Kras gene codon 12 mutation detection enabled by gold nanoparticles conducted in a nanobioarray chip

Analytical Biochemistry

Volumn 448, Issue 1, 2014, Pages 58-64

  Sedighi, Abootaleb ^a   Li, Paul C H ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Gold nanoparticle; Kras gene; Microarray; Nanobioarray chip; Single nucleotide polymorphism; Target DNA

Indexed keywords

FIBER OPTIC SENSORS; GENES; GLASS; GLASS INDUSTRY; GOLD NANOPARTICLES; METAL NANOPARTICLES; MICROARRAYS; NANOFLUIDICS; OLIGONUCLEOTIDES; POLYDIMETHYLSILOXANE; POLYMORPHISM; PROBES; SILICONES;

K-RAS GENE; MUTATION DETECTION; NANOBIOARRAY CHIP; NANOFLUIDIC CHANNEL; OLIGONUCLEOTIDE PROBES; POLYDIMETHYLSILOXANE PDMS; SINGLE NUCLEOTIDE POLYMORPHISMS; TEMPERATURE OPTIMIZATION;

POLYMERASE CHAIN REACTION;

DIMETICONE; GOLD NANOPARTICLE; K RAS PROTEIN; OLIGONUCLEOTIDE;

ALLELE; ARTICLE; CODON; CONTROLLED STUDY; DNA HYBRIDIZATION; GENE; GENE MUTATION; HIGH TEMPERATURE; MOLECULAR PROBE; NANOBIOARRAY CHIP; NANOCHIP; NANOFLUIDICS; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; ROOM TEMPERATURE; SURFACE PROPERTY; WILD TYPE;

GOLD NANOPARTICLE; KRAS GENE; MICROARRAY; NANOBIOARRAY CHIP; SINGLE NUCLEOTIDE POLYMORPHISM; TARGET DNA;

ALLELES; CODON; DNA; GENETIC TECHNIQUES; GOLD; HUMANS; METAL NANOPARTICLES; MICROFLUIDIC ANALYTICAL TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTO-ONCOGENE PROTEINS; RAS PROTEINS; TEMPERATURE;

EID: 84891672470     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2013.11.019     Document Type: Article

References (34)

1. F.S. Collins Medical and societal consequences of the Human Genome Project N. Engl. J. Med. 341 1999 28 37 (Pubitemid 29293718)
2. S. White, M. Kalf, Q. Liu, M. Villerius, D. Engelsma, M. Kriek, E. Vollebregt, B. Bakker, G.J.B. van Ommen, M.H. Breuning, and J.T. den Dunnen Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization Am. J. Hum. Genet. 71 2002 365 374 (Pubitemid 34800252)
3. S. Ye, S. Dhillon, X. Ke, A.S. Collins, and Y.N.M. Day An efficient procedure for genotyping single nucleotide polymorphisms Nucleic Acids Res. 29 2001 7773 7782
4. C.J. Allegra, J.M. Jessup, M.R. Somerfield, S.R. Hamilton, E.H. Hammond, D.F. Hayes, P.K. McAllister, R.F. Morton, and R.L. Schilsky American Society of Clinical Oncology provisional clinical opinion: testing for KRAS gene mutations in patients with metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy J. Clin. Oncol. 27 2009 2091 2096
5. K. Sato, M. Onoguchi, Y. Sato, K. Hosokawa, and M. Maeda Non-cross-linking gold nanoparticle aggregation for sensitive detection of single-nucleotide polymorphisms: optimization of the particle diameter Anal. Biochem. 350 2006 162 164 (Pubitemid 43247640)
6. N.N. Iscove, M. Barbara, M. Gu, M. Gibson, C. Modi, and N. Winegarden Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA Nat. Biotechnol. 20 2002 940 943 (Pubitemid 35001134)
7. L. Wang, and P.C.H. Li Microfluidic DNA microarray analysis: a review Anal. Chim. Acta 687 2011 12 27
8. S. Russell, and L.A. Meadows Microarray Technology in Practice 2009 Academic Press/Elsevier Amsterdam
9. A. Sedighi, and P.C.H. Li Challenges and future trends in DNA microarray analysis C. Simó, A. Cifuentes, V. García-Cañas, Fundamentals of Advanced Omic Technologies: From Genes to Metabolites 2013 Elsevier Science San Diego
10. C. Situma, Y. Wang, M. Hupert, F. Barany, R.L. McCarley, and S.A. Soper Fabrication of DNA microarrays onto poly(methyl methacrylate) with ultraviolet patterning and microfluidics for the detection of low-abundant point mutations Anal. Biochem. 340 2005 123 135 (Pubitemid 40404108)
11. A. Sedighi, L. Wand, and P.C.H. Li 2D nanofluidic bioarray for nucleic acid analysis K. Iniewski, S. Selimovic, Nanopatterning and Nanoscale Devices for Biological Applications 2013 Taylor & Francis/CRC Press Boca Raton, FL
12. O.Y.F. Henry, and C.K. O-Sullivan Rapid DNA hybridization in microfluidics Trends Anal. Chem. 33 2012 9 22
13. S. Link, and M.A. El-Sayed Spectral properties and relaxation dynamics of surface plasmon electronic oscillations in gold and silver nanodots and nanorods J. Phys. Chem. B 103 1999 8410 8426 (Pubitemid 129613873)
14. R. Elghanian, J.J. Storhoff, R.C. Mucic, R.L. Letsinger, and C.A. Mirkin Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles Science 277 1997 1078 1081 (Pubitemid 27371624)
15. K. Sato, K. Hosokawa, and M. Maeda Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization J. Am. Chem. Soc. 125 2003 8102 8103 (Pubitemid 36828566)
16. K. Sato, K. Hosokawa, and M. Maeda Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions Nucleic Acids Res. 33 2005 e4
17. C. Wang, Y. Chen, T. Wang, Z. Ma, and Z. Su Biorecognition-driven self-assembly of gold nanorods: a rapid and sensitive approach toward antibody sensing Chem. Mater. 19 2007 5809 5811 (Pubitemid 350241408)
18. C.C. Huang, Y.F. Huang, Z. Cao, W. Tan, and H.T. Chang Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors Anal. Chem. 77 2005 5735 5741 (Pubitemid 41266072)
19. H.X. Li, and L. Rothberg Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles Proc. Natl. Acad. Sci. USA 101 2004 14036 14039 (Pubitemid 39305025)
20. H.X. Li, and L.J. Rothberg Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction J. Am. Chem. Soc. 126 2004 10958 10961 (Pubitemid 39180580)
21. H. Lee, S.W. Joob, S.Y. Lee, C.H. Lee, K.A. Yoon, and K. Lee Colorimetric genotyping of single nucleotide polymorphism based on selective aggregation of unmodified gold nanoparticles Biosens. Bioelectron. 26 2010 730 735
22. P.C. Ray Diagnostics of single base-mismatch DNA hybridization on gold nanoparticles by using the hyper-Rayleigh scattering technique Angew. Chem. Int. Ed. 45 2006 1151 1154 (Pubitemid 44104911)
23. L. Wang, and P.C.H. Li Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device Biomicrofluidics 4 2010 032209
24. L. Wang, and P.C.H. Li Optimization of a microfluidic microarray device for the fast discrimination of fungal pathogenic DNA Anal. Biochem. 400 2010 282 288
25. A. Sedighi, and P.C.H. Li Kinetic and thermodynamic analyses of DNA hybridization reveal the mechanism of gold nanoparticle-assisted single base-pair discrimination in the Nanobioarray chip μTAS 2013 865 867
26. L. Yanez, J. Groffen, and D.M. Valenzuela C-K-ras mutations in human carcinomas occur preferentially in codon 12 Oncogene 1 1987 315 318 (Pubitemid 17149194)
27. L. Wang, and P.C.H. Li Flexible microarray construction and fast DNA hybridization conducted on a microfluidic chip for greenhouse plant fungal pathogen detection J. Agric. Food Chem. 55 2007 10509 10516
28. H. Urakawa, S. El Fantroussi, H. Smidt, J.C. Smoot, E.H. Tribou, J.J. Kelly, P.A. Noble, and D.A. Stahl Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays Appl. Environ. Microbiol. 69 2003 2848 2856 (Pubitemid 36560365)
29. H. Chen, L. Wang, and P.C.H. Li Nucleic acid microarrays created in the double-spiral format on a circular microfluidic disk Lab Chip 8 2008 826 829 (Pubitemid 351585465)
30. X.Y. Peng, P.C.H. Li, H.Z. Yu, M. Parameswaran, and W.L. Chou Spiral microchannels on a CD for DNA hybridizations Sens. Actuat. B 128 2007 64 69 (Pubitemid 350051791)
31. R. Zinsky, S. Bolukbas, H. Bartsch, J. Schirren, and A. Fisseler-Eckhoff Analysis of KRAS mutations of exon 2 codons 12 and 13 by SNaPshot analysis in comparison to common DNA sequencing Gastroenterol. Res. Pract. 2010 2010 789363
32. M. Maekawa, T. Nagaoka, T. Taniguchi, H. Higashi, H. Sugimura, K. Sugano, H. Yonekawa, T. Satoh, T. Horii, N. Shirai, A. Takeshita, and T. Kanno Three-dimensional microarray compared with PCR-single-strand conformation polymorphism analysis/DNA sequencing for mutation analysis of K-ras codons 12 and 13 Clin. Chem. 50 2004 1322 1327 (Pubitemid 38970638)
33. J.H. Park, I.J. Kim, H.C. Kang, Y. Shin, H.W. Park, S.G. Jang, J.L. Ku, S.B. Lim, S.Y. Jeong, and J.G. Park Oligonucleotide microarray-based mutation detection of the K-ras gene in colorectal cancers with use of competitive DNA hybridization Clin. Chem. 50 2004 1688 1691 (Pubitemid 39121247)
34. P.C. McCabe Production of single-stranded DNA by asymmetric PCR M.A. Innis, D.H. Gelfand, J.J. Sninsky, T.J. White, PCR Protocols 1990 Academic Press San Diego