Discrimination of single nucleotide mutation by using a new class of immobilized shared-stem double-stranded DNA probes

Journal of Biomedical Nanotechnology

Volumn 7, Issue 5, 2011, Pages 640-647

  Bai, Yunfei ^a   Lin, Dai ^a   Han, Qin ^a   Jia, Yaojuan ^a   Tu, Jing ^a   Luo, Junfeng ^a   Ge, Qinyu ^b   Zhang, Dingdong ^c   Lu, Zuhong ^a,b  

^a SOUTHEAST UNIVERSITY   (China)

^b Southeast University   (China)

^c JINLING INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Double stranded DNA microarray; Shared stem DNA probe; Single nucleotide mutation

Indexed keywords

AGAROSE; ANNEALING PROPERTIES; DISCRIMINATION RATIO; DOUBLE STRANDED DNA; HAIRPIN-LIKE; PERFECT MATCHES; SHARED-STEM DNA PROBE; SINGLE NUCLEOTIDES;

CHROMOPHORES; DNA; NUCLEOTIDES;

PROBES;

DOUBLE STRANDED DNA; SHORT HAIRPIN RNA; DNA; MAGNESIUM;

AGAR GEL ELECTROPHORESIS; ARTICLE; CHROMATOPHORE; DNA HYBRIDIZATION; DNA MICROARRAY; DNA PROBE; MISMATCH REPAIR; NUCLEIC ACID IMMOBILIZATION; NUCLEOTIDE SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; BASE MISPAIRING; CONFORMATION; FLUORESCENCE; GENETICS; HOMOZYGOTE; HUMAN; METABOLISM; METHODOLOGY; MUTATION; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE;

BASE PAIR MISMATCH; DNA; DNA PROBES; FLUORESCENCE; HOMOZYGOTE; HUMANS; MAGNESIUM; MUTATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; TEMPERATURE;

EID: 84863064277     PISSN: 15507033     EISSN: 15507041     Source Type: Journal    
DOI: 10.1166/jbn.2011.1327     Document Type: Article

References (34)

1. S. C. Christopher, A. E. Michael, K. Leonid, and A. N. Deborah, Mapping complex disease loci in whole-genome association studies. Nature 429, 446 (2004).
2. P. Y. Kwok, Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics. Hum. Genet. 2, 235 (2001).
3. L. Cheng, Q. Ge, B. Sun, P. Yu, X. Ke, and Z. Lu, Polyacrylamide gel-based microarray: A novel method applied to the association study between the polymorphisms of BDNF gene and autism. J. Biomed. Nanotechnol. 5, 542 (2009).
4. L. Tian, S. Li, H. Liu, Z. Wang, and N. He, An automated magstation for High-throughput single nucleotide polymorphism genotyping and the dual-color hybridization. J. Biomed. Nanotechnol. 5, 511 (2009).
5. S. Li, H. Liu, Z. Wang, P. Hou, Y. Guo, Q. He, and N. He, Magnetic particles-based high-throughput genotyping method with dual-color fluorescence hybridization. Anal. Biochem. 359, 277 (2006).
6. T. Pastinen, M. Raitio, K. Lindroos, P. Tainola, L. Peltonen, and A. C. Syvanen, A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10, 1031 (2000).
7. H. Liu, S. Li, L. Liu, L. Tian, and N. He, Multiplex single nucleotide polymorphisms genotyping using solid-phase single base extension on magnetic nanoparticles. Anal. Biochem. 386, 126 (2009).
8. F. Erdogan, R. Kirchner, W. Mann, H. H. Ropers, and U. A. Nuber, Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays. Nucleic Acids Res. 29, e36 (2001).
9. J. N. Hirschhorn, P. Sklar, K. Lindblad-Toh, Y. M. Lim, M. Ruiz-Gutierrez, S. Bolk, B. Langhorst, S. Schaffner, E. Winchester, and E. S. Lander, SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. 97, 12164 (2000).
10. K. Lindblad-Toh, D. M. Tanenbaum, M. J. Daly, E. Winchester, W. O. Lui, A. Villapakkam, S. E. Stanton, C. Larsson, T. J. Hudson, B. E. Johnson, E. S. Lander, and M. Meyerson, Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol. 18, 1001 (2000).
11. D. Jaccoud, K. Peng, D. Feinstein, and A. Kilian, Diversity arrays: A solid state technology for sequence information independent genotyping. Nucleic Acids Res. 29, e25 (2001).
12. H. Liu, S. Li, L. Liu, L. Tian, and N. He, An integrated and sensitive detection platform for biosensing application based on Fe@Au magnetic nanoparticles as bead array carries. Biosens. Bioelectron. 26, 1442 (2010).
13. S. Li, H. Liu, L. Liu, L. Tian, and N. He, A novel automated assay with dual-color hybridization for single-nucleotide 4 polymorphisms genotyping on gold magnetic nanoparticle array. Anal. Biochem. 405, 141 (2010).
14. H. Liu, S. Li, M. Ji, L. Nie, J. Chen, Y. Miao, and N. He, Fabrication and application of single nucleotide polymorphisms library on magnetic nanoparticles using adaptor PCR. J. Nanosci. Nanotechnol. 8, 405 (2008).
15. S. Li, M. Ji, N. He, and Z. Lu, Application of microarray-based method for methylenetetrahydrofolate reductase (MTHFR) polymorphisms in the risk of gastric carcinoma in east china population. J. Nanosci. Nanotechnol. 7, 3245 (2007).
16. 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 using competitive DNA hybridization (CDH). Clin. Chem. 50, 1688 (2004).
17. J. F. Andrew, N. B. Viacheslav, B. Allan, J. Runchun, R. Joanne, T. H. Noel Ellis, and I. Peter, A microarray based high throughput molecular marker genotyping method: The tagged microarray marker (TAM) approach. Nucleic Acids Res. 31, e115 (2003).
18. F. Zhang, S. W. Hu, J. Huang, H. Wang, Z. Wen, G. Y. Yao, and S. Q. Wang, Development and clinical evaluation of oligonucleotide microarray for HLA-AB genotyping. Pharmacogenomics 7, 973 (2006).
19. S. Tyagi and F. R. Kramer, Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303 (1996).
20. B. T. Grégoire, K. Oleg, and L. Albert, Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl. Acad. Sci. 95, 8602 (1998).
21. S. Tyagi, D. P. Bratu, and F. R. Kramer, Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49 (1998).
22. J. A. Vet, A. R. Majithia, S. A. Marras, S. Tyagi, S. Dube, B. J. Poiesz, and F. R. Kramer, Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc. Natl. Acad. Sci. 96, 6394 (1999).
23. I. Täpp, L. Malmberg, E. Rennel, M. Wik, and A. C. Syvänen, Homogeneous scoring of single nuclceotide polymorphism markers: The 5′-nuclease "TaqMan" assay versus Molecular Beacon probes. BioTechniques 28, 732 (2000).
24. H. Wang, J. Li, H. Liu, Q. Liu, Q. Mei, Y. Wang, J. Zhu, N. He, and Z. Lu, Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res. 30, e61 (2002).
25. Y. Wang, H. Wang, L. Gao, H. Liu, Z. Lu, and N. He, Polyacrylamide gel film immobilized molecular beacon array for single nucleotide mismatch detection. J. Nanosci. Nanotechnol. 5, 653 (2005).
26. S. Catherine, J. M. Amanda, A. F. N. Mohamed, and A. S. Steven, Immobilized molecular beacons: A new strategy using UV-activated poly(methyl methacrylate) surfaces to provide large fluorescence sensitivities for reporting on molecular association events. Anal. Biochem. 363, 35 (2007).
27. B. Benjamin, G. Thomas, S. Edzard, and B. Reinhard, Immobilized stem-loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA. Nucleic Acids Res. 33, e101 (2005).
28. A. Tsourkas, M. A. Behlke, and G. Bao, Structure-function relationships of shared-stem and conventional molecular beacons. Nucleic Acids Res. 30, 4208 (2002).
29. J. K Wang, Y. F. Bai, T. X. Li, and Z. Lu, DNA microarrays with unimolecular hairpin double-stranded DNA probes: fabrication and exploration of sequence-specific DNA/protein interactions. J. Biochem. Bioph. Meth. 55, 215 (2003).
30. Y. Bai, Q. Ge, Q. Liu, T. Li, J. Wang, and Z. Lu, A free-labeled method for DNA-binding protein detection using a double-stranded DNA microarray. J. Nanosci. Nanotechnol. 5, 1216 (2005).
31. Y. F. Bai, Q. Y. Ge, Q. J. Liu, T. X. Li, J. K. Wang, and Z. H. Lu, Evaluating the binding affinities of NF-κB p50 homodimer to the wild-type and single-nucleotide mispair DNA binding sites by the unimolecular double-stranded DNA. J. Nanosci. Nanotechnol. 6, 1014 (2006).
32. M. Julian and B. Michael, Design of a combinatorial DNA microarray for protein-DNA interaction studies. BMC Bioinformatics 7, 429 (2006).
33. M. L. Bulyk, DNA microarray technologies for measuring protein-DNA interactions. Curr. Opin. Biotechnol. 17, 422 (2006).
34. Z. Wu, J. Luo, Q. Ge, D. Zhang, Y. Wang, C. Jia, and Z. Lu, Allele-specific extension on microarray for DNA methylation analysis. Anal. Chim. Acta. 603, 199 (2007).