DOE Patents title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid

Abstract

Embodiments of the present invention are directed toward devices, systems, and methods for purifying nucleic acids to conduct polymerase chain reaction (PCR) assays. In one example, a method includes generating complexes of silica beads and nucleic acids in a lysis buffer, transporting the complexes through an immiscible fluid to remove interfering compounds from the complexes, further transporting the complexes into a density medium containing components required for PCR where the nucleic acids disassociate from the silica beads, and thermocycling the contents of the density medium to achieve PCR. Signal may be detected from labeling agents in the components required for PCR.

Inventors:
; ; ;
Issue Date:
Research Org.:
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1637827
Patent Number(s):
10590477
Application Number:
15/717,524
Assignee:
National Technology & Engineering Solutions of Sandia, LLC (Albuquerque, NM)
Patent Classifications (CPCs):
B - PERFORMING OPERATIONS B01 - PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL B01L - CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
DOE Contract Number:  
NA0003525
Resource Type:
Patent
Resource Relation:
Patent File Date: 09/27/2017
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Koh, Chung-Yan, Light, Yooli Kim, Piccini, Matthew Ernest, and Singh, Anup K. Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid. United States: N. p., 2020. Web.
Koh, Chung-Yan, Light, Yooli Kim, Piccini, Matthew Ernest, & Singh, Anup K. Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid. United States.
Koh, Chung-Yan, Light, Yooli Kim, Piccini, Matthew Ernest, and Singh, Anup K. Tue . "Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid". United States. https://www.osti.gov/servlets/purl/1637827.
@article{osti_1637827,
title = {Method and apparatus for purifying nucleic acids and performing polymerase chain reaction assays using an immiscible fluid},
author = {Koh, Chung-Yan and Light, Yooli Kim and Piccini, Matthew Ernest and Singh, Anup K.},
abstractNote = {Embodiments of the present invention are directed toward devices, systems, and methods for purifying nucleic acids to conduct polymerase chain reaction (PCR) assays. In one example, a method includes generating complexes of silica beads and nucleic acids in a lysis buffer, transporting the complexes through an immiscible fluid to remove interfering compounds from the complexes, further transporting the complexes into a density medium containing components required for PCR where the nucleic acids disassociate from the silica beads, and thermocycling the contents of the density medium to achieve PCR. Signal may be detected from labeling agents in the components required for PCR.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Mar 17 00:00:00 EDT 2020},
month = {Tue Mar 17 00:00:00 EDT 2020}
}

Works referenced in this record:

Optical bio-discs and fluidic circuits for analysis of cells and methods relating thereto
patent, January 2007


On-Chip Coupling of Isoelectric Focusing and Free Solution Electrophoresis for Multidimensional Separations
journal, March 2003


Capillary columns with in situ formed porous monolithic packing for micro high-performance liquid chromatography and capillary electrochromatography
journal, September 1999


Diagnostic Analyzers With Pretreatment Carousels and Related Methods
patent-application, September 2014


Systems and Methods for Handling Microfluidic Droplets
patent-application, October 2013


Portable Simultaneous Multiple Analyte Whole-Blood Analyzer for Point-of-Care Testing
journal, September 1992


How Hofmeister ion interactions affect protein stability
journal, October 1996


Centrifugation Apparatus For Containers Of Biological Material
patent-application, February 2011


Shiga toxin 1 acting on DNA in vitro is a heat-stable enzyme not requiring proteolytic activation
journal, April 2004


Compact disk based platform for separating and detecting immunomagnetic bead labeled cells
patent-application, June 2010


Microparticle-based methods and systems and applications thereof
patent-application, December 2005


Heterogeneous binding assay
patent, April 1987


Centripetally-motivated microfluidics system for performing in vitro hybridization and amplification of nucleic acids
patent, February 2008


Ricin A-Chain Activity on Stem−Loop and Unstructured DNA Substrates
journal, March 2005


Monolithic microfluidic concentrators and mixers
patent, May 2005


A molecular approach to bioseparations: Protein–protein and protein–salt interactions
journal, February 2006


Functional integration of DNA purification and concentration into a real time micro-PCR chip
journal, January 2011


Detecting Single Stranded DNA with a Solid State Nanopore
journal, October 2005


Clockwork PCR Including Sample Preparation
journal, May 2008


Centrifugal hematology disposable
patent, November 2000


Reagents for labeling biomolecules having aldehyde or ketone Moieties
patent-application, September 2002


Comparison of sample fixation and the use of LDS-751 or anti-CD45 for leukocyte identification in mouse whole blood for flow cytometry
journal, January 2007


A B Cell-Based Sensor for Rapid Identification of Pathogens
journal, July 2003


Cell-Free DNA—A Marker to Predict Ischemic Brain Damage in a Rat Stroke Experimental Model
journal, January 2011


Multistage Isoelectric Focusing in a Polymeric Microfluidic Chip
journal, December 2005


Bead-based microfluidic immunoassays: The next generation
journal, February 2007


Systems, Devices, and Methods For Agglutination Assays Using Sedimentation
patent-application, March 2016


Microfluidic devices and methods
patent-application, January 2003


Systems, devices, and methods for agglutination assays using sedimentation
patent, January 2016


Infrared controlled waxes for liquid handling and storage on a CD-microfluidic platform
journal, January 2011


Integrated Preconcentration SDS−PAGE of Proteins in Microchips Using Photopatterned Cross-Linked Polyacrylamide Gels
journal, July 2006


Multi-parameter assays including analysis discs and methods relating thereto
patent-application, October 2002


Toxin Activity Assays, Devices, Methods And Systems Therefor
patent-application, June 2016


Effects of separation length and voltage on isoelectric focusing in a plastic microfluidic device
journal, September 2006


Class characterization of circulating cancer cells isolated from body fluids and methods of use
patent-application, July 2002


Design Strategies and Performance of Custom DNA Sequencing Primers
journal, September 1999


One-step purification of nucleic acid for gene expression analysis via Immiscible Filtration Assisted by Surface Tension (IFAST)
journal, January 2011


Apparatus for precise transfer and manipulation of fluids by centrifugal and or capillary forces
patent, December 2012


Separation Device
patent-application, May 2010


Parallel processing in the isoelectric focusing chip
journal, November 2003


Integration of nanoporous membranes for sample filtration/preconcentration in microchip electrophoresis
journal, December 2006


Lab On A CD
journal, August 2006


Method for separating cells
patent-application, July 2003


Devices and Method For Using Centripetal Acceleration To Drive Fluid Movement In A Microfluidics System With On-Board Informatics
patent-application, December 2001


Analytical methods and compositions
patent-application, November 2002


Microfluidic particle-analysis systems
patent-application, April 2004


Centrifuge with removable core for scalable centrifugation
patent-application, September 2005


Microfluidic devices, systems, and methods for quantifying particles using centrifugal force
patent, November 2015


Rapid isoelectric trapping in a micropreparative-scale multicompartment electrolyzer
journal, June 2007


Protecting agent
patent-application, August 2005


Method for detecting analytes in a sample
patent-application, December 2009


Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock
journal, April 2008


Plastic microfluidics enabling two-dimensional protein separations in proteome analysis
patent-application, November 2002


Parallel isoelectric focusing chip
journal, September 2004


Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation
patent, February 2015


On-Chip Isoelectric Focusing Using Photopolymerized Immobilized pH Gradients
journal, May 2008


Density-based cell detection system
patent, March 2010


Microfluidic immunoassays as rapid saliva-based clinical diagnostics
journal, March 2007


Preparative-scale isoelectric trapping separations using a modified Gradiflow unit
journal, December 2002


Multichannel control in microfluidics
patent-application, October 2002


Staphylococcal Enterotoxin B as a Biological Weapon: Recognition, Management, and Surveillance of Staphylococcal Enterotoxin
journal, September 2006


Micro freef-low IEF enhanced by active cooling and functionalized gels
journal, December 2006


Leukocyte analysis and differentiation using high speed microfluidic single cell impedance cytometry
journal, January 2009


Microfluidics devices and methods for performing cell based assays
patent-application, August 2002


Centrifugal Separation System
patent-application, August 2009


Measurement of Circulating Cell-Free DNA Levels by a New Simple Fluorescent Test in Patients With Primary Colorectal Cancer
journal, February 2011


Parallel Nanoliter Microfluidic Analysis System
journal, June 2007


Microfluidic particle-analysis systems
patent, December 2007


Whole Blood Immunoassay Based on Centrifugal Bead Sedimentation
journal, March 2011


Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function
journal, June 2011


Read-out concepts for multiplexed bead-based fluorescence immunoassays on centrifugal microfluidic platforms
journal, February 2006


Method for Separating Cells
patent-application, May 2008


Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays
journal, January 2007


Polyethyleneimine functionalized iron oxide nanoparticles as agents for DNA delivery and transfection
journal, January 2007


Toxin activity assays, devices, methods and systems therefor
patent, April 2016


Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin
journal, December 2014


Method and Apparatus For Precise Transfer and Manipulation Of Fluids By Centrifugal and Or Capillary Forces
patent-application, January 2009


Assay system and method for conducting assays
patent, March 1999


Detection of Listeria monocytogenes and the toxin listeriolysin O in food
journal, February 2006


A new biodosimetric method: branched DNA-based quantitative detection of B1 DNA in mouse plasma
journal, August 2010


Method Of Detecting Analyte-Molecule Interactions
patent-application, June 2008


Formation of Natural pH Gradients in a Microfluidic Device under Flow Conditions:  Model and Experimental Validation
journal, February 2001


Centrifugal microfluidics for biomedical applications
journal, January 2010


Quantitative Comparison of Long-wavelength Alexa Fluor Dyes to Cy Dyes: Fluorescence of the Dyes and Their Bioconjugates
journal, December 2003


Assay of blood or other biologic samples for target analytes
patent, June 1997


Integrated planar microfluidic bioanalytical systems
patent-application, August 2006


Parallel isoelectric focusing II
journal, November 2004


Fully Integrated Lab-on-a-Disc for Nucleic Acid Analysis of Food-Borne Pathogens
journal, March 2014


Plasma DNA as a Prognostic Marker in Trauma Patients
journal, March 2000


Fully integrated lab-on-a-disc for simultaneous analysis of biochemistry and immunoassay from whole blood
journal, January 2011


Devices, systems, and methods for conducting sandwich assays using sedimentation
patent, February 2015


High resolution two-dimensional electrophoresis of proteins.
journal, May 1975


A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids
journal, September 2009


Molecular Detection of Bacterial Pathogens Using Microparticle Enhanced Double-Stranded DNA Probes
journal, August 2011


Photopolymerized diffusion-defined polyacrylamide gradient gels for on-chip protein sizing
journal, January 2008


Circulating DNA: a new diagnostic gold mine?
journal, October 2002


A fully automated immunoassay from whole blood on a disc
journal, January 2009


Loading Disk for Photometric Analyzer of Rotary Cuvette Type
patent, July 1973


Microfluidic Devices, Systems, And Methods For Quantifying Particles Using Centrifugal Force
patent-application, December 2015