# US 9,434,938 B2 · Systems and methods for enhanced SCODA > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 9,434,938 B2 - Document ID: US9434938B2 - Status: Granted - Kind: B2 - Application number: 13/968,907 - Filed: 2013-08-16 - Published: 2013-12-05 - Granted: 2016-09-06 - Earliest claimed: 2011-05-20 - Assignees: The University of British Columbia - Applicants: The University of British Columbia - Inventors: Andrea Marziali; Joel Pel; Jason Donald Thompson; Gosuke Shibahara - Web page: https://patentgrep.com/patent/US9434938B2 ## CPC - C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) - B03C 7/023: {Non-uniform field separators} - C12N 15/1003: {Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor} - C12N 15/101: {by chromatography, e.g. electrophoresis, ion-exchange, reverse phase} - C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence) - G01N 33/5308: {for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites} - G01N 33/543: with an insoluble carrier for immobilising immunochemicals - G01N 33/575: for cancer - G01N 33/689: {related to pregnancy or the gonads} - G01N 2800/385: Congenital anomalies - 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 - B03C: MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS (separating isotopes B01D59/00; combinations of magnetic or electrostatic separation with separation of solids by other means B03B, B07B) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - 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 Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like. ## Claims ### Claim 1 A method of separating differentially methylated nucleic acid molecules, comprising: providing first and second nucleic acid molecules, the first and second nucleic acids molecules being at least 95% identical in sequence but being differentially methylated, contacting a matrix comprising an oligonucleotide probe with the first and second nucleic acids, wherein the difference between the binding energy of the first nucleic acid molecule to the oligonucleotide probe and the binding energy of the second nucleic acid molecule to the oligonucleotide probe is less than about 4 kcal/mol; and applying a time-varying electric field to the matrix while synchronously varying the mobility of the first and second nucleic acids, thereby separating the first and second nucleic acid molecules. ### Claim 2 (depends on 1) The method of claim 1, further comprising collecting the first nucleic acid molecule from the matrix. ### Claim 3 (depends on 1) The method of claim 1, further comprising collecting the second nucleic acid molecule from the matrix. ### Claim 4 (depends on 1) The method of claim 1, wherein the time-varying electric field varies the mobility of the first and second nucleic acids. ### Claim 5 (depends on 4) The method of claim 4, wherein the time-varying electric field varies the mobility by causing Joule heating within the matrix. ### Claim 6 A method of separating differentially methylated nucleic acid molecules, comprising: providing first and second nucleic acid molecules, the first and second nucleic acids molecules being at least 95% identical in sequence but being differentially methylated, contacting a matrix comprising an oligonucleotide probe with the first and second nucleic acids, wherein the difference between the melting temperature of the first nucleic acid molecule complexed with the oligonucleotide probe and the melting temperature of the second nucleic acid molecule complexed with the oligonucleotide probe is less than about 10° C.; and applying a time-varying electric field to the matrix while synchronously varying the mobility of the first and second nucleic acids, thereby separating the first and second nucleic acid molecules. ### Claim 7 (depends on 6) The method of claim 6, wherein the difference in temperatures is less than about 3° C. ### Claim 8 (depends on 1) The method of claim 1, wherein the first and second nucleic acid molecules are between 100 and 1000 nucleotides in length. ### Claim 9 (depends on 1) The method of claim 1, wherein the first and second nucleic acid molecules are less than 100 nucleotides in length. ### Claim 10 A method of separating differentially methylated nucleic acid molecules, comprising: providing first and second nucleic acid molecules, the first nucleic acid molecule and the second nucleic acid molecule are methylated at different nucleotides; contacting a matrix comprising an oligonucleotide probe with the first and second nucleic acids; and applying a time-varying electric field to the matrix while synchronously varying the mobility of the first and second nucleic acids, thereby separating the first and second nucleic acid molecules. ### Claim 11 (depends on 1) The method of claim 1, wherein the oligonucleotide probe is complimentary to at least a portion of the first and second nucleic acid molecules. ### Claim 12 (depends on 1) The method of claim 1, wherein the first nucleic acid molecule originates from a fetus, the second nucleic acid molecule originates from a mother of the fetus and both the first and second nucleic acids are obtained from a blood sample from the mother. ### Claim 13 (depends on 1) The method of claim 1, wherein both the first and the second nucleic acids comprise a gene implicated in cancer. ### Claim 14 (depends on 1) The method of claim 1, further comprising amplifying or sequencing the first or the second nucleic acid. ### Claim 15 A method of separating differentially methylated nucleic acid molecules, comprising: providing first and second nucleic acid molecules, the first and second nucleic acids molecules being at least 95% identical in sequence but being differentially methylated; contacting a matrix comprising a plurality of different oligonucleotide probes with the first and second nucleic acids; and applying a time-varying electric field to the matrix while synchronously varying the mobility of the first and second nucleic acids, thereby separating the first and second nucleic acid molecules. ### Claim 16 (depends on 15) The method of claim 15, wherein a first portion of the plurality of different oligonucleotide probes is complimentary to the first nucleic acid molecule and a second portion of the plurality of different oligonucleotide probes is complementary to a third nucleic acid molecule, and wherein the method additionally comprises separating the third nucleic acid molecule from a fourth nucleic acid molecule. ### Claim 17 (depends on 16) The method of claim 16, further comprising separating the first nucleic acid molecule from the third nucleic acid molecule. ### Claim 18 (depends on 1) The method of claim 1, wherein the first and second nucleic acids molecules are at least 98% identical in sequence.