Abstract
An AFM-imaging-based method for single nucleotide polymorphism (SNP) analysis is described. A stem-loop-forming 34-mer oligonucleotide (p34s) was designed. P34s contains the complementary sequence for K-ras (5′-GGT GGC-3′, t6G), one of the human oncogenes, at the 5′-end for target-recognition and five successive phosphorothioate linkages in the loop. The functional probe, either alone or hybridized with target DNA (p34s/t6G), relaxed upon treatment with “opener” DNA. The template/target DNA interstrand hybridization product is covalently connected by ligase if the correct target is used, but not hybridized species including mismatches. With these results, developed was a solid-phase SNP assay by transferring an aliquot of the product onto an Au(111) substrate for self-assembly, followed by AFM imaging. Clear contrasts that allow the detection of SNPs, were observed for the ligated and non-ligated species representing the loop-to-linear conformational change. Simple statistical surface-roughness analysis determined the lowest concentration of the sample to be 5 × 10−10 M, whose necessary sample quantity was 5 fmol.
Similar content being viewed by others
References
T. A. Brown, “Genomes 3”, 2006, Chaps. 3 and 4, Garland Science, New York.
M. Endo and H. Sugiyama, ChemBioChem., 2009, 10, 2420.
S. Tyagi and F. R. Kramer, Nat. Biotechnol., 1996, 14, 303.
A. S. Piatek, S. Tyagi, A. C. Pol, A. Telenti, L. P. Miller, F. R. Kramer, and D. Alland, Nat. Biotechnol., 1998, 16, 359.
H. Du, C. M. Strohsahl, J. Camera, B. L. Miller, and T. D. Krauss, J. Am. Chem. Soc., 2005, 127, 7932.
M. P. Raphael, J. A. Christodoulides, S. N. Qadri, S. A. Qadri, M. M. Miller, L. K. Kurihara, and J. M. Byers, Biosens. Bioelectron., 2008, 24, 888.
S. A. E. Marras, F. R. Kramer, and S. Tyagi, Genet. Anal. Biomol. Eng., 1999, 14, 151.
A. Tsourkas, M. A. Behlke, Y. Xu, and G. Bao, Anal. Chem,. 2003, 75, 3697.
Y. Wu, C. J. Yang, L. L. Moroz, and W. Tan, Anal. Chem., 2008, 80, 3025.
C. B. Swearingen, D. P. Wernette, D. M. Cropek, Y. Lu, J. V. Sweedler, and P. W. Bohn, Anal. Chem., 2005, 77, 442.
R. Y. Lai, E. T. Lagally, S. H. Lee, H. T. Soh, K. W. Plaxco, and A. J. Heeger, Proc. Natl. Acad. Sci. U. S. A., 2006, 103, 4017.
M. Zuker, Nucleic Acids Res., 2003, 31, 3406.
W. A. Kibbe, Nucleic Acids Res., 2007, 35, W43.
J. B. Schlenoff, M. Li, and H. Ly, J. Am. Chem. Soc., 1995, 117, 12528.
K. Nakano, T. Yoshitake, Y. Yamashita, and E. F. Bowden, Langmuir, 2007, 23, 6270.
Image SXM, S. D. Barrett, 2008, http://www.ImageSXM.org.uk/.
K. Nakano, H. Yamanouchi, H. Yoshinaga, N. Soh, and T. Imato, Chem. Commun., 2010, 46, 5683.
T. Ihara, M. Nakayama, M. Murata, K. Nakano, and M. Maeda, Chem. Commun., 1997, 1609.
M. Nakayama, T. Ihara, K. Nakano, and M. Maeda, Talanta, 2002, 56, 857.
W. Saenger, “Principles of Nucleic Acid Structure”, 1984, Springer-Verlag, New York, 242.
K. Nakano, Y. Katasumi, N. Soh, and T. Imato, Bull. Chem. Soc. Jpn., 2010, 3, 273.
K. Nakano, H. Matsunaga, M. Murata, N. Soh, and T. Imato, Anal. Sci., 2009, 25, 993.
J. G. Hacia, B. Sun, N. Hunt, K. Edgemon, D. Mosbrook, C. Robbins, S. P. A. Fodor, D. A. Tagle, and F. S. Collins, Genome Res., 1998, 8, 1245.
D. G. Wang, J. B. Fan, C. J. Siao, A. Berno, P. Young, R. Sapolsky, G. Ghandour, N. Perkins, E. Winchester, J. Spencer, L. Kruglyak, L. Stein, L. Hsie, T. Topaloglou, E. Hubbell, E. Robinson, M. Mittmann, M. S. Morris, N. Shen, D. Kilburn, J. Rioux, C. Nusbaum, S. Rozen, T. J. Hudson, R. Lipshutz, M. Chee, and E. S. Lander, Science, 1998, 280, 1077.
S. Tyagi, D. P. Bratu, and F. R. Kramer, Nat. Biotechnol., 1998, 16, 49.
X. Chen, K. J. Livak, and P. Y. Kwok, Genome Res., 1998, 8, 549.
M. A. Iannone, J. D. Taylor, J. Chen, M. S. Li, P. Rivers, K. A. Slentz-Kesler, and M. P. Weiner, Cytometry, 2000, 39, 131.
X. Chen, B. Zehnbauer, A. Gnirke, and P. Y. Kwok, Proc. Natl. Acad. Sci. U. S. A., 1997, 94, 10756.
J. B. Fan, X. Chen, M. K. Halushka, A. Berno, X. Huang, T. Ryder, R. J. Lipshutz, D. J. Lockhart, and A. Chakravarti, Genome Res., 2000, 10, 853.
J. Chen, M. A. Iannone, M. S. Li, J. D. Taylor, P. Rivers, A. J. Nelsen, K. A. Slentz-Kesler, A. Roses, and M. P. Weiner, Genome Res., 2000, 10, 549.
T. Morris, B. Robertson, and M. Gallagher, J. Clin. Microbiol., 1996, 34, 2933.
K. J. Livak, J. Marmaro, and J. A. Todd, Nat. Genet., 1995, 9, 341.
V. Lyamichev, A. L. Mast, J. G. Hall, J. R. Prudent, M. W. Kaiser, T. Takova, R. W. Kwiatkowski, T. J. Sander, M. de Aruda, D. A. Arco, B. P. Neri, and M. A. D. Brow, Nat. Biotechnol., 1999, 17, 292.
V. Lyamichev, M. A. D. Brow, V. E. Varvel, and E. Dahlberg, Proc. Natl. Acad. Sci. U. S. A., 1999, 96, 6143.
T. J. Griffin, J. G. Hall, J. R. Prudent, and L. M. Smith, Proc. Natl. Acad. Sci. U. S. A., 1999, 96, 6301.
T. Ando, T. Uchihashi, and T. Fukuma, Prog. Surf. Sci., 2008, 83, 337.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Yoshinaga, H., Nakano, K., Soh, N. et al. AFM-Imaging Diagnosis Method for Single Nucleotide Polymorphism Using Molecular Beacon DNA as an Intramolecular Ligation Template of Target DNA and a Viewable Indicator. ANAL. SCI. 28, 939–945 (2012). https://doi.org/10.2116/analsci.28.939
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.2116/analsci.28.939