# US 12,006,542 B2 · Force-modulated hybridization for visualizing nucleic acid length and function > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,006,542 B2 - Document ID: US12006542B2 - Status: Granted - Kind: B2 - Application number: 16/620,571 - Filed: 2018-06-11 - Published: 2023-05-25 - Granted: 2024-06-11 - Earliest claimed: 2017-06-09 - Assignees: University of Houston System - Applicants: University of Houston System - Inventors: Shoujun Xu; Qiongzheng Hu; Yuhong Wang - Web page: https://patentgrep.com/patent/US12006542B2 ## CPC - C12Q 1/6816: characterised by the detection means (C12Q1/6804 takes precedence) - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - B01L 3/502761: {specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads or physically stretching molecules} - B01L 7/52: {with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples} - C12Q 1/6811: Selection methods for production or design of target specific oligonucleotides or binding molecules - B01L 2200/0663: Stretching or orienting elongated molecules or particles - B01L 2300/044: pierceable, e.g. films, membranes - B01L 2300/0654: Lenses; Optical fibres - B01L 2300/0672: Integrated piercing tool - B01L 2300/18: Means for temperature control - B01L 2400/0439: ultrasonic vibrations, vibrating piezo elements - C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) - C12Q 1/6818: involving interaction of two or more labels, e.g. resonant energy transfer - 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 - B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE ## Abstract Embodiments of the present disclosure pertain to methods of utilizing force-modulated hybridization to determine the length of an analyte strand, to determine an unknown nucleic acid sequence, or to determine the binding of a nucleotide to an active agent. Additional embodiments of the present disclosure pertain to sample holder devices and methods of utilizing such devices. Further embodiments of the present disclosure pertain to detection devices. ## Claims ### Claim 1 A method of determining the length of an analyte strand, comprising: (a) incubating a magnetically labeled oligonucleotide strand, the analyte strand, and one of a series of oligonucleotide ruler strands to form a mixture, wherein the magnetically labeled oligonucleotide strand is complementary in sequence to the analyte strand, wherein the series of oligonucleotide ruler strands are complementary in sequence to the magnetically labeled oligonucleotide strand and comprise different lengths, and wherein either the analyte strand or the oligonucleotide ruler strands are labeled with at least one label; (b) transferring the mixture to a surface functionalized to couple with the at least one label; (c) applying a mechanical force to the mixture; and (d) inspecting the surface for immobilized particles, wherein if the analyte strand is labeled, then the longest oligonucleotide ruler strand producing immobilized particles on the surface represents the length of the analyte strand, and wherein if the oligonucleotide ruler strands are labeled, then the longest oligonucleotide ruler strand not producing immobilized particles represents the length of the analyte strand; and (e) wherein a different oligonucleotide ruler strand is used to repeat steps (a)-(d) until the length of the analyte strand is determined. ### Claim 2 (depends on 1) The method of claim 1, wherein the mechanical force modulates oligonucleotide hybridization; wherein the oligonucleotide hybridization results in the presence of immobilized particles when the analyte strand is labeled and the oligonucleotide ruler strand is not longer than the analyte strand, and wherein the immobilized particles represent a hybrid structure between the magnetically labeled oligonucleotide strand and the analyte strand; wherein the oligonucleotide hybridization results in the absence of immobilized particles when the analyte strand is labeled and the oligonucleotide ruler strand is longer than the analyte strand; wherein the oligonucleotide hybridization results in the presence of immobilized particles when the oligonucleotide ruler strands are labeled and the oligonucleotide ruler strand is longer than the analyte strand, and wherein the immobilized particles represent a hybrid structure between the magnetically labeled oligonucleotide strand and the oligonucleotide ruler strand; and wherein the oligonucleotide hybridization results in the absence of immobilized particles when the oligonucleotide ruler strands are labeled and the oligonucleotide ruler strand is shorter than or the same length as the analyte strand. ### Claim 3 (depends on 1) The method of claim 1, wherein the analyte strand is labeled with the at least one label. ### Claim 4 (depends on 1) The method of claim 1, wherein the oligonucleotide ruler strands are labeled with the at least one label. ### Claim 5 (depends on 1) The method of claim 1, wherein the immobilized particles are represented by a yellow color on the surface, and wherein the yellow color is derived from the magnetically labeled oligonucleotide strand. ### Claim 6 (depends on 1) The method of claim 1, wherein the analyte strand is a DNA strand or an RNA strand; wherein the magnetically labeled oligonucleotide strand is a DNA strand or an RNA strand; wherein the magnetically labeled oligonucleotide strand has a longer length than the analyte strand; wherein the magnetically labeled oligonucleotide strand is 12-50 nucleotides long; and wherein the magnetically labeled oligonucleotide strand is labeled with a magnetic particle. ### Claim 7 (depends on 1) The method of claim 1, wherein the oligonucleotide ruler strands are selected from the group consisting of DNA strands, RNA strands, and combinations thereof; wherein the oligonucleotide ruler strands are complementary in sequence to the analyte strand; and wherein the oligonucleotide ruler strands comprise oligonucleotides longer than the analyte strand, oligonucleotides shorter than the analyte strand, and oligonucleotides the same length as the analyte strand. ### Claim 8 (depends on 1) The method of claim 1, wherein the surface is functionalized with a molecule that binds to the at least one label; and wherein the at least one label is selected from the group consisting of biotin, streptavidin, digoxigenin, avidin, maleic imide, gold, proteins, nucleic acids, functional groups, and combinations thereof. ### Claim 9 (depends on 1) The method of claim 1, wherein the mechanical force is selected from the group consisting of gravitational force, centrifugal force, shaking force, ultrasound radiation force, magnetic force, and combinations thereof; and wherein the mechanical force applied is between 10 fN and 500 pN. ### Claim 10 (depends on 1) The method of claim 1, wherein the at least one label is biotin, and wherein the surface is functionalized with streptavidin. ### Claim 11 (depends on 1) The method of claim 1, wherein the inspecting occurs by visual inspection.