1. In The Name of Allah Scanning Tunneling Microscope Pooria Gill Ph.D. of Nanobiotechnology Faculty of Medicine Mazandaran University of Medical sciences P.Gill@mazums.ac.ir

2. Microscopy  Optical Microscopy  Scanning Electron Microscopy  Scanning Probe Microscopy

3. Scanning Probe Microscope  Atomic Force Microscope (AFM)  Electrostatic Force Microscope (EFM)  Magnetic Force Microscope (MFM)  Scanning Tunneling Microscope (STM)  Near-field Scanning Optical Microscope (SNOM)

4. History The scanning tunneling microscope was developed at IBM Zürich in 1981 by Gerd Binning and Heinrich Rohrer who shared the Nobel Prize for physics in 1986 because of the microscope. Gerd BinningHeinrich Rohrer

5. The STM is an electron microscope that uses a single atom tip to attain atomic resolution. Scanning Tunneling Microscope (STM)

6. SPM Systems SPM Systems Piezoelectric Scanner

7. General Overview An extremely fine conducting probe is held about an atom’s diameter from the sample. Electrons tunnel between the surface and the tip, producing an electrical signal. While it slowly scans across the surface, the tip is raised and lowered in order to keep the signal constant and maintain the distance. This enables it to follow even the smallest details of the surface it is scanning.

8. The Tip As we will see later, is very important that the tip of the probe be a single atom. Tungsten is commonly used because you can use Electro-chemical etching techniques to create very sharp tips like the one above.

9. Note A STM does not measure nuclear position directly. Rather it measures the electron density clouds on the surface of the sample. In some cases, the electron clouds represent the atom locations pretty well, but not always.

10. Converse Piezoelectricity Piezoelectricity is the ability of certain crystals to produce a voltage when subjected to mechanical stress. When you apply an electric field to a piezoelectric crystal, the crystal distorts. This is known as converse piezoelectricity. The distortions of a piezo is usually on the order of micrometers, which is in the scale needed to keep the tip of the STM a couple Angstroms from the surface. The tip Pizos Electric Field

11. Scanning Modes Scanning Modes   STM Constant Current Mode

12.  STM Constant Height Mode

13. System Components System Components  Mechanical Parts  Electronics Parts  Computer + software

14. Needle replacement Needle replacement Needle type Platinum-iridium (PtIr) Tungsten tips Gold Needle preparation Electrochemical etching Mechanical shearing

15. System Software Execution

16. Sample preparation

17.  Gold Nano crystals 6-14nm

18. Advantages of Scanning Probe Microscopy The resolution of the microscopesThe resolution of the microscopes Create small structures nanolithographyCreate small structures nanolithography Do not require a partial vacuumDo not require a partial vacuum Disadvantages of Scanning Probe Microscopy The detailed shape of the scanning tip The detailed shape of the scanning tip Slower in acquiring images Slower in acquiring images The maximum image size The maximum image size

19. STM: Applications in Biomedicine

20. Nanoscopy of Nanostructured Biomolecules  Structural Analyses  Interactiomics  Partial Sequencing  Immobilization Characterization  Peptide Characteristics  Microbial Characteristics  Viral Characteristics  …

21. Single strand of calf thymus DNA deposited along a surface step of HOPG. (50 x 50 nm, constant current mode, current 0.1 nA, bias voltage 500 mV.) Methods In Molecular Biology, Vol 22. Microscopy, Opt/cat Spectroscopy, and Macmscop/c Technrqoes Edlted by: C Jones, I3 Mulloy, and A H. Thomas Copynght 01994 Humana Press Inc., Totowa, NJ.

22. STM of λ-DNA (GeneRuler DNA) on HOPG P. Gill, B. Ranjbar, R. Saber. IET Nanobiotechnol., 2011, Vol. 5, Iss. 1, pp. 8–13.

23. 3D image of a single antibody (IgG) molecule after the filtering and coloring process, which shows orientation of this molecule after physical adsorption on the rigid surface from the hinge region imaged by NAMA-STM R. Saber, S. Sarkar, P. Gill, B. Nazari, F. Faridani. Scientia Iranica F (2011) 18 (6), 1643–1646.

24. 3D image of a single antibody (IgM) molecule, imaged by NAMA-STM. (b) Standard configuration of human immunoglobulin M with pentameric domains R. Saber, S. Sarkar, P. Gill, B. Nazari, F. Faridani. Scientia Iranica F (2011) 18 (6), 1643–1646.

25. STM comparison of passive antibody adsorption and biotinylated antibody linkage to streptavidin on microtiter wells STM images of antiferritin antibodies passively adsorbed to a microwell surface STM images of biotinylated antiferritin antibodies immobilized to a streptavidin coated microwell surface Davies et al., Journal of Immunological Methods, 167 (1994) 263-269.

26. Individual Peptide Structures Visible by STM

27. Reconstructed surface topography of coated T4 polybead capsomeres; (a) the TEM and (b) STM representations. The slight variation in the representation may be due to the overlying carbon film, which is observed by STM but not by TEM. Height range is 2.3 nm. (Reprinted with permission from Stemmer et al., 1989.) M. FIRTEL and T. J. BEVERIDGE. Scanning Probe Microscopy in Microbiology. Micron, Vol. 26, No. 4, pp. 347-362, 1995.

28. References References 1.Pooria Gill, Bijan Ranjbar, Reza Saber. Scanning Tunneling Microscopy of Cauliflower-like DNA Nanostructures Synthesized by Loop-mediated Isothermal Amplification. IET Nanobiotechnology 2011; 5 (1), 8-13. 2.Reza Saber, Saeed Sarkar, Pooria Gill, Behzad Nazari, Faramarz Faridani. High Resolution Imaging of IgG and IgM Molecules by Scanning Tunneling Microscopy in Air Condition. Scientia Iranica (Transaction F: Nanotechnology) 2011; 18 (6), 1643–1646. 3.M.Q. Li. Scanning probemicroscopy (STM=AFM) and applications in biology, Appl. Phys. A 68, 255– 258 (1999). 4.Errez Shapir et al., High-Resolution STM Imaging of Novel Single G4-DNA Molecules, J. Phys. Chem. B, Vol. 112, No. 31, 2008. 5.D. P. ALLISON. Immobilization of DNA for scanning probe microscopy, Proc. Nadl. Acad. Sci. USA, Vol. 89, pp. 10129-10133, November 1992. 6.Hiroyuki Tanaka. Visualization of the Detailed Structure of Plasmid DNA, J. Phys. Chem. B 16788 2008, 112, 16788–16792. 7.Hiroyuki Tanaka. High-resolution scanning tunneling microscopy imaging of DNA molecules on Cu(111) surfaces, Surface Science 432 (1999) L611–L616. 8.Handbook of microscopy for nanotechnology / edited by Nan Yao. Zhong Lin Wang. 2005 Kluwer Academic Publishers. 9.Scanning probe microscopes : applications in science and technology / K.S. Birdi. 2003 by CRC Press LLC. 10.SCANNING PROBE MICROSCOPY, 2007 Springer Science+Business Media, LLC.

29. Thanks for your Attentions Mazandaran University of Medical Sciences and Health Care Sari, I.R. Iran www.mazums.ac.ir