Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques.

While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes. On graphene, the images of the origami plates show severe unwanted distortions, where the rectangular shape of the nanoplates is significantly distorted. From a number of comparative control experiments, it is demonstrated that neither staining agents, nor screening ions, nor the level of electron-beam irradiation cause this distortion. Instead, it is suggested that origami nanoplates are distorted due to hydrophobic interaction of the DNA bases with graphene upon adsorption of the DNA origami nanoplates.

[1]  F. Benfenati,et al.  Imaging and structural studies of DNA-protein complexes and membrane ion channels. , 2017, Nanoscale.

[2]  Robert M Glaeser,et al.  How good can cryo-EM become? , 2015, Nature Methods.

[3]  T. LaBean,et al.  Electronically addressable nanomechanical switching of i-motif DNA origami assembled on basal plane HOPG. , 2015, Chemical communications.

[4]  Sergei Lopatin,et al.  The structure of DNA by direct imaging , 2015, Science Advances.

[5]  N. Seeman,et al.  Programmable materials and the nature of the DNA bond , 2015, Science.

[6]  J. Aldrich-Wright,et al.  Metal complex interactions with DNA. , 2015, Dalton transactions.

[7]  Tolou Shokuhfar,et al.  High‐Resolution Electron Microscopy and Spectroscopy of Ferritin in Biocompatible Graphene Liquid Cells and Graphene Sandwiches , 2014, Advanced materials.

[8]  A. Turchanin,et al.  Dry-cleaning of graphene , 2014 .

[9]  H. Stahlberg,et al.  Rendering graphene supports hydrophilic with non-covalent aromatic functionalization for transmission electron microscopy , 2014, 1403.6976.

[10]  P. Peters,et al.  The use of a central beam stop for contrast enhancement in TEM imaging. , 2013, Ultramicroscopy.

[11]  K. Novoselov,et al.  Control of radiation damage in MoS(2) by graphene encapsulation. , 2013, ACS nano.

[12]  U. Kaiser,et al.  The pristine atomic structure of MoS2 monolayer protected from electron radiation damage by graphene , 2013, 1310.2411.

[13]  M. Ishigami,et al.  Superb resolution and contrast of transmission electron microscopy images of unstained biological samples on graphene-coated grids. , 2013, Biochimica et biophysica acta.

[14]  Igor L. Medintz,et al.  TEM imaging of unstained DNA nanostructures using suspended graphene , 2013 .

[15]  Remo Proietti Zaccaria,et al.  Direct imaging of DNA fibers: the visage of double helix. , 2012, Nano letters.

[16]  Peng Chen,et al.  Biological and chemical sensors based on graphene materials. , 2012, Chemical Society reviews.

[17]  D. Nečas,et al.  Gwyddion: an open-source software for SPM data analysis , 2012 .

[18]  Marya Lieberman,et al.  DNA origami nanopatterning on chemically modified graphene. , 2012, Angewandte Chemie.

[19]  P. Rothemund,et al.  Programmable molecular recognition based on the geometry of DNA nanostructures. , 2011, Nature chemistry.

[20]  Carl W. Magnuson,et al.  Graphene: Substrate preparation and introduction. , 2011, Journal of structural biology.

[21]  Mark Bathe,et al.  A primer to scaffolded DNA origami , 2011, Nature Methods.

[22]  N. Seeman,et al.  Crystalline two-dimensional DNA-origami arrays. , 2011, Angewandte Chemie.

[23]  P. Annibale,et al.  ssDNA binding reveals the atomic structure of graphene. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[24]  Rolf Erni,et al.  Aberration-Corrected Imaging in Transmission Electron Microscopy: An Introduction , 2010 .

[25]  Feng Wang,et al.  A direct transfer of layer-area graphene , 2010 .

[26]  Adam H. Marblestone,et al.  Rapid prototyping of 3D DNA-origami shapes with caDNAno , 2009, Nucleic acids research.

[27]  R M Westervelt,et al.  Graphene Nanoelectronics , 2008, Science.

[28]  Radostin Danev,et al.  Phase contrast electron microscopy: development of thin-film phase plates and biological applications , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[29]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[30]  R. Egerton,et al.  Beam-Induced Damage to Thin Specimens in an Intense Electron Probe , 2005, Microscopy and Microanalysis.

[31]  M. Malac,et al.  Radiation damage in the TEM and SEM. , 2004, Micron.

[32]  J. Griffith,et al.  Visualizing nucleic acids and their complexes using electron microscopy. , 1997, Current opinion in structural biology.

[33]  R. Glaeser,et al.  Limitations to significant information in biological electron microscopy as a result of radiation damage. , 1971, Journal of ultrastructure research.

[34]  M. Norton,et al.  Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: a review. , 2015, Analytica chimica acta.

[35]  Brian F. G. Johnson,et al.  Z-Contrast tomography: a technique inthree-dimensional nanostructural analysis based on Rutherfordscattering , 2001 .