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

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

Patent · 17 March 2020

OSTI ID:1637827

Koh, Chung-Yan; Light, Yooli Kim; Piccini, Matthew Ernest; Singh, Anup K.

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.

View Patent

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

DOE Contract Number:: NA0003525

Assignee:: National Technology & Engineering Solutions of Sandia, LLC (Albuquerque, NM)

Patent Number(s):: 10,590,477

Application Number:: 15/717,524

OSTI ID:: 1637827

Country of Publication:: United States

Language:: English

References (61)

Whole Blood Immunoassay Based on Centrifugal Bead Sedimentation Schaff, U. Y.; Sommer, G. J. Clinical Chemistry, Vol. 57, Issue 5, p. 753-761 https://doi.org/10.1373/clinchem.2011.162206	journal	March 2011
Shiga toxin 1 acting on DNA in vitro is a heat-stable enzyme not requiring proteolytic activation Brigotti, Maurizio; Carnicelli, Domenica; Vara, Antonio González Biochimie, Vol. 86, Issue 4-5, p. 305-309 https://doi.org/10.1016/j.biochi.2004.03.009	journal	April 2004
Design Strategies and Performance of Custom DNA Sequencing Primers Buck, G. A.; Fox, J. W.; Gunthorpe, M. BioTechniques, Vol. 27, Issue 3 https://doi.org/10.2144/99273rr01	journal	September 1999
Molecular Detection of Bacterial Pathogens Using Microparticle Enhanced Double-Stranded DNA Probes Riahi, Reza; Mach, Kathleen E.; Mohan, Ruchika Analytical Chemistry, Vol. 83, Issue 16, p. 6349-6354 https://doi.org/10.1021/ac2012575	journal	August 2011
Integration of nanoporous membranes for sample filtration/preconcentration in microchip electrophoresis Long, Zhicheng; Liu, Dayu; Ye, Nannan ELECTROPHORESIS, Vol. 27, Issue 24, p. 4927-4934 https://doi.org/10.1002/elps.200600252	journal	December 2006
Fully Integrated Lab-on-a-Disc for Nucleic Acid Analysis of Food-Borne Pathogens Kim, Tae-Hyeong; Park, Juhee; Kim, Chi-Ju Analytical Chemistry, Vol. 86, Issue 8, p. 3841-3848 https://doi.org/10.1021/ac403971h	journal	March 2014
Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function Yu, Eizadora T.; Hadi, Masood Z. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, Vol. 722, Issue 2, p. 140-146 https://doi.org/10.1016/j.mrgentox.2010.06.015	journal	June 2011
A molecular approach to bioseparations: Protein–protein and protein–salt interactions Curtis, R. A.; Lue, L. Chemical Engineering Science, Vol. 61, Issue 3, p. 907-923 https://doi.org/10.1016/j.ces.2005.04.007	journal	February 2006
How Hofmeister ion interactions affect protein stability Baldwin, R. L. Biophysical Journal, Vol. 71, Issue 4, p. 2056-2063 https://doi.org/10.1016/S0006-3495(96)79404-3	journal	October 1996
A B Cell-Based Sensor for Rapid Identification of Pathogens Rider, Todd H.; Petrovick, Martha S.; Nargi, Frances E. Science, Vol. 301, Issue 5630, p. 213-215 https://doi.org/10.1126/science.1084920	journal	July 2003
Fully integrated lab-on-a-disc for simultaneous analysis of biochemistry and immunoassay from whole blood Lee, Beom Seok; Lee, Yang Ui; Kim, Han-Sang Lab on a Chip, Vol. 11, Issue 1, p. 70-78 https://doi.org/10.1039/C0LC00205D	journal	January 2011
Parallel processing in the isoelectric focusing chip Zilberstein, Gleb V.; Baskin, Emmanuil M.; Bukshpan, Shmuel ELECTROPHORESIS, Vol. 24, Issue 21, p. 3735-3744 https://doi.org/10.1002/elps.200305663	journal	November 2003
Microfluidic immunoassays as rapid saliva-based clinical diagnostics Herr, A. E.; Hatch, A. V.; Throckmorton, D. J. Proceedings of the National Academy of Sciences, Vol. 104, Issue 13, p. 5268-5273 https://doi.org/10.1073/pnas.0607254104	journal	March 2007
Multistage Isoelectric Focusing in a Polymeric Microfluidic Chip Cui, Huanchun; Horiuchi, Keisuke; Dutta, Prashanta Analytical Chemistry, Vol. 77, Issue 24, p. 7878-7886 https://doi.org/10.1021/ac050781s	journal	December 2005
On-Chip Coupling of Isoelectric Focusing and Free Solution Electrophoresis for Multidimensional Separations Herr, Amy E.; Molho, Joshua I.; Drouvalakis, Katerina A. Analytical Chemistry, Vol. 75, Issue 5, p. 1180-1187 https://doi.org/10.1021/ac026239a	journal	March 2003
Centrifugal microfluidics for biomedical applications Gorkin, Robert; Park, Jiwoon; Siegrist, Jonathan Lab on a Chip, Vol. 10, Issue 14, p. 1758-1773 https://doi.org/10.1039/b924109d	journal	January 2010
Ricin A-Chain Activity on Stem−Loop and Unstructured DNA Substrates Amukele, Tim K.; Roday, Setu; Schramm, Vern L. Biochemistry, Vol. 44, Issue 11, p. 4416-4425 https://doi.org/10.1021/bi0474362	journal	March 2005
On-Chip Isoelectric Focusing Using Photopolymerized Immobilized pH Gradients Sommer, Greg J.; Singh, Anup K.; Hatch, Anson V. Analytical Chemistry, Vol. 80, Issue 9, p. 3327-3333 https://doi.org/10.1021/ac702523g	journal	May 2008
Leukocyte analysis and differentiation using high speed microfluidic single cell impedance cytometry Holmes, David; Pettigrew, David; Reccius, Christian H. Lab on a Chip, Vol. 9, Issue 20, p. 2881-2889 https://doi.org/10.1039/b910053a	journal	January 2009
Staphylococcal Enterotoxin B as a Biological Weapon: Recognition, Management, and Surveillance of Staphylococcal Enterotoxin Ahanotu, Ejem; Alvelo-Ceron, Damaris; Ravita, Timothy Applied Biosafety, Vol. 11, Issue 3, p. 120-126 https://doi.org/10.1177/153567600601100303	journal	September 2006
Measurement of Circulating Cell-Free DNA Levels by a New Simple Fluorescent Test in Patients With Primary Colorectal Cancer Czeiger, David; Shaked, Gad; Eini, Hadar American Journal of Clinical Pathology, Vol. 135, Issue 2, p. 264-270 https://doi.org/10.1309/AJCP4RK2IHVKTTZV	journal	February 2011
Capillary columns with in situ formed porous monolithic packing for micro high-performance liquid chromatography and capillary electrochromatography Gusev, Isabelle; Huang, Xian; Horváth, Csaba Journal of Chromatography A, Vol. 855, Issue 1, p. 273-290 https://doi.org/10.1016/S0021-9673(99)00697-4	journal	September 1999
Integrated Preconcentration SDS−PAGE of Proteins in Microchips Using Photopatterned Cross-Linked Polyacrylamide Gels Hatch, Anson V.; Herr, Amy E.; Throckmorton, Daniel J. Analytical Chemistry, Vol. 78, Issue 14, p. 4976-4984 https://doi.org/10.1021/ac0600454	journal	July 2006
Portable Simultaneous Multiple Analyte Whole-Blood Analyzer for Point-of-Care Testing Schembri, C. T.; Ostoich, V.; Lingane, P. J. Clinical Chemistry, Vol. 38, Issue 9 https://doi.org/10.1093/clinchem/38.9.1665	journal	September 1992
Detection of Listeria monocytogenes and the toxin listeriolysin O in food Churchill, Robin L. T.; Lee, Hung; Hall, J. Christopher Journal of Microbiological Methods, Vol. 64, Issue 2, p. 141-170 https://doi.org/10.1016/j.mimet.2005.10.007	journal	February 2006
Parallel isoelectric focusing chip Zilberstein, Gleb; Korol, Leonid; Bukshpan, Shmuel PROTEOMICS, Vol. 4, Issue 9, p. 2533-2540 https://doi.org/10.1002/pmic.200300794	journal	September 2004
Comparison of sample fixation and the use of LDS-751 or anti-CD45 for leukocyte identification in mouse whole blood for flow cytometry Maes, Melissa L.; Davidson, Lisa B.; McDonagh, Paul F. Journal of Immunological Methods, Vol. 319, Issue 1-2, p. 79-86 https://doi.org/10.1016/j.jim.2006.10.016	journal	January 2007
Clockwork PCR Including Sample Preparation Pipper, Juergen; Zhang, Yi; Neuzil, Pavel Angewandte Chemie International Edition, Vol. 47, Issue 21 https://doi.org/10.1002/anie.200705016	journal	May 2008
Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays Suzuki, Shingo; Ono, Naoaki; Furusawa, Chikara BMC Genomics, Vol. 8, Issue 1, Article No. 373 https://doi.org/10.1186/1471-2164-8-373	journal	January 2007
Infrared controlled waxes for liquid handling and storage on a CD-microfluidic platform Abi-Samra, Kameel; Hanson, Ryan; Madou, Marc Lab on a Chip, Vol. 11, Issue 4, p. 723-726 https://doi.org/10.1039/C0LC00160K	journal	January 2011
Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin Koh, Chung-Yan; Schaff, Ulrich Y.; Piccini, Matthew E. Analytical Chemistry, Vol. 87, Issue 2, p. 922-928 https://doi.org/10.1021/ac504054u	journal	December 2014
A Method for Global Analysis of Complex Proteomes Using Sample Prefractionation by Solution Isoelectrofocusing Prior to Two-Dimensional Electrophoresis Zuo, Xun; Speicher, David W. Analytical Biochemistry, Vol. 284, Issue 2 https://doi.org/10.1006/abio.2000.4714	journal	September 2000
Photopolymerized diffusion-defined polyacrylamide gradient gels for on-chip protein sizing Lo, Catherine T.; Throckmorton, Daniel J.; Singh, Anup K. Lab on a Chip, Vol. 8, Issue 8, p. 1273-1279 https://doi.org/10.1039/b804485f	journal	January 2008
A rapid direct fluorescent assay for cell-free DNA quantification in biological fluids Goldshtein, H.; Hausmann, M. J; Douvdevani, A. Annals of Clinical Biochemistry, Vol. 46, Issue 6, p. 488-494 https://doi.org/10.1258/acb.2009.009002	journal	September 2009
RNA N-glycosidase activity of ricin A-chain. Mechanism of action of the toxic lectin ricin on eukaryotic ribosomes. Endo, Y.; Tsurugi, K. Journal of Biological Chemistry, Vol. 262, Issue 17 https://doi.org/10.1016/S0021-9258(18)47538-2	journal	June 1987
The Alpher, Bethe, Gamow of isoelectric focusing, the alpha-Centaury of electrokinetic methodologies. Part I Righetti, Pier Giorgio ELECTROPHORESIS, Vol. 27, Issue 5-6, p. 923-938 https://doi.org/10.1002/elps.200500525	journal	March 2006
Polyethyleneimine functionalized iron oxide nanoparticles as agents for DNA delivery and transfection McBain, S. C.; Yiu, H. H. P.; El Haj, A. Journal of Materials Chemistry, Vol. 17, Issue 24, p. 2561-2565 https://doi.org/10.1039/b617402g	journal	January 2007
Detecting Single Stranded DNA with a Solid State Nanopore Fologea, Daniel; Gershow, Marc; Ledden, Bradley Nano Letters, Vol. 5, Issue 10, p. 1905-1909 https://doi.org/10.1021/nl051199m	journal	October 2005
High resolution two-dimensional electrophoresis of proteins. O'Farrell, Ph Journal of Biological Chemistry, Vol. 250, Issue 10 https://doi.org/10.1016/S0021-9258(19)41496-8	journal	May 1975
Bead-based microfluidic immunoassays: The next generation Lim, C. T.; Zhang, Y. Biosensors and Bioelectronics, Vol. 22, Issue 7, p. 1197-1204 https://doi.org/10.1016/j.bios.2006.06.005	journal	February 2007
A fully automated immunoassay from whole blood on a disc Lee, Beom Seok; Lee, Jung-Nam; Park, Jong-Myeon Lab on a Chip, Vol. 9, Issue 11, p. 1548-1555 https://doi.org/10.1039/b820321k	journal	January 2009
Lab On A CD Madou, Marc; Zoval, Jim; Jia, Guangyao Annual Review of Biomedical Engineering, Vol. 8, Issue 1, p. 601-628 https://doi.org/10.1146/annurev.bioeng.8.061505.095758	journal	August 2006
Rapid isoelectric trapping in a micropreparative-scale multicompartment electrolyzer Lim, Peniel; North, Robert; Vigh, Gyula ELECTROPHORESIS, Vol. 28, Issue 12, p. 1851-1859 https://doi.org/10.1002/elps.200600846	journal	June 2007
Cell-Free DNA—A Marker to Predict Ischemic Brain Damage in a Rat Stroke Experimental Model Boyko, Matthew; Ohayon, Sharon; Goldsmith, Tomer Journal of Neurosurgical Anesthesiology, Vol. 23, Issue 3, p. 222-228 https://doi.org/10.1097/ANA.0b013e31821b536a	journal	January 2011
The Alpher, Bethe and Gamow of IEF, the alpha-Centaury of electrokinetic methodologies. Part II: Immobilized pH gradients Righetti, Pier Giorgio ELECTROPHORESIS, Vol. 28, Issue 4, p. 545-555 https://doi.org/10.1002/elps.200600256	journal	February 2007
Parallel Nanoliter Microfluidic Analysis System Andersson, Per; Jesson, Gerald; Kylberg, Gunnar Analytical Chemistry, Vol. 79, Issue 11, p. 4022-4030 https://doi.org/10.1021/ac061692y	journal	June 2007
Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock Saukkonen, K.; Lakkisto, P.; Pettila, V. Clinical Chemistry, Vol. 54, Issue 6, p. 1000-1007 https://doi.org/10.1373/clinchem.2007.101030	journal	April 2008
Functional integration of DNA purification and concentration into a real time micro-PCR chip Min, Junhong; Kim, Joon-Ho; Lee, Youngsun Lab on a Chip, Vol. 11, Issue 2, p. 259-265 https://doi.org/10.1039/C0LC00320D	journal	January 2011
A new biodosimetric method: branched DNA-based quantitative detection of B1 DNA in mouse plasma Zhang, L.; Zhang, M.; Yang, S. The British Journal of Radiology, Vol. 83, Issue 992, p. 694-701 https://doi.org/10.1259/bjr/49886569	journal	August 2010
Plasma DNA as a Prognostic Marker in Trauma Patients Lo, Y. M. Dennis; Rainer, Timothy H.; Chan, Lisa Y. S. Clinical Chemistry, Vol. 46, Issue 3 https://doi.org/10.1093/clinchem/46.3.319	journal	March 2000
Circulating DNA: a new diagnostic gold mine? Ziegler, Annemarie; Zangemeister-Wittke, Uwe; Stahel, Rolf A. Cancer Treatment Reviews, Vol. 28, Issue 5, p. 255-271 https://doi.org/10.1016/S0305-7372(02)00077-4	journal	October 2002
Formation of Natural pH Gradients in a Microfluidic Device under Flow Conditions: Model and Experimental Validation Cabrera, Catherine R.; Finlayson, Bruce; Yager, Paul Analytical Chemistry, Vol. 73, Issue 3, p. 658-666 https://doi.org/10.1021/ac000495a	journal	February 2001
Depurination of A4256 in 28 S rRNA by the Ribosome-inactivating Proteins from Barley and Ricin Results in Different Ribosome Conformations Holmberg, Lovisa; Nygård, Odd Journal of Molecular Biology, Vol. 259, Issue 1, p. 81-94 https://doi.org/10.1006/jmbi.1996.0303	journal	May 1996
Effects of separation length and voltage on isoelectric focusing in a plastic microfluidic device Das, Champak; Fan, Z. Hugh ELECTROPHORESIS, Vol. 27, Issue 18, p. 3619-3626 https://doi.org/10.1002/elps.200600013	journal	September 2006
Characterization of EBV-genome negative “null” and “T” cell lines derived from children with acute lymphoblastic leukemia and leukemic transformed non-Hodgkin lymphoma Schneider, Ulrich; Schwenk, Hans-Ulrich; Bornkamm, Georg International Journal of Cancer, Vol. 19, Issue 5, p. 621-626 https://doi.org/10.1002/ijc.2910190505	journal	May 1977
Read-out concepts for multiplexed bead-based fluorescence immunoassays on centrifugal microfluidic platforms Riegger, L.; Grumann, M.; Nann, T. Sensors and Actuators A: Physical, Vol. 126, Issue 2, p. 455-462 https://doi.org/10.1016/j.sna.2005.11.006	journal	February 2006
Preparative-scale isoelectric trapping separations using a modified Gradiflow unit Ogle, David; Ho, Agnes; Gibson, Toby Journal of Chromatography A, Vol. 979, Issue 1-2, p. 155-161 https://doi.org/10.1016/S0021-9673(02)01601-1	journal	December 2002
Parallel isoelectric focusing II Zilberstein, Gleb V.; Baskin, Emmanuil M.; Bukshpan, Shmuel ELECTROPHORESIS, Vol. 25, Issue 21-22, p. 3643-3651 https://doi.org/10.1002/elps.200406117	journal	November 2004
One-step purification of nucleic acid for gene expression analysis via Immiscible Filtration Assisted by Surface Tension (IFAST) Berry, Scott M.; Alarid, Elaine T.; Beebe, David J. Lab on a Chip, Vol. 11, Issue 10, p. 1747-1753 https://doi.org/10.1039/c1lc00004g	journal	January 2011
Quantitative Comparison of Long-wavelength Alexa Fluor Dyes to Cy Dyes: Fluorescence of the Dyes and Their Bioconjugates Berlier, Judith E.; Rothe, Anca; Buller, Gayle Journal of Histochemistry & Cytochemistry, Vol. 51, Issue 12, p. 1699-1712 https://doi.org/10.1177/002215540305101214	journal	December 2003
Micro freef-low IEF enhanced by active cooling and functionalized gels Albrecht, Jacob W.; Jensen, Klavs F. ELECTROPHORESIS, Vol. 27, Issue 24, p. 4960-4969 https://doi.org/10.1002/elps.200600436	journal	December 2006

Similar Records

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

Patent · 2017 · OSTI ID:1406570

Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

Patent · 2011 · OSTI ID:1013411

Devices, systems, and methods for detecting nucleic acids using sedimentation

Patent · 2017 · OSTI ID:1404945

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES

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

Citation Formats

References (61)

Similar Records

Related Subjects