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Unusual DNA Structures Formed on Bare Highly Oriented Pyrolytic Graphite Surfaces Studied by Atomic Force Microscopy

Published online by Cambridge University Press:  27 March 2013

Zhiguo Liu*
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
Lin Zhao
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
Yuangang Zu*
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
Shengnan Tan
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
Yuanlin Wang
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
Yiming Zhang
Affiliation:
Key Laboratory of Forest Plant Ecology of Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China State Engineering Laboratory of Bio-Resource Eco-Utilization, Harbin 150040, People's Republic of China
*
*Corresponding author. E-mail: [email protected]
**Corresponding author. E-mail: [email protected]
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Abstract

It is important to know the detailed DNA structure on carbonaceous surfaces for further application of DNA-functionalized carbonaceous materials in diverse research areas. In this study, the topographic and structural characteristics of the separated single DNA molecules and their assembly on highly oriented pyrolytic graphite (HOPG) surfaces have been investigated by atomic force microscopy (AFM). AFM results indicate that both circular and linear DNA molecules tend to form hexagonal patterns along with some unusual structures that include node, protrusion, cruciform, parallel single-stranded DNA (ssDNA), and compact zigzag. Furthermore, parallel ssDNA patterns and their crossed structures have been obtained under high-temperature conditions. Our AFM results reveal that a bare HOPG surface can induce DNA molecules to form various unusual structures. This finding is helpful for understanding the adsorption behavior of DNA on other carbonaceous surfaces such as carbon nanotubes and graphene. In addition, the hexagonal DNA patterns in this study are similar to those formed on the alkylamine-modified HOPG surface, which implies that a bare HOPG, without any chemical modification, has a strong ability to align biomolecules. This study could expand our knowledge of the diversities of DNA structures and the aligning ability of carbonaceous surfaces.

Type
Biological Applications
Copyright
Copyright © Microscopy Society of America 2013 

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References

Adamcik, J., Klinov, D.V., Witz, G., Sekatskii, S.K. & Dietler, G. (2006). Observation of single-stranded DNA on mica and highly oriented pyrolytic graphite by atomic force microscopy. FEBS Lett 580, 56715675.CrossRefGoogle ScholarPubMed
Adamcik, J., Tobenas, S., Santo, G.D., Klinov, D. & Dietler, G. (2009). Temperature-controlled assembly of high ordered/disordered dodecylamine layers on HOPG: Consequences for DNA patterning. Langmuir 25, 31593162.CrossRefGoogle ScholarPubMed
Brett, A.M.O. & Chiorcea, A.-M. (2003). Atomic force microscopy of DNA immobilized onto a highly oriented pyrolytic graphite electrode surface. Langmuir 19, 38303839.CrossRefGoogle Scholar
Chiorcea-Paquim, A.-M., Corduneanu, O., Oliveira, S.C.B., Diculescu, V.C. & Oliveira-Brett, A.M. (2009). Electrochemical and AFM evaluation of hazard compounds—DNA interaction. Electrochim Acta 54, 19781985.CrossRefGoogle Scholar
Clemmer, C.R. & Beebe, T.P. (1991). Graphite: A mimic for DNA and other biomolecules in scanning tunneling microscope studies. Science 251, 640642.CrossRefGoogle ScholarPubMed
Dubrovin, E.V., Gerritsen, J.W., Zivkovic, J., Yaminsky, I.V. & Speller, S. (2010). The effect of underlying octadecylamine monolayer on the DNA conformation on the graphite surface. Colloids Surf B 76, 6369.CrossRefGoogle ScholarPubMed
Hembacher, S., Giessibl, F.J., Mannhart, J. & Quate, C.F. (2003). Revealing the hidden atom in graphite by low-temperature atomic force microscopy. Proc Natl Acad Sci USA 100, 1253912542.CrossRefGoogle ScholarPubMed
Jiang, X. & Lin, X. (2004). Atomic force microscopy of DNA self-assembled on a highly oriented pyrolytic graphite electrode surface. Electrochem Commun 6, 873879.CrossRefGoogle Scholar
Klinov, D.V., Neretina, T.V., Prokhorov, V.V., Dobrynina, T.V., Aldarov, K.G. & Demin, V.V. (2009). High resolution atomic force microscopy of DNA. Biochemistry (Moscow) 74, 11501154.CrossRefGoogle ScholarPubMed
Liu, Z., Li, Z., Wei, G., Song, Y., Wang, L. & Sun, L. (2005). Imaging DNA molecules on mica surface by atomic force microscopy in air and in liquid. Microsc Res Tech 66, 179185.CrossRefGoogle ScholarPubMed
Liu, Z., Zu, Y., Fu, Y., Zhang, Z. & Meng, R. (2008). Assembling and imaging of His-Tag green fluorescent protein on mica surfaces studied by atomic force microscopy and fluorescence microscopy. Microsc Res Tech 71, 802809.CrossRefGoogle ScholarPubMed
Lu, C.-H., Yang, H.-H., Zhu, C.-L., Chen, X. & Chen, G.-N. (2009). A graphene platform for sensing biomolecules. Angew Chem Int Ed 48, 47854787.CrossRefGoogle ScholarPubMed
Lyubchenko, Y.L. & Shlyakhtenko, L.S. (1997). Visualization of supercoiled DNA with atomic force microscopy in situ . Proc Natl Acad Sci USA 94(2), 496501.CrossRefGoogle ScholarPubMed
Mao, C.D., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000). Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407(6803), 493496.CrossRefGoogle ScholarPubMed
Mirkin, S.M. (1994). H-DNA and related structures. Annu Rev Biophys Biomol Struct 23, 541576.CrossRefGoogle ScholarPubMed
Pong, W.-T. & Durkan, C. (2005). A review and outlook for an anomaly of scanning tunnelling microscopy (STM): Superlattices on graphite. J Phys D 38, R329R355.CrossRefGoogle Scholar
Pope, L.H., Davies, M.C., Laughton, C.A., Roberts, C.J., Tendler, S.J.B. & Williams, P.M. (1999). Intercalation-induced changes in DNA supercoiling observed in real-time by atomic force microscopy. Anal Chim Acta 400, 2732.CrossRefGoogle Scholar
Postma, H.W.C. (2010). Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett 10, 420425.CrossRefGoogle ScholarPubMed
Rippe, K., Mücke, N. & Langowski, J. (1997). Superhelix dimensions of a 1868 base pair plasmid determined by scanning force microscopy in air and in aqueous solution. Nucl Acids Res 25, 17361744.CrossRefGoogle ScholarPubMed
Rivetti, C., Guthold, M. & Bustamante, C. (1996). Scanning force microscopy of DNA deposited onto Mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol 264, 919932.CrossRefGoogle ScholarPubMed
Rose, F., Martin, P., Fujita, H. & Kawakatsu, H. (2006). Adsorption and combing of DNA on HOPG surfaces of bulk crystals and nanosheets: Application to the bridging of DNA between HOPG/Si heterostructures. Nanotechnology 17, 33253332.CrossRefGoogle Scholar
Rosi, N.L. & Mirkin, C.A. (2005). Nanostructures in biodiagnostics. Chem Rev 105, 15471562.CrossRefGoogle ScholarPubMed
Seeman, N.C. (1998). DNA nanotechnology: Novel DNA constructions. Annu Rev Biophys Biomol Struct 27, 225248.CrossRefGoogle ScholarPubMed
Seeman, N.C. (2003). DNA in a material world. Nature 421(6921), 427431.CrossRefGoogle Scholar
Severin, N., Barner, J., Kalachev, A.A. & Rabe, J.P. (2004). Manipulation and overstretching of genes on solid substrates. Nano Lett 4, 577579.CrossRefGoogle Scholar
Shlyakhtenko, L.S., Hsieh, P., Grigoriev, M., Potaman, V.N., Sinden, R.R. & Lyubchenko, Y.L. (2000). A cruciform structural transition provides a molecular switch for chromosome structure and dynamics. J Mol Biol 296, 11691173.CrossRefGoogle ScholarPubMed
Song, Y.H., Li, Z., Liu, Z.G., Wei, G., Wang, L., Sun, L.L., Guo, C.L., Sun, Y.J. & Yang, T. (2006). A novel strategy to construct a flat-lying DNA monolayer on a mica surface. J Phys Chem B 110(22), 1079210798.CrossRefGoogle ScholarPubMed
Storhoff, J.J. & Mirkin, C.A. (1999). Programmed materials synthesis with DNA. Chem Rev 99, 18491862.CrossRefGoogle ScholarPubMed
Tan, S., Liu, Z., Zu, Y., Fu, Y., Xing, Z., Zhao, L., Sun, T. & Zhou, Z. (2011). Adsorption of chitosan onto carbonaceous surfaces and its application: Atomic force microscopy study. Nanotechnology 22, 155703. CrossRefGoogle ScholarPubMed
Tiner, W.J. Sr., Potaman, V.N., Sinden, R.R. & Lyubchenko, Y.L. (2001). The structure of intramolecular triplex DNA: Atomic force microscopy study. J Mol Biol 314, 353357.CrossRefGoogle ScholarPubMed
Ueno, T., Yokota, S., Kitaoka, T. & Wariishi, H. (2007). Conformational changes in single carboxymethylcellulose chains on a highly oriented pyrolytic graphite surface under different salt conditions. Carbohyd Res 342, 954960.CrossRefGoogle ScholarPubMed
Wang, H., An, H., Zhang, F., Zhang, Z., Ye, M., Xiu, P., Zhang, Y. & Hu, J. (2008). Study of substrate-directed ordering of long double-stranded DNA molecules on bare highly oriented pyrolytic graphite surface based on atomic force microscopy relocation imaging. J Vac Sci Technol B 26, 4144.CrossRefGoogle Scholar
Wu, A.G., Li, Z., Yu, L.H., Wang, H.D. & Wang, E. (2001). Plasmid DNA network on a mica substrate investigated by atomic force microscopy. Anal Sci 17(5), 583584.CrossRefGoogle ScholarPubMed
Yokota, S., Ueno, T., Kitaoka, T. & Wariishi, H. (2007). Molecular imaging of single cellulose chains aligned on a highly oriented pyrolytic graphite surface. Carbohyd Res 342(17), 25932598.CrossRefGoogle ScholarPubMed
Zheng, G., Ussery, D.W. & Sinden, R.R. (1991). Estimation of superhelical density in vivo from analysis of the level of cruciforms existing in living cells. J Mol Biol 221, 122129.Google ScholarPubMed
Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C. & Seeman, N.C. (2009). From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 7477.CrossRefGoogle ScholarPubMed