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Self-Assembly of DNA Bases via Hydrogen Bonding Studied by Scanning Tunneling Microscopy

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Nucleic Acid Nanotechnology

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 29))

Abstract

Nature is the master of self-assembly, and in biological system, a great many of hierarchical structures of biomolecules including DNA, peptide, and protein are attributed to the self-assembly from molecular level to nanoscale. One successful example is inspired by nature; DNA can be an excellent agent to self-assemble into the desirable amazing two-dimensional and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. Therefore, the self-assembly of DNA bases has played a significant role in constructing the hierarchical nanostructures, and maybe they are also the key to the earliest appearance of life. In this chapter, we will study on DNA base self-assembly by scanning tunneling microscopy (STM) at the liquid/solid interface and present the nanoscale patterns that can be created by assembly of the individual DNA base (G, guanine; C, cytosine; A, adenine; T, thymine) and coabsorption of DNA complementary bases (G-C and A-T) based on the specific hydrogen bond interactions. Scanning tunneling microscopy is the powerful technique to visualize atomic-scale structure with submolecular resolution. At the liquid/solid interface, one can be in the ambient condition that is more close to the physiological environment rather than the extreme condition in vacuum system. On the other hand, the influence of the various types of intermolecular interactions is revealed such as hydrogen bond, stacking interaction, etc. Therefore, the utilization of STM at liquid/solid interface has the good advantage to investigate the DNA base self-assemblies on the surface, and the variety of novel two-dimensional nanostructure-based DNA base assemblies will be introduced in this chapter. Furthermore, the theoretical calculation will also provide the assembly models of DNA base to make better understanding of the mechanism of self-assembly of DNA bases.

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Acknowledgments

The authors acknowledge financial support from the Centre for DNA Nanotechnology and Danish-Chinese Centre for Self-Assembly and Function of Molecular Nanostructures on Surfaces from iNANO through the Danish National Research Foundation and Carlsberg Foundation. M.D. acknowledges the support from the STENO Independent Research grant and Young Investigator Program of Villum Kann Rasmussen Foundation.

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Authors and Affiliations

  1. iNANO Center, Aarhus University, Gustav Wieds vej 14, Building 1590, 8000, Aarhus, Denmark

    Lei Liu, Flemming Besenbacher & MingDong Dong

  2. CDNA Center, Aarhus University, Gustav Wieds vej 14, Building 1590, 8000, Aarhus, Denmark

    Lei Liu, Flemming Besenbacher & MingDong Dong

Authors
  1. Lei Liu
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  2. Flemming Besenbacher
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  3. MingDong Dong
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Corresponding author

Correspondence to MingDong Dong .

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Editors and Affiliations

  1. Dept. of Molecular Biology, University of Aarhus, Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Aarhus C, Denmark

    Jørgen Kjems

  2. Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark

    Elena Ferapontova

  3. Center for DNA Nanotechnology, Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, Aarhus C, Denmark

    Kurt V. Gothelf

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Liu, L., Besenbacher, F., Dong, M. (2014). Self-Assembly of DNA Bases via Hydrogen Bonding Studied by Scanning Tunneling Microscopy. In: Kjems, J., Ferapontova, E., Gothelf, K. (eds) Nucleic Acid Nanotechnology. Nucleic Acids and Molecular Biology, vol 29. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38815-6_1

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