Measurement of Temperature Induced Unfolding of DNA Hairpins by Microcantilever Sensors

Joseph D. Ng, Jeffrey J. Dowell, Asit K. Kar, Karolyn Hansen, Thomas Thundat, Michael A. George

Department of Biology, University of Dayton, Dayton, USA.
Department of Chemical and Materials Engineering University of Alberta, Edmonton, Canada.
Department of Chemistry, University of Alabama, Huntsville, USA.
Laboratory for Structural Biology and the Department of Biological Science, University of Alabama, Huntsville, USA.

DOI: 10.4236/ojab.2013.23010                

Abstract

The technical feasibility of monitoring DNA melting and cooling transitions using a microcantilever substrate has been demonstrated and these results were compared with those measured in solution by circular dichroism. DNA hairpins have been immobilized on the surface of gold-coated microcantilever surfaces and their DNA melting and cooling transitions were monitored by nanomechanical deflections. The hairpins comprised of a 16 base-pair GACA repeat motif stem duplex with a 29
nucleotide variable region. Microcantilever deflection profiles, measured by the microcantilever response as a function of temperature, were unique to different hairpins indicative of the molecules’ general stability and denaturation characteristics. The major melting and cooling transition temperatures for all three immobilized oligonucleotides were between 41^。C - 52^。C. The composition and flexibility of the DNA stem loops were shown to influence the thermal transitions.

Keywords

Hairpin DNA; Microcantilever; Thermal Melting; Unfolding

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	M. Alvarez, L. G. Carrascosa, M. Moreno, A. Calle, A. Zaballos, L. M. Lechuga, A. C. Martinez and J. Tamayo, “Nanomechanics of the Formation of DNA Self-Assembled Monolayers and Hybridization on Micro-Cantilevers,” Langmuir, Vol. 20, No. 22, 2004, pp. 9663-9668. doi:10.1021/la0489559
[2]	G. Wu, H. Ji, K. Hansen, T. Thundat, R. Datar, R. Cote, M. F. Hagan, A. K. Chakraborty and A. Majumdar, “Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 4, 2001, pp. 1560-1564. doi:10.1073/pnas.98.4.1560
[3]	A. Kooser, K. Manygoats, M. P. Eastman and T. L. Porter, “Investigation of the Antigen Antibody Reaction between Anti-Bovine Serum Albumin (a-BSA) and Bovine Serum Albumin (BSA) Using Piezoresistive Microcantilever Based Sensors,” Biosensors and Bioelectronics, Vol. 19, No. 5, 2003, pp. 503-508.
[4]	C. Grogan, R. Raiteri, G. M. O’Connor, T. J. Glynn, V. Cunningham, M. Kane, M. Charlton and D. Leech, “Characterisation of an Antibody Coated Micro-Cantilever as a Potential Immuno-Based Biosensor,” Biosensors and Bioelectronics, Vol. 17, No. 3, 2002, pp. 201-207. doi:10.1016/S0956-5663(01)00276-7
[5]	F. Liu, Y. Zhang and Z. C. Ou-Yang, “Flexoelectric Origin of Nanomechanic Deflection in DNA-Microcantilever System,” Biosensors and Bioelectronics, Vol. 18, No. 5-6, 2003, pp. 655-660. doi:10.1016/S0956-5663(03)00047-2
[6]	M. Hegner and Y. Arntz, “Advanced Biosensing Using Micromechanical Cantilever Arrays,” Methods in Molecular Biology, Vol. 242, 2004, pp. 39-49.
[7]	J. Pei, F. Tian and T. Thundat, “Glucose Biosensor Based on the Microcantilever,” Analytical Chemistry, Vol. 76, No. 2, 2004, pp. 292-297. doi:10.1021/ac035048k
[8]	R. McKendry, J. Zhang, Y. Arntz, T. Strunz, M. Hegner, H. P. Lang, M. K. Baller, U. Certa, E. Meyer, H. J. Guntherodt and C. Gerber, “Multiple Label-Free Biodetection and Quantitative DNA-Binding Assays on a Nanomechanical Cantilever Array,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 15, 2002, pp. 9783-9788. doi:10.1073/pnas.152330199
[9]	C. A. Savran, S. M. Knudsen, A. D. Ellington and S. R. Manalis, “Micromechanical Detection of Proteins Using Aptamer-Based Receptor Molecules,” Analytical Chemistry, Vol. 76, No. 11, 2004, pp. 3194-3198. doi:10.1021/ac049859f
[10]	M. Zuker, “Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction,” Nucleic Acids Research, Vol. 31, No. 13, 2003, pp. 3406-3415. doi:10.1093/nar/gkg595