Detection of mutations regarding one or more deoxyribonucleic acid sequences using deterministic lateral displacement arrays

Patent metadata

Field	Value
Publication number	US-11180796-B2
Application number	US-201816007389-A
Country	US
Kind code	B2
Filing date	Jun 13, 2018
Priority date	Jun 13, 2018
Publication date	Nov 23, 2021
Grant date	Nov 23, 2021

Abstract

Techniques regarding screening for mutations using nanoscale deterministic arrays are provided. For example, one or more embodiments described herein can comprise a method, which can comprise cleaving a deoxyribonucleic acid segment hybridized with a molecular probe to form a sample fluid. The cleaving can occur at a first end and a second end of the molecular probe. Also, the cleaving can comprise a cleaving agent that targets base pair mismatches. The method can also comprise supplying the sample fluid to a nanoscale deterministic lateral displacement array to screen for a single nucleotide polymorphism.

First claim

What is claimed is:

1. A method, comprising:
cleaving a deoxyribonucleic acid segment hybridized with a molecular probe to form a sample fluid, wherein the cleaving occurs at a first end of the molecular probe and a second end of the molecular probe, wherein the sample fluid has a plurality of base pair mismatches with respect to the deoxyribonucleic acid segment and the molecular probe, wherein a first base pair mismatch from the plurality of base pair mismatches is located at the first end of the molecular probe and a second base pair mismatch from the plurality of the base pair mismatches is located at the second end of the molecular probe, and wherein the cleaving comprises a cleaving agent that targets base pair mismatches with respect to the deoxyribonucleic acid segment and the molecular probe, wherein the base pair mismatches include the plurality of base pair mismatches;
supplying the sample fluid to a nanoscale deterministic lateral displacement array to screen for a single nucleotide polymorphism; and
determining whether the deoxyribonucleic acid segment comprises the single nucleotide polymorphism at a position between the first base pair mismatch and the second base pair mismatch based on a flow path of the molecular probe through the nanoscale deterministic lateral displacement array.

2. The method of claim 1 , wherein the molecular probe remains intact between the first end of the molecular probe and the second end of the molecular probe subsequent to the cleaving, and wherein the molecular probe flows through the nanoscale deterministic lateral displacement array in a bumped path.

3. The method of claim 1 , wherein a third base pair mismatch from the plurality of base pair mismatches is located between the first base pair mismatch and the second base pair mismatch, wherein the cleaving further cleaves the molecular probe between the first end of the molecular probe and the second end of the molecular probe, and wherein the molecular probe within the sample fluid is too small to be laterally displaced by the nanoscale deterministic lateral displacement array.

4. The method of claim 1 , further comprising:
detecting a location of the molecular probe; and
determining the flow path based on the location.

5. The method of claim 1 , wherein the molecular probe comprises an identifier selected from a group consisting of a fluorescent tag and a magnetic bead.

6. The method of claim 1 , wherein the cleaving agent is selected from a group consisting of a chemical cleaving agent and an enzymatic cleaving agent.

7. The method of claim 6 , wherein the cleaving agent is selected from a second group consisting of piperidine and endonucleases.

8. The method of claim 1 , comprising:
forming a second sample fluid by cleaving a second deoxyribonucleic acid segment hybridized to a second molecular probe, wherein the deoxyribonucleic acid segment and the second deoxyribonucleic acid segment are defined by a same nucleic acid sequence, wherein the cleaving occurs at a first end of the second molecular probe and a second end of the second molecular probe, wherein the second sample fluid has a second plurality of base pair mismatches with respect to the second deoxyribonucleic acid segment and the second molecular probe, wherein a first base pair mismatch from the second plurality of base pair mismatches is located at the first end of the second molecular probe and a second base pair mismatch from the second plurality of the base pair mismatches is located at the second end of the second molecular probe, and wherein the forming comprises a second cleaving agent that targets the second plurality of base pair mismatches; and
screening for the single nucleotide polymorphism in the same nucleic acid sequence by supplying the second sample fluid to a second nanoscale deterministic lateral displacement array.

9. The method of claim 8 , wherein the molecular probe is hybridized to a first portion of the same nucleic acid sequence, wherein the second molecular probe is hybridized to a second portion of the same nucleic acid sequence, and wherein the first portion of the same nucleic acid sequence overlaps the second portion of the same nucleic acid sequence.

10. The method of claim 9 , wherein the molecular probe remains intact subsequent to the cleaving of the deoxyribonucleic acid segment, wherein the second molecular probe remains intact subsequent to the cleaving of the second deoxyribonucleic acid segment, wherein the molecular probe flows through the nanoscale deterministic lateral displacement array in a first bumped path, and wherein the second molecular probe flows through the second nanoscale deterministic lateral displacement array in a second bumped path.

11. The method of claim 9 , wherein the molecular probe remains intact subsequent to the cleaving of the deoxyribonucleic acid segment, wherein the cleaving of the second deoxyribonucleic acid segment further comprises cleaving the second molecular probe between first end of the second molecular probe and the second end of the second molecular probe, wherein a third base pair mismatch from the second plurality of base pair mismatches is located between the first base pair mismatch from the second plurality of base pair mismatches and the second base pair mismatch from the second plurality of base pair mismatches, wherein the molecular probe flows through the nanoscale deterministic lateral displacement array in a bumped path, and wherein the second molecular probe flows through the second nanoscale deterministic lateral displacement array in a zig-zag path.

12. The method of claim 9 , wherein the cleaving of the deoxyribonucleic acid segment further comprises cleaving the molecular probe between first end of the molecular probe and the second end of the molecular probe, wherein a third base pair mismatch from the plurality of base pair mismatches is located between the first base pair mismatch from the plurality of base pair mismatches and the second base pair mismatch from the plurality of base pair mismatches, wherein the cleaving of the second deoxyribonucleic acid segment further comprises cleaving the second molecular probe between first end of the second molecular probe and the second end of the second molecular probe, wherein a third base pair mismatch from the second plurality of base pair mismatches is located between the first base pair mismatch from the second plurality of base pair mismatches and the second base pair mismatch from the second plurality of base pair mismatches, wherein the molecular probe flows through the nanoscale deterministic lateral displacement array in a first zig-zag path, and wherein the second molecular probe flows through the second nanoscale deterministic lateral displacement array in a second zig-zag path.

13. The method of claim 9 , wherein the molecular probe comprises a first identifier selected from a first group consisting of a fluorescent tag and a magnetic bead, wherein the second molecular probe comprises a second identifier selected from a second group consisting of the fluorescent tag and the magnetic bead, and wherein the first cleaving agent is selected from a third group consisting of a first chemical cleaving agent and a first enzymatic cleaving agent, and wherein the second cleaving agent is selected from a fourth group consisting of a second chemical cleaving agent and a second enzymatic cleaving agent.

Assignees

• IBM

Inventors

• Gifford Stacey
• Wunsch Benjamin
• Smith Joshua T
• Kim Sung-Cheol

Classifications

• C12Q1/6823 Primary

  Release of bound markers · CPC title

• C12Q1/683 Primary

  involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP] · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q1/6816

  characterised by the detection means (C12Q1/6804 takes precedence) · CPC title