Molecular Biology Protocols

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Pyth-Ion is an open source nanopore data analysis package created by Robert Henley and currently maintained and updated by Ali Fallahi for the Wanunu Lab.


Equipment and Facilities

Major equipment in our lab:
  • Fluorescence microscope (Olympus IX71 body) with multi-color laser-based wide-field illumination (Coherent) and em-CCD detection (Andor iXon 897)
  • Fiber-illuminated inverted fluorescence microscope (Olympus IX81 body) equipped with R+G+B lasers (Coherent) and emCCD detection (Hamamatsu ImagEM)
  • Patch-clamp systems for ion-current measurements through nanoporous membranes (Axopatch 200B’s, temperature-controlled measurement cells)
  • Fast-scanning AFM system (Bruker FastScan and Dimension Icon modules)
  • Reactive ion etch system with fluorine and oxygen chemistry (Technics micro-RIE 800)
  • Atomic-layer deposition system for conformal thin-film deposition (Arradiance Gemstar)
  • UV-vis spectrophotometer with multi-cell temperature control (Varian Cary 100)
  • Ellipsometer (Rudolph Research AutoEL III)
  • Dynamic and static contact angle meter (home built)
  • Mask aligner and full photolithography unit (home built)
  • Gel scanner equipped with 3 lasers (Biorad Pharos FX)
  • Realtime PCR system (Biorad CFX96 Touch)


On-campus facilities that we use:
  • JEOL 2010FEG transmission electron microscope with Gatan Ultrascan 2k x 2k CCD (@ Northeastern’s EM Center)
  • Electron beam lithography system (Zeiss Supra 25 with NABITY system)
  • Kostas facility for micro/nano-fabrication (photolithography, thermal oxidation, metal deposition)


Off-campus facilities that we frequently use:
  • Center for Nanoscale Systems, Harvard University
  • Center for Nanoscale Fabrication, Cornell University

Our Little Library (books that we have around just in case…)

  • Bevington, Philip R., and D. Keith Robinson. Data reduction and error analysis for the physical sciences. New York: McGraw-Hill, 2003.
  • Mendelson, Mel I. Learning Bio-micro-nanotechnology. CRC Press, 2013.
  • Murphy, Douglas B., and Michael W. Davidson. Fundamentals of light microscopy and electronic imaging. John Wiley & Sons, 2012.
  • Muthukumar, Murugappan. Polymer translocation. CRC Press, 2011.
  • Nelson, Philip. Biological physics. New York: WH Freeman, 2014.
  • Phillips, Rob, et al. Physical biology of the cell. New York: Garland Science, 2009.
  • Sakmann, Bert, and Erwin Neher, eds. Single-channel recording. New York: Springer, 2009.
  • Sambrook, Joseph, David W. Russell, and David W. Russell. Molecular cloning: a laboratory manual (3-volume set). Vol. 999. Cold Spring Harbor, New York:: Cold spring harbor laboratory press, 2001.
  • Wanunu, Meni, and Yitzhak Tor, eds. Methods for studying nucleic acid/drug interactions. CRC Press, 2011.
  • Weiss, T. Fisher. Cellular Biophysics. Vol. 1 and 2. MIT Press, 1996.