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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Arnott S (1984) Sprung from chain. Nature 312:174–174
Bernstein J, Davis RE, Shimoni L et al (1995) Patterns in hydrogen bonding – functionality and graph set analysis in crystals. Angew Chem Int Ed 34:1555–1573
Binnig G, Rohrer H (1982) Scanning tunneling microscopy. Helv Phys Acta 55:726–735
Binning G, Rohrer H, Gerber C et al (1982) Surface studies by scanning tunneling microscopy. Phys Rev Lett 49:57–61
Douglas SM, Dietz H, Liedl T et al (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414–418
Fritz J, Baller MK, Lang HP et al (2000) Translating biomolecular recognition into nanomechanics. Science 288:316–318
Furukawa M, Tanaka H, Kawai T (2000) Formation mechanism of low-dimensional superstructure of adenine molecules and its control by chemical modification: a low-temperature scanning tunneling microscopy study. Surf Sci 445:1–10
Furukawa M, Tanaka H, Kawai T (2001) The role of dimer formation in the self-assemblies of DNA base molecules on Cu(111) surfaces: a scanning tunneling microscope study. J Chem Phys 115:3419–3423
Kawai T, Tanaka H, Nakagawa T (1997) Low dimensional self-organization of DNA-base molecules on Cu(111) surfaces. Surf Sci 386:124–136
Kelly REA, Kantorovich LN (2006) Homopairing possibilities of the DNA base thymine and the RNA base uracil: an ab initio density functional theory study. J Phys Chem B 110:2249–2255
Kelly REA, Lee YJ, Kantorovich LN (2005a) Homopairing possibilities of the DNA base adenine. J Phys Chem B 109:11933–11939
Kelly REA, Lee YJ, Kantorovich LN (2005b) Homopairing possibilities of the DNA bases cytosine and guanine: an ab initio DFT study. J Phys Chem B 109:22045–22052
Lamond AI (2002) Swimming lessons. Nature 417:383–383
Leonard GA, Zhang S, Peterson MR et al (1995) Self-association of a DNA loop creates a quadruplex – crystal-structure of D(Gcatgct) at 1.8-angstrom resolution. Structure 3:335–340
Liu L, Zhang L, Mao XB et al (2009) Chaperon-mediated single molecular approach toward modulating a beta peptide aggregation. Nano Lett 9:4066–4072
Liu L, Busuttil K, Zhang S et al (2011a) The role of self-assembling polypeptides in building nanomaterials. Phys Chem Chem Phys 13:17435–17444
Liu L, Zhang L, Niu L et al (2011b) Observation of reduced cytotoxicity of aggregated amyloidogenic peptides with chaperone-like molecules. ACS Nano 5:6001–6007
Ma XJ, Liu L, Mao XB et al (2009) Amyloid beta (1-42) folding multiplicity and single-molecule binding behavior studied with STM. J Mol Biol 388:894–901
Mamdouh W, Dong MD, Xu SL et al (2006) Supramolecular nanopatterns self-assembled by adenine-thymine quartets at the liquid/solid interface. J Am Chem Soc 128:13305–13311
McNutt A, Haq S, Raval R (2003) RAIRS investigations on the orientation and intermolecular interactions of adenine on Cu(110). Surf Sci 531:131–144
Nishimura M, Tanaka H, Kawai T (2002) Structure of linear double-stranded deoxyribonucleic acid adsorbed on Cu(111) surfaces: a low-temperature scanning tunneling microscopy study. Jpn J Appl Phys 41:7510–7511
Otero R, Schock M, Molina LM et al (2005) Guanine quartet networks stabilized by cooperative hydrogen bonds. Angew Chem Int Ed 44:2270–2275
Pauling L (1992) The nature of the chemical-bond – 1992. J Chem Educ 69:519–521
Perdigao LMA, Staniec PA, Champness NR et al (2006) Experimental and theoretical identification of adenine monolayers on Ag-terminated Si(111). Phys Rev B 73 195423(1–7)
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
Samori B, Zuccheri G (2005) DNA codes for nanoscience. Angew Chem Int Ed 44:1166–1181
Sowerby SJ, Heckl WM (1998) The role of self-assembled monolayers of the purine and pyrimidine bases in the emergence of life. Orig Life Evol Biosph 28:283–310
Wandlowski T, Lampner D, Lindsay SM (1996) Structure and stability of cytosine adlayers on Au(111): an in-situ STM study. J Electroanal Chem 404:215–226
Watson JD, Crick FHC (2003) Molecular structure of nucleic acids – a structure for deoxyribose nucleic acid. Revista De Investigacion Clinica 55:108–109 (Reprinted from Nature, vol 171, pg 737–738, 1953)
Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295:2418–2421
Whitesides GM, Mathias JP, Seto CT (1991) Molecular self-assembly and nanochemistry – a chemical strategy for the synthesis of nanostructures. Science 254:1312–1319
Winfree E, Liu FR, Wenzler LA et al (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544
Xu SL, Dong MD, Rauls E et al (2006) Coadsorption of guanine and cytosine on graphite: ordered structure based on GC pairing. Nano Lett 6:1434–1438
Yang YL, Wang C (2009) Hierarchical construction of self-assembled low-dimensional molecular architectures observed by using scanning tunneling microscopy. Chem Soc Rev 38:2576–2589
Zain R, Sun JS (2003) Do natural DNA triple-helical structures occur and function in vivo? Cell Mol Life Sci 60:862–870
Zhao XJ, Zhang SG (2006) Molecular designer self-assembling peptides. Chem Soc Rev 35:1105–1110
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/978-3-642-38815-6_1
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-38814-9
Online ISBN: 978-3-642-38815-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)