Abstract
We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes at the same time according to a loading protocol generated by the user. Biotinylated deoxyribonucleic acid (DNA) is directed to the pad(s) via the electronic field(s) and bound to streptavidin in the hydrogel layer. Subsequently, fluorescently labeled reporter oligos and a stabilizer oligo are hybridized to the bound DNA. Base stacking between the short reporter and the longer stabilizer oligo stabilizes the binding of a matching reporter, whereas the binding of a reporter carrying a mismatch in the SNP position will be relatively weak. Thermal stringency is applied to the NanoChip array according to a reader protocol generated by the user and the fluorescent label on the matching reporter is detected.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Chen, X., and Sullivan, P. F. (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J. 3, 77–96.
Kwok, P. Y. and Chen, X. (2003) Detection of single nucleotide polymorphisms. Curr. Issues Mol. Biol. 5, 43–60.
Yershov, G., Barsky, V., Belgovskiy, A., Kirillov, E., Kreindlin, E., Ivanov, I., et al. (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. USA 93, 4913–4918.
Lane, M. J., Paner, T., Kashin, I., Faldasz, B. D., Li, B., Gallo, F. J., and Benight, A. S. (1997) The thermodynamic advantage of DNA oligonucleotide’ stacking hybridization' reactions: energetics of a DNA nick. Nucleic Acid Res. 25, 611–616.
Sosnowski, R. G., Tu, E., Butler, W. F., O'Connell, J. P., and Heller, M. J. (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl. Acad. Sci. USA 94, 1119–1123.
Gilles, P. N., Wu, D. J., Foster, C. B., Dillon, P. J., and Chanock, S. J. (1999) Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol. 17, 365–370.
Huang, Y., Sunghae, J., Duhon, M., Heller, M., Wallace, B., and Xu, X. (2002) Dielectronic cell separation and gene expression profiling on microelectronic chip arrays. Anal. Chem. 74, 3362–3371.
Westin, L., Xu, X., Miller, C., Wang, L., Edman, C. F. and Nerenberg, M. (2000) Anchored multiplex amplification on a microelectronic chip array. Nat. Biotechnol. 18, 199–204.
Weidenhammer E. M., Kahl B. F., Wang L., Wang L., Duhon M., Jackson J. A., et al. (2002) Multiplexed, targeted gene expression profiling and genetic analysis on electronic microarrays. Clin. Chem. 48, 1873–1882.
Yang J. M., Bell J., Huang Y., Tirado M., Thomas D., Forster A. H., et al. (2002) An integrated, stacked microlaboratory for biological agent detection with DNA and immunoassays. Biosensors Bioelectronics 17, 605–618.
Radtkey R., Feng L., Muralhidar M., Duhon M., Canter D., DiPierro D., et al. (2000) Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acid Res. 28, e17.
Behrensdorf, H. A., Pignot, M., Windhab, N., and Kappel, A. (2002) Rapid parallel mutation scanning of gene fragments using a microelectronic protein-DNA chip format. Nucleic Acid Res. 30, e64.
Saenger W. (1984) Forces stabilizing base associations: hydrogen bonding and basestacking, in Principles of nucleic acid structure. Springer-Verlag, New York}, pp 116–158.
BØrsting, C., Sanchez, J. J., and Morling, N. (2004) Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray. Int. J. Legal Med. 118, 75–82.
Thistlethwaite W. A., Moses L. M., Hoffbuhr K. C., Devaney J. M., and Hoffman E. P. (2003) Rapid genotyping of common MeCP2 mutations with an electronic DNA microchip using serial differential hybridization. J. Mol. Diag. 5, 121–126.
Santacroce R., Ratti A., Caroli F., Foglieni B., Ferraris A., Cremonesi L., et al. (2002) Analysis of clinically relevant single-nucleotide polymorphisms by use of microelectronic array technology. Clin. Chem. 48, 2124–2130.
Cooper K. L. F., and Goering R. V. (2003) Development of a universal probe for electronic microarray and its application in characterization of the Staphylococcus aureus polC gene. J. Mol. Diag. 5, 28–33.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
BØrsting, C., Sanchez, J.J., Morling, N. (2005). SNP Typing on the NanoChip Electronic Microarray. In: Carracedo, A. (eds) Forensic DNA Typing Protocols. Methods in Molecular Biology, vol 297. Humana Press. https://doi.org/10.1385/1-59259-867-6:155
Download citation
DOI: https://doi.org/10.1385/1-59259-867-6:155
Publisher Name: Humana Press
Print ISBN: 978-1-58829-264-3
Online ISBN: 978-1-59259-867-0
eBook Packages: Springer Protocols