Genotyping by Alkaline Dehybridization Using Graphically Encoded Particles

Zhang, Huaibin; DeConinck, Adam J.; Slimmer, Scott C.; Doyle, Patrick S.; Lewis, Jennifer A.; Nuzzo, Ralph G.

doi:10.1002/chem.201002848

Genotyping by Alkaline Dehybridization Using Graphically Encoded Particles

Journal Article · Tue Feb 08 00:00:00 EST 2011 · Chemistry - A European Journal

DOI:https://doi.org/10.1002/chem.201002848· OSTI ID:1875443

Zhang, Huaibin ^[1]; DeConinck, Adam J. ^[2]; Slimmer, Scott C. ^[2]; Doyle, Patrick S. ^[3]; Lewis, Jennifer A. ^[2]; Nuzzo, Ralph G. ^[2]

Univ. of Illinois at Urbana-Champaign, IL (United States); University of Illinois
Univ. of Illinois at Urbana-Champaign, IL (United States)
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. Here, we further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: NIH; National Science Foundation; USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division

Grant/Contract Number:: FG02-07ER46471

OSTI ID:: 1875443

Journal Information:: Chemistry - A European Journal, Journal Name: Chemistry - A European Journal Journal Issue: 10 Vol. 17; ISSN 0947-6539

Publisher:: ChemPubSoc EuropeCopyright Statement

Country of Publication:: United States

Language:: English

References (33)

SNP Genotyping by Using Photochemical Ligation Ogasawara, Shinzi; Fujimoto, Kenzo Angewandte Chemie, Vol. 118, Issue 27 https://doi.org/10.1002/ange.200600790	journal	July 2006
SNP Genotyping by Using Photochemical Ligation Ogasawara, Shinzi; Fujimoto, Kenzo Angewandte Chemie International Edition, Vol. 45, Issue 27 https://doi.org/10.1002/anie.200600790	journal	July 2006
DNA Analysis by Dynamic Chemistry Bowler, Frank R.; Diaz-Mochon, Juan J.; Swift, Michael D. Angewandte Chemie International Edition, Vol. 49, Issue 10 https://doi.org/10.1002/anie.200905699	journal	March 2010
Theoretical aspects of genomic variation screening using DNA microarrays Vainrub, Arnold; Pettitt, B. Montgomery Biopolymers, Vol. 73, Issue 5 https://doi.org/10.1002/bip.20008	journal	January 2004
UNAFold Markham, Nicholas R.; Zuker, Michael Bioinformatics https://doi.org/10.1007/978-1-60327-429-6_1	book	January 2008
Suspension array technology: evolution of the flat-array paradigm Nolan, John P.; Sklar, Larry A. Trends in Biotechnology, Vol. 20, Issue 1 https://doi.org/10.1016/S0167-7799(01)01844-3	journal	January 2002
Rapid discrimination of single-nucleotide mismatches using a microfluidic device with monolayered beads Ng, Johnson Kian-Kok; Feng, Hanhua; Liu, Wen-Tso Analytica Chimica Acta, Vol. 582, Issue 2 https://doi.org/10.1016/j.aca.2006.09.016	journal	January 2007
Point-of-care molecular diagnostic systems — past, present and future Holland, Carol A.; Kiechle, Frederick L. Current Opinion in Microbiology, Vol. 8, Issue 5 https://doi.org/10.1016/j.mib.2005.08.001	journal	October 2005
Evaluation of the Nanosphere Verigene® System and the Verigene® F5/F2/MTHFR Nucleic Acid Tests Lefferts, Joel A.; Jannetto, Paul; Tsongalis, Gregory J. Experimental and Molecular Pathology, Vol. 87, Issue 2 https://doi.org/10.1016/j.yexmp.2009.06.002	journal	October 2009
Microfluidic Device for the Discrimination of Single-Nucleotide Polymorphisms in DNA Oligomers Using Electrochemically Actuated Alkaline Dehybridization Zhang, Huaibin; Mitrovski, Svetlana M.; Nuzzo, Ralph G. Analytical Chemistry, Vol. 79, Issue 23 https://doi.org/10.1021/ac701660x	journal	October 2007
Spatial DNA Melting Analysis for Genotyping and Variant Scanning Crews, Niel; Wittwer, Carl T.; Montgomery, Jesse Analytical Chemistry, Vol. 81, Issue 6 https://doi.org/10.1021/ac801495w	journal	February 2009
Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification Pregibon, Daniel C.; Doyle, Patrick S. Analytical Chemistry, Vol. 81, Issue 12 https://doi.org/10.1021/ac9005292	journal	May 2009
Accessing genetic variation: genotyping single nucleotide polymorphisms Syvänen, Ann-Christine Nature Reviews Genetics, Vol. 2, Issue 12 https://doi.org/10.1038/35103535	journal	December 2001
Dynamic allele-specific hybridization Howell, W. Mathias; Jobs, Magnus; Gyllensten, Ulf Nature Biotechnology, Vol. 17, Issue 1 https://doi.org/10.1038/5270	journal	January 1999
A haplotype map of the human genome No authors listed Nature, Vol. 437, Issue 7063, p. 1299-1320 https://doi.org/10.1038/nature04226	journal	October 2005
Continuous-flow lithography for high-throughput microparticle synthesis Dendukuri, Dhananjay; Pregibon, Daniel C.; Collins, Jesse Nature Materials, Vol. 5, Issue 5, p. 365-369 https://doi.org/10.1038/nmat1617	journal	April 2006
SNP genotyping: six technologies that keyed a revolution Perkel, Jeffrey Nature Methods, Vol. 5, Issue 5 https://doi.org/10.1038/nmeth0508-447	journal	May 2008
Stop-flow lithography in a microfluidic device Dendukuri, Dhananjay; Gu, Shelley S.; Pregibon, Daniel C. Lab on a Chip, Vol. 7, Issue 7 https://doi.org/10.1039/b703457a	journal	January 2007
Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control Sosnowski, Ronald G.; Tu, Eugene; Butler, William F. Proceedings of the National Academy of Sciences, Vol. 94, Issue 4 https://doi.org/10.1073/pnas.94.4.1119	journal	February 1997
Nucleic Acid Isothermal Amplification Technologies—A Review Gill, Pooria; Ghaemi, Amir Nucleosides, Nucleotides and Nucleic Acids, Vol. 27, Issue 3 https://doi.org/10.1080/15257770701845204	journal	February 2008
SNP identification in unamplified human genomic DNA with gold nanoparticle probes Bao, Y. P. Nucleic Acids Research, Vol. 33, Issue 2 https://doi.org/10.1093/nar/gni017	journal	January 2005
Robust and Accurate Single Nucleotide Polymorphism Genotyping by Dynamic Allele-Specific Hybridization (DASH): Design Criteria and Assay Validation Prince, Jonathan A.; Feuk, Lars; Howell, W. Mathias Genome Research, Vol. 11, Issue 1 https://doi.org/10.1101/gr.150201	journal	January 2001
DASH-2: Flexible, Low-Cost, and High-Throughput SNP Genotyping by Dynamic Allele-Specific Hybridization on Membrane Arrays Jobs, Magnus; Howell, W. Mathias; Strömqvist, Linda Genome Research, Vol. 13, Issue 5 https://doi.org/10.1101/gr.801103	journal	May 2003
Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis Pregibon, Daniel C.; Toner, Mehmet; Doyle, Patrick S. Science, Vol. 315, Issue 5817, p. 1393-1396 https://doi.org/10.1126/science.1134929	journal	March 2007
Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome Wang, D. G. Science, Vol. 280, Issue 5366 https://doi.org/10.1126/science.280.5366.1077	journal	May 1998
Scanometric DNA Array Detection with Nanoparticle Probes Taton, T. A. Science, Vol. 289, Issue 5485 https://doi.org/10.1126/science.289.5485.1757	journal	September 2000
Genotyping Technologies for Genetic Research Ragoussis, Jiannis Annual Review of Genomics and Human Genetics, Vol. 10, Issue 1 https://doi.org/10.1146/annurev-genom-082908-150116	journal	September 2009
SNP Genotyping: Technologies and Biomedical Applications Kim, Sobin; Misra, Ashish Annual Review of Biomedical Engineering, Vol. 9, Issue 1 https://doi.org/10.1146/annurev.bioeng.9.060906.152037	journal	August 2007
M ETHODS FOR G ENOTYPING S INGLE N UCLEOTIDE P OLYMORPHISMS Kwok, Pui-Yan Annual Review of Genomics and Human Genetics, Vol. 2, Issue 1 https://doi.org/10.1146/annurev.genom.2.1.235	journal	September 2001
RNAstructure: software for RNA secondary structure prediction and analysis Reuter, Jessica S.; Mathews, David H. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-129	journal	March 2010
Emerging technologies for point-of-care genetic testing Dobson, Mark G.; Galvin, Paul; Barton, David E. Expert Review of Molecular Diagnostics, Vol. 7, Issue 4 https://doi.org/10.1586/14737159.7.4.359	journal	July 2007
SNP Discovery and Typing Technologies for Pharmacogenomics Twyman, Richard Current Topics in Medicinal Chemistry, Vol. 4, Issue 13 https://doi.org/10.2174/1568026043387656	journal	September 2004
DNA Diagnostics by Surface-Bound Melt-Curve Reactions Strömqvist Meuzelaar, Linda; Hopkins, Katie; Liebana, Ernesto The Journal of Molecular Diagnostics, Vol. 9, Issue 1 https://doi.org/10.2353/jmoldx.2007.060057	journal	February 2007

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Fluorescent monomers as building blocks for dye labeled polymers: synthesis and application in energy conversion, biolabeling and sensors Breul, Alexander M.; Hager, Martin D.; Schubert, Ulrich S. Chemical Society Reviews, Vol. 42, Issue 12 https://doi.org/10.1039/c3cs35478d	journal	January 2013

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