Enrichment of nucleic acid targets

Patent metadata

Field	Value
Publication number	US-10337054-B2
Application number	US-201615284980-A
Country	US
Kind code	B2
Filing date	Oct 4, 2016
Priority date	Feb 2, 2004
Publication date	Jul 2, 2019
Grant date	Jul 2, 2019

Abstract

Methods and apparatus providing for the isolation of an unknown mutation from a sample comprising wild type nucleic acids and mutated nucleic acids through the application of time-varying driving fields and periodically varying mobility-altering fields to the sample within in an affinity matrix.

First claim

What is claimed is:

1. A method for isolating a second molecule from a first molecule in a sample, the method comprising: applying a time-varying driving field to the sample in the presence of an affinity matrix comprising immobilized probes, the probes having a first binding affinity for the first molecule that is greater than a second binding affinity for the second molecule; applying a periodically varying, mobility-altering field that modifies the first and second binding affinities; wherein application of the time-varying driving field and the periodically varying, mobility-altering field concentrates the second molecule within the affinity matrix and separate from the first molecule;
wherein the sample further comprises a background molecule with a third binding affinity that is less than the first and second binding affinities and wherein application of the time-varying driving field and periodically varying mobility-altering field concentrates the second molecule within the affinity matrix and separate from the first molecule and the background molecule.

2. The method of claim 1 , wherein the periodically varying mobility-altering field is a temperature gradient.

3. The method of claim 2 , wherein the time-varying driving field comprises an electric field and the magnitude of the electric field is selected to produce the temperature gradient within the affinity matrix.

4. The method of claim 1 , wherein the time-varying driving field comprises an electric field.

5. The method of claim 1 , wherein the time-varying driving field varies direction with time.

6. The method of claim 5 , further comprising:
calculating a velocity of the first and second molecules in the affinity matrix as a function of magnitude of the mobility-altering field;
determining a value for the magnitude of the mobility-altering field at which the difference in mobility of the first and second molecules is highest; and
varying the magnitude of the mobility altering field around the value while varying the direction of the driving field to separate the first and second molecules within the affinity matrix.

7. The method of claim 1 , further comprising applying a washing field to cause net motion of the first and second molecules through the affinity matrix.

8. The method of claim 1 , wherein the first and second molecules comprise nucleic acids comprising between 30 and 5000 bases.

9. The method of claim 1 , wherein the first and second molecules comprise nucleic acids that differ in sequence by at least one base.

10. The method of claim 1 , wherein the first and second molecules comprise nucleic acids and the first molecule is identical to or shares at least 95% sequence similarity with the second molecule.

11. The method of claim 1 , wherein the first and second molecules comprise oligonucleotides, and wherein the immobilized probes each comprise a nucleic acid that is complementary to at least a portion of the first molecule.

12. The method of claim 11 , wherein the immobilized probes each comprise a nucleic acid comprising between 30 and 150 bases.

13. The method of claim 1 , wherein the ratio of the second molecule in the sample to the first molecule in the sample is 1:1,000 or less.

14. The method of claim 1 , wherein a concentration of the second molecule relative to a concentration of the first molecule within the affinity matrix has been increased by a factor of at least 100:1 over the concentration of the second molecule relative to the concentration of the first molecule in the sample.

15. The method of claim 1 , wherein at least one of the first and second molecules is fluorescently labeled, the method further comprising periodically monitoring the location of the fluorescently labeled molecules in the affinity matrix and adjusting the application of the time-varying driving field and the periodically varying, mobility-altering field based on the location of the fluorescently labeled molecule.

16. The method of claim 1 , wherein two or more target molecules are present in the sample and are simultaneously concentrated at different, unique locations within the affinity matrix.

17. A method for isolating a second molecule from a first molecule in a sample, the method comprising:
applying a time-varying driving field to the sample in the presence of an affinity matrix comprising immobilized probes, the probes having a first binding affinity for the first molecule that is greater than a second binding affinity for the second molecule;
applying a periodically varying, mobility-altering field that modifies the first and second binding affinities;
wherein application of the time-varying driving field and the periodically varying, mobility-altering field concentrates the second molecule within the affinity matrix and separate from the first molecule; wherein the first molecule is a wild type nucleic acid and the second molecule comprises a mutant nucleic acid.

18. A method for isolating a second molecule from a first molecule in a sample, the method comprising:
applying a time-varying driving field to the sample in the presence of an affinity matrix comprising immobilized probes, the probes having a first binding affinity for the first molecule that is greater than a second binding affinity for the second molecule;
applying a periodically varying, mobility-altering field that modifies the first and second binding affinities;
wherein application of the time-varying driving field and the periodically varying, mobility-altering field concentrates the second molecule within the affinity matrix and separate from the first molecule;
wherein the sample comprises issue, blood, sputum, sweat, urine, feces, tears, aspirate, or a combination thereof.

19. A method for isolating a second molecule from a first molecule in a sample, the method comprising:
applying a time-varying driving field to the sample in the presence of an affinity matrix comprising immobilized probes, the probes having a first binding affinity for the first molecule that is greater than a second binding affinity for the second molecule;
applying a periodically varying, mobility-altering field that modifies the first and second binding affinities; wherein application of the time-varying driving field and the periodically varying, mobility-altering field concentrates the second molecule within the affinity matrix and separate from the first molecule;
wherein the affinity matrix comprises two or more different immobilized probes configured to work simultaneously and wherein application of the time-varying driving field and the periodically varying, mobility-altering field simultaneously concentrates a plurality of different target molecules from the sample.

Assignees

• Quantum Si Inc

Inventors

• Marziali Andrea
• Despotovic Milenko
• Pel Joel

Classifications

• C12Q1/6837

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• B01L2200/0631

  Purification arrangements, e.g. solid phase extraction [SPE] · CPC title

• B01L2300/1805

  Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks · CPC title

• B03C2201/18

  Magnetic separation whereby the particles are suspended in a liquid · CPC title

• B01L2400/0421

  electrophoretic flow · CPC title