# US 2019/0169684 A1 · Systems and methods for measurement and sequencing of bio-molecules > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0169684 A1 - Document ID: US20190169684A1 - Status: Published application - Kind: A1 - Application number: 16/169,756 - Filed: 2018-10-24 - Published: 2019-06-06 - Earliest claimed: 2016-04-27 - Assignees: Quantum Biosystems Inc. - Applicants: Quantum Biosystems Inc. - Inventors: Mark F. OLDHAM; Eric S. NORDMAN; Timothy M. WOUDENBERG; Gaurav GOYAL; Masoud VAKILI; Toshihiko HONKURA; Sam WOO; Hisao KAWASAKI; Kazusuke MIHARA - Web page: https://patentgrep.com/patent/US20190169684A1 ## CPC - C12Q 1/6869: Methods for sequencing - C12Q 1/68: involving nucleic acids - C12Q 1/6823: Release of bound markers - G01N 27/3275: {Sensing specific biomolecules, e.g. nucleic acid strands, based on an electrode surface reaction} - G01N 27/3276: {being a hybridisation with immobilised receptors (using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68)} - G01N 27/3278: {involving nanosized elements, e.g. nanogaps or nanoparticles (nanopores G01N33/48721; magnetic beads G01N27/745)} - G01N 33/00: Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00 - G01N 33/48721: {Investigating individual macromolecules, e.g. by translocation through nanopores (Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68)} - C12Q 2565/631: being a biochannel or pore - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) ## Abstract The present disclosure provides systems and methods for sequencing nucleic acid molecules using tunneling labels. A sequence of a nucleic acid molecule may be identified with high accuracy using a chip comprising sensors, wherein each individual sensor may comprise at least two electrodes separated by a gap. The electrodes may be configured to generate at least one electrical signal upon binding of a tunneling label associated with a nucleotide. Epigenetic information can also be determined at the same time as a nucleic acid sequence. ## Claims ### Claim at position 1 -28. (canceled) ### Claim 29 A method for sequencing a sample nucleic acid, comprising: (a) using a polymerase adjacent to two electrodes on a substrate to bind a nucleotide to a complementary base of the sample nucleic acid, the nucleotide having a tunneling label attached thereto; (b) measuring a tunneling current between the two electrodes caused by a localization of the tunneling label to the two electrodes; and (c) using at least the tunneling current measured in (b) to identify the complementary base. ### Claim 30 (depends on 29) The method of claim 29, wherein the tunneling label is larger than a size of a gap between the two electrodes. ### Claim 31 (depends on 30) The method of claim 30, wherein the tunneling label comprises a zwitterionic compound. ### Claim 32 (depends on 29) The method of claim 29, wherein the tunneling label comprises a nucleic acid strand. ### Claim 33 (depends on 32) The method of claim 32, wherein the nucleic acid strand is greater than 10 bases long. ### Claim 34 (depends on 32) The method of claim 32, wherein the nucleic acid strand has a double stranded portion and a single stranded portion. ### Claim 35 (depends on 29) The method of claim 29, further comprising binding the polymerase to a dielectric between the two electrodes. ### Claim 36 (depends on 29) The method of claim 29, further comprising binding the polymerase to one of the two electrodes. ### Claim 37 (depends on 29) The method of claim 29, wherein a gap between the two electrodes has a first portion having a width that is greater than a size of the polymerase and a second portion having a width that is smaller than the size of the polymerase. ### Claim 38 (depends on 29) The method of claim 29, wherein a self assembled monolayer is bound to the electrodes. ### Claim 39 (depends on 38) The method of claim 38, wherein the self assembled monolayer is bound by a thiol to the electrodes. ### Claim 40 (depends on 38) The method of claim 38, wherein the self assembled monolayer comprises at least in part a nucleic acid which binds to at least a part of a nucleic acid strand comprised in the tunneling label. ### Claim 41 (depends on 40) The method of claim 40, wherein said binding is transient. ### Claim 42 (depends on 29) The method of claim 29, wherein said nucleotide further comprises a terminator. ### Claim 43 (depends on 42) The method of claim 42, wherein said terminator is bound to the 3′ of a ribose of the nucleotide. ### Claim 44 An apparatus for sequencing a sample nucleic acid, comprising: two electrodes disposed on a substrate separated by a non-conductive gap; wherein the two electrodes and the non-conductive gap are configured to accommodate a polymerase in adjacent to the two electrodes, which polymerase binds a nucleotide to a complementary base of the sample nucleic acid, the nucleotide having a tunneling label attached thereto; and wherein the two electrodes are configured to measure a tunneling current between the two electrodes caused by a localization of the tunneling label to the two electrodes. ### Claim 45 (depends on 44) The apparatus of claim 44, wherein the polymerase is disposed in the non-conductive gap, and wherein said non-conductive gap is etched down between said electrodes to a depth of 10 nanometers (nm) or more. ### Claim 46 (depends on 45) The apparatus of claim 45, wherein the non-conductive gap has a size that is smaller than a size of the polymerase such that the polymerase is disposed over the non-conductive gap, and wherein said non-conductive gap is etched to a depth of 10 nm or less. ### Claim 47 (depends on 44) The apparatus of claim 44, wherein the non-conductive gap has a wider portion and a narrower portion. ### Claim 48 A method comprising: (a) using a polymerase adjacent to two electrodes on a substrate to bind a nucleobase having an tunneling label attached thereto, said nucleobase complementary to an interrogated base of a sample nucleic acid; (b) measuring a current signal comprising a combination of at least one tunneling current and at least one hopping current between the two electrodes caused by localization of the tunneling label to the two electrodes; and (c) identifying a matching nucleobase on a single stranded portion of the sample nucleic acid based at least in part on the measured current signal.