Construction of branched DNA for SNP determination on glass-chip using photochemical ligation

Biochip Journal

Volumn 5, Issue 3, 2011, Pages 206-213

  Ahmed, Minhaz Uddin ^a,b   Yoshimura, Yoshinaga ^a   Hossain, M Mosharraf ^c   Tamiya, Eiichi ^c   Fujimoto, Kenzo ^a  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b INRS EMT   (Canada)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

Branched DNA; Glass chip; ODN; Photochemical ligation; SNP

Indexed keywords

CHEMICAL DETECTION; DIAGNOSIS; DNA;

BRANCHED DNA; GLASS CHIP; ODN; PHOTOCHEMICAL LIGATION; SNP;

GLASS;

ARTICLE; BRANCHED DNA SIGNAL AMPLIFICATION ASSAY; DNA DETERMINATION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; ONCOGENE K RAS; PHOTOCHEMISTRY; PROCESS OPTIMIZATION; REACTION ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 80052139681     PISSN: 19760280     EISSN: 20927843     Source Type: Journal    
DOI: 10.1007/s13206-011-5303-0     Document Type: Article

References (47)

1. Stephens, J. C. Single-nucleotide polymorphisms, haplotypes, and their relevance to pharmacogenetics. Molecular Diagnosis4, 309-317 (1999).
2. McCarthy, J. J. & Hilfiker, R. The use of single-nucleotide polymorphism maps in pharmacogenomics. Nature Biotech. 18, 505-508 (2000).
3. Twyman, R. M. SNP discovery and typing technologies for pharmacogenomics. Current Topics in Medicinal Chemistry4, 1421-1429 (2004).
4. Evans, W. E. & Relling, M. V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science286, 487-491 (1999).
5. Venter, J. C. et al. The sequence of the human genome. Science291, 1304-1351 (2001).
6. Conti, R., Veenstra, R. D. L., Armstrong, K., Lesko, L. J. & Grosse, S. D. Personalized medicine and genomics: challenges and opportunities in assessing effectiveness, cost-effectiveness, and future research priorities. Med. Decis Making doi: 10. 1177/0272989X093 47014 (2010).
7. Haff, L. & Smirnov, I. Multiplex genotyping of PCR products with MassTag-labeled primers. Nucl. Acids Res. 25, 3749-3750 (1997).
8. Ross, P., Hall, L., Smirnov, I. & Haff, L. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16, 1347-1351 (1998).
9. Rao, V. Strategies for direct sequencing of PCR-amplified DNA. Genome Research4, S15-S23 (1994).
10. Syvänen, A. From gels to chips: "Minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphims. Human Mutation13, 1-10 (1999).
11. Yershov, G. et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Nat. Aca. Sci. 93, 4913 (1996).
12. Newton, C. et al. Analysis of any point mutation in DNA. The amplification refractry mutation system (ARMS). Nucleic Acids Research17, 2503-2516 (1989).
13. Lndegren, U., Kaiser, R., Sanders, J. & Hood, L. A ligase-mediated gene detection technique. Science241, 1077-1080 (1988).
14. Iannone, M. A. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry39, 131-140 (2000).
15. Ahmed, M. U. et al. Electrochemical DNA biosensor using a disposable electrochemical printed (DEP) chip for the detection of SNPs from unpurified PCR amplicons. The Analyst132, 431-438 (2007).
16. Chen, X., Levine, L. & Kwok, P. Fluorescence polarization in homogeneous nuclei acid analysis. Genome Research9, 492-498 (1999).
17. Tyagi, S. & Kramer, F. Molecular beacons: probes that fluoresce upon hybridzation. Nature Biotechnology14, 303-308 (1996).
18. Tyagi, S., Bratu, D. & Kramer, F. Multicolor molecular beacons for allele discriination. Nature Biotechnology16, 49-53 (1998).
19. Zhou, G. H. et al. Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Research29, e93 (2001).
20. Ogasawara, S. & Fujimoto, K. SNP genotyping by using photochemical ligation. Angewandte Chemie (International ed. Print)45, 4512-4515 (2006).
21. Elghanian, R., Storhoff, J., Mucic, R., Letsinger, R. & Mirkin, C. A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science277, 1078-1081 (1997).
22. Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature382, 607-609 (1996).
23. Storhoff, J., Lucas, A., Garimella, V., Bao, Y. & Müller, U. Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes. Nature Biotechnology22, 883-887 (2004).
24. Li, J. et al. A colorimetric method for point mutation detection using high-fidelity DNA ligase. Nucl. Acids Res. 33, e168 (2005).
25. Han, M., Lytton-Jean, A., Oh, B., Heo, J. & Mirkin, C. Towards polymer-based hydrogen storage materials: engineering ultramicroporous cavities within polymers of intrinsic microporosity. Angewandte Chemie45, 1804-1807 (2006).
26. Frutos, A., Smith, L. & Corn, R. Enzymatic ligation reactions of DNA "Words" on surfaces for DNA computing. J. Am. Chem. Soc. 120, 10277-10282 (1998).
27. Nilsson, M., Barbany, G., Antson, D., Gertow, K. & Landegren, U. Enhanced detection and distinction of RNA by enzymatic probe ligation. Nature Biotechnology18, 791-793 (2000).
28. Zhan, Z. Y. J. & Lynn, D. G. Chemical amplification through template-directed synthesis. J. Am. Chem. Soc. 119, 12420-12421 (1997).
29. Luo, P., Leitzel, J. C., Zhan, Z.-Y. J. & Lynn, D. G. Analysis of the structure and stability of a backbone-modified oligonucleotide: implications for avoiding product inhibition in catalytic template-directed synthesis. J. Am. Chem. Soc. 120, 3019-3031 (1998).
30. Sando, S. & Kool, E. T. Imaging of RNA in bacteria with self-ligating quenched probes. J. Am. Chem. Soc. 124, 2096-2097 (2002).
31. Rozenman, M. M. & Liu, D. R. DNA-templated synthesis in organic solvents. ChemioChem. 7, 253-256 (2006).
32. Li, X. & Liu, D. R. DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. Angewandte Chemie116, 4956-4979 (2004).
33. Li, X. & Liu, D. R. DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. Angewandte Chemie International Edition43, 4848-4870 (2004).
34. Fujimoto, K., Matsuda, S., Takahashi, N. & Saito, I. Template-directed photoreversible ligation of deoxyoligonucleotides via 5-Vinyldeoxyuridine. J. Am. Chem. Soc. 122, 5646-5647 (2000).
35. Ogasawara, S. & Fujimoto, K. Multiple-branched DNA (MB-DNA) by reversible photochemical ligation. ChemBioChem. 6, 1756-1760 (2005).
36. Ogino, M., Yoshimura, Y., Nakazawa, A., Saito, I. & Fujimoto, K. Template-directd DNA photoligation via alpha-5-cyanovinyldeoxyuridine. Organic Letters7, 2853-2856 (2005).
37. Yoshimura, Y., Noguchi, Y., Sato, H. & Fujimoto, K. Template-directed DNA photoligation in rapid and selective detection of RNA point mutations. Chem-BioChem. 7, 598-601 (2006).
38. Yoshimura, Y., Noguchi, Y. & Fujimoto, K. Highly sequence specific RNA terminal labeling by DNA photoligation. Organic & Biomolecular Chemistry5, 139-142 (2007).
39. Urdea, M. Branched DNA signal amplification. Nature Biotechnology12, 926-928 (1994).
40. Collins, M. et al. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucl. Acids Res. 25, 2979-2984 (1997).
41. Horn, T., Chang, C. & Urdea, M. Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays. Nucl. Acids Res., 25, 4842-4849 (1997).
42. Ardyen, S., Jonoska, P. & Seeman, N. C. The construction of graphs whose edges are DNA helix axes. J. Am. Chem. Soc. 126, 6648-6657 (2004).
43. Scheffler, M., Dorenbeck, A., Jordan, S., Wüstefeld, M. & von Kiedrowski, G. Self-assembly of trisoligonucleotidyls "nano-acetylene" and "nano-cyclobutadiene". Angewandte Chemie111, 3513-3518 (1999).
44. Mitra, D., Cesare, N. D. & Sleiman, H. F. Self-assembly of cyclic metal-DNA nanostructures using ruthenium tris(bipyridine)-branched oligonucleotides. Angewandte Chemie116, 5928-5932 (2004).
45. Scheffler, M., Dorenbeck, A., Jordan, S., Wüstefeld, M. & Kiedrowski, G. V. Self-assembly of trisoligonucleotidyls: the case for nano-acetylene and nano-cyclobutadiene. Angeandte Chemie International Edition38, 3311-3315 (1999).
46. Nakamura, F. et al. Preparation of a branched DNA self-assembled monolayer toward sensitive DNA biosensors. Nano Letters3, 1083-1086 (2003).
47. Becerril, H. A. et al. DNA-templated three-branched nanostructures for nanoelectronic devices. J. Am. Chem. Soc. 127, 2828-2829 (2005).