Methods of macromolecular analysis using nanochannel arrays

• US 10,000,804 B2
• Filed: 03/07/2016
• Issued: 06/19/2018
• Est. Priority Date: 03/28/2007
• Status: Active Grant

• Current Assignee: BioNano Genomics, Inc.
• Original Assignee: BioNano Genomics, Inc.
• Inventors: Cao, Han, Deshpande, Parikshit A., Austin, Michael D., Boyce-Jacino, Michael
• Primary Examiner(s): Bhat, Narayan
• Application Number:
  US15/062,622
• Publication Number:
  US 20160289756A1
• Time in Patent Office: 834 Days
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2200/12 Specific details about manufacturing devices
• CPC Class Codes: B01L 2300/041 Connecting closures to device or container
• CPC Class Codes: B01L 2300/0627 Sensor or part of a sensor is integrated
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0861 Configuration of multiple channels and/or chambers in a single devices
• CPC Class Codes: B01L 2300/0864 comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2300/089 Virtual walls for guiding liquids
• CPC Class Codes: B01L 2300/0896 Nanoscaled
• CPC Class Codes: B01L 2300/161 Control and use of surface tension forces, e.g. hydrophobic, hydrophilic
• CPC Class Codes: B01L 2400/0406 capillary forces
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/50273 characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6876 : Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2600/172 : Haplotypes
• CPC Class Codes: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/645 : Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 33/582 : with fluorescent label

Abstract

Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.

Claims

1. A method of characterizing a genomic DNA using a nanofluidic device, the method comprising:

providing a sample comprising the genomic DNA;

labeling one or more regions of the genomic DNA comprising a haplotype;

translocating at least a portion of the labeled DNAs through an array of fluidic nanochannel segments disposed substantially parallel to a substrate surface, wherein the fluidic nanochannel segment is capable of containing and elongating at least a portion of the region of the nucleic acid, and wherein the fluidic nanochannel segment has a characteristic cross-sectional dimension of less than about 1000 nm and a length of at least about 10 nm, wherein said translocating comprises introducing the labeled isolated nucleic acid molecules into separate fluidic nanochannel segments each having a cross-sectional diameter of less than about 200 nm so as to at least substantially linearize at least a part of the labeled nucleic acid molecules,

said translocating comprising fluidic flow in a nanoscale environment that precludes turbulence and shear forces, thereby maintaining the genomic DNA intact,

capturing single-molecule signals evolved from the haplotype of the intact genomic DNA; and

ascertaining a structural pattern of the intact genomic DNA based on the captured single-molecule signals.

2. The method of claim 1, wherein labeling comprises labeling with at least one of a fluorescent label, a magnetic label, or a radioactive label.

3. The method of claim 1, wherein the labeled isolated nucleic acid molecules are from a single cell.

4. The method of claim 1, wherein translocating is selected from the group consisting of:

a fluid flow, a magnetic field, an electric field, a radioactive field, a mechanical force, an electroosmotic force, an electrophoretic force, an electrokinetic force, a temperature gradient, a pressure gradient, a surface property gradient, a capillary flow, and any combination thereof.

5. The method of claim 1, wherein the translocating comprises controllably moving at least a portion of the genomic DNA into at least a portion of a fluidic nanochannel segment.

6. The method of claim 1, wherein the translocating comprises moving at least a portion of the genomic DNA through at least a portion of a fluidic nanochannel segment at a controlled speed and a controlled direction.

7. The method of claim 1, wherein the signal is generated by a substance selected from the group consisting of:

an electron spin resonance molecule, a fluorescent molecule, a chemiluminescent molecule, a radioisotope, an enzyme substrate, a biotin molecule, an avidin molecule, an electrical charged transferring molecule, a semiconductor nanocrystal, a semiconductor nanoparticle, a colloid gold nanocrystal, a ligand, a microbead, a magnetic bead, a paramagnetic particle, a quantum dot, a chromogenic substrate, an affinity molecule, a protein, a peptide, a nucleic acid, a carbohydrate, an antigen, a hapten, an antibody, an antibody fragment, a lipid, and any combination thereof.

8. The method of claim 1, wherein capturing single-molecule signals evolved from the genomic DNA comprises capturing signals from more than one DNA.

9. The method of claim 8, wherein said translocating, permits simultaneous viewing of multiple regions of DNAs within the nanofluidic device.