Systems and methods for enhanced SCODA

Patent metadata

Field	Value
Publication number	US-9434938-B2
Application number	US-201313968907-A
Country	US
Kind code	B2
Filing date	Aug 16, 2013
Priority date	May 20, 2011
Publication date	Sep 6, 2016
Grant date	Sep 6, 2016

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.

First claim

What is claimed is:

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.

2. The method of claim 1 , further comprising collecting the first nucleic acid molecule from the matrix.

3. The method of claim 1 , further comprising collecting the second nucleic acid molecule from the matrix.

4. The method of claim 1 , wherein the time-varying electric field varies the mobility of the first and second nucleic acids.

5. The method of claim 4 , wherein the time-varying electric field varies the mobility by causing Joule heating within the matrix.

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.

7. The method of claim 6 , wherein the difference in temperatures is less than about 3° C.

8. The method of claim 1 , wherein the first and second nucleic acid molecules are between 100 and 1000 nucleotides in length.

9. The method of claim 1 , wherein the first and second nucleic acid molecules are less than 100 nucleotides in length.

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.

11. The method of claim 1 , wherein the oligonucleotide probe is complimentary to at least a portion of the first and second nucleic acid molecules.

12. 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.

13. The method of claim 1 , wherein both the first and the second nucleic acids comprise a gene implicated in cancer.

14. The method of claim 1 , further comprising amplifying or sequencing the first or the second nucleic acid.

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.

16. 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.

17. The method of claim 16 , further comprising separating the first nucleic acid molecule from the third nucleic acid molecule.

18. The method of claim 1 , wherein the first and second nucleic acids molecules are at least 98% identical in sequence.

Assignees

• Univ British Columbia

Inventors

• Marziali Andrea
• Pel Joel
• Thompson Jason Donald
• Shibahara Gosuke

Classifications

• G01N33/575

  for cancer · CPC title

• C12N15/1003 Primary

  Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor · CPC title

• G01N33/5308

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title

• G01N33/543

  with an insoluble carrier for immobilising immunochemicals · CPC title

• G01N2800/385

  Congenital anomalies · CPC title