chemistry, on color-barcoded beads. Beads that capture molecular species from a complex sample using selective binders are exposed to a test sample, and the captured molecular species is tagged using second affinity probes that are linked to photocleavable nucleic acid particles. In the embodiment, the beads are then introduced to a counter system that comprises a microcavity/nanopore device. Once a bead is captured by the micropore, nucleic acid particles, e.g., reporter nucleic acid nanoparticles (rNANPs), are released using photocleavage, and are detected by the nanopore. Each electrical spike that is uniquely produced by the nucleic acid nanoparticle is counted as a single molecular species, and the total count represents the overall number of molecular species in the sample. Various molecular species can be detected at the same time.

System and method for identifying and quantifying species with nanopores, using complexes of nanoparticles with carrier particles

A method for etching a light absorbing material permits directly writing a pattern of etching of silicon nitride and other light absorbing materials, without the need of a lithographic mask, and allows the creation of etched features of less than one micron in size. The method can be used for etching deposited silicon nitride films, freestanding silicon nitride membranes, and other light absorbing materials, with control over the thickness achieved by optical feedback. The etching is promoted by solvents including electron donor species, such as chloride ions. The method provides the ability to etch silicon nitride and other light absorbing materials, with fine spatial and etch rate control, in mild conditions, including in a biocompatible environment. The method can be used to create nanopores and nanopore arrays.

Nanoscale etching of light absorbing materials using light and an electron donor solvent

The invention provides methods for direct growth of low noise, atomically thin freestanding membranes of two-dimensional monocrystalline or polycrystalline materials, such as transition metal chalcogenides including molybdenum disulfide. The freestanding membranes are directly grown over an aperture by reacting two precursors in a chemical vapor deposition process carried out at atmospheric pressure. Membrane growth is preferentially over apertures in a thin sheet of solid state material. The resulting membranes are one or a few atomic layers thick and essentially free of defects. The membranes are useful for sequencing of biopolymers through nanopores.

Low noise ultrathin freestanding membranes composed of atomically-thin 2D materials

An apparatus and a method are provided for selectively and rapidly applying heat to a nanoscale environment in a controlled manner. The technology utilizes laser irradiation of a solid state material to heat a nanoscale point of interest by an optothermal effect. The technology can be used to the tip of an atomic force microscope, a spot on a flat surface, or a nanopore, or molecules in their vicinity. The apparatus and method are capable of rapidly scanning the temperature of a nanoscale object such as a molecule or biomolecular complex and to interrogate properties of the object at high throughput. The methods can be used in nanofabrication processes or to drive single molecule chemistry.

Apparatus and method for optothermal heating of nanoscale environments

Provided is a highly multiplex approach to disease condition diagnostics that combines nanopore sensing and nucleic acid nanoparticle (NANP) design and synthesis to detect multiple biomarkers to diagnose diseases. The system works by taking a sample containing biomarkers that is mixed with a plurality of nucleic acid nanoparticle (NANP) populations, with each population designed and synthesized to be able to detect a particular biomarker. Upon incubation, the mixture is used with nanopore measurements, with recordings of the ionic current through the nanopore. The ionic current recordings are analyzed, which determines the presence and/or concentration of biomarkers in the sample.

Nucleic acid nanoparticles for analyte detection

Devices and methods useful for sequencing and characterizing single nucleic acid molecules involve large arrays of nanopore zero-mode waveguides (NZMWs). The methods and devices are made possible by fabrication of nanoporous membranes of appropriate porosity for use in nucleotide sequencing. The fabrication methods eliminate the need for serial nanopore formation and make possible the mass production of highly efficient DNA and RNA single molecule sequencing devices.

Pinhole zero-mode waveguides

Described herein are systems for analysis of biopolymers and complexes containing biopolymers based on optical measurement of ion flux through pores. Also described are methods of using such devices for analysis of biopolymers and complexes containing biopolymers, including methods of determining the nucleotide sequences of polynucleotides.

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Needham, MA, United States of America

Meni Wanunu