1Department of Biology, California Institute of Technology, 2Department of Bioengineering, California Institute of Technology, 3Synthetic Biology Center, Department of Bioengineering, Massachusetts Institute of Technology, 4School of Physics and Astronomy, University of Minnesota
This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.
Published September 16, 2013. Keywords: Cellular Biology, Bioengineering, Synthetic Biology, Chemistry Techniques, Synthetic, Molecular Biology, control theory, TX-TL, cell-free expression, in vitro, transcription-translation, cell-free protein synthesis, synthetic biology, systems biology, Escherichia coli cell extract, biological circuits, biomolecular breadboard
1Department of Electrical Engineering and Computer Science, University of Michigan - Ann Arbor
We describe the device fabrication and measurement protocol for carbon nanotube based high frequency biosensors. The high frequency sensing technique mitigates the fundamental ionic (Debye) screening effect and allows nanotube biosensor to be operated in high ionic strength solutions where conventional electronic biosensors fail. Our technology provides a unique platform for point-of-care (POC) electronic biosensors operating in physiologically relevant conditions.
Published July 22, 2013. Keywords: Bioengineering, Chemical Engineering, Biochemistry, Biophysics, Electrical Engineering, Nanotechnology, Biosensing Techniques, carbon nanotubes (synthesis and properties), bioelectronic instruments (theory and techniques), Carbon nanotube, biosensor, frequency mixing, biotin, streptavidin, poly-dimethylsiloxane
1Department of Chemical and Biomolecular Engineering, Ohio University, 2Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, 3Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School
Compared with traditional affinity chromatography using protein A agarose bead-packed columns, protein A membrane adsorbers can significantly speed laboratory-scale isolation of antibodies and other Fc fragment-expressing proteins. Appropriate analysis and quantification methods can further accelerate protein processing, allowing isolation/characterization to be completed in one workday, instead of 20+ work hours.
Published January 8, 2014. Keywords: Bioengineering, affinity chromatography, membrane adsorber, bioseparations, protein A, galectin-1, Gal-1hFc
JoVE Applied Physics
1Department of Physics, University of Ottawa, 2Ottawa-Carleton Institute of Biomedical Engineering, University of Ottawa
A methodology for preparing solid-state nanopores in solution for biomolecular translocation experiments is presented. By applying short pulses of high electric fields, the nanopore diameter can be controllably enlarged with subnanometer precision and its electrical noise characteristics significantly improved. This procedure is performed in situ using standard laboratory equipment under experimental conditions.
Published October 31, 2013. Keywords: Physics, Nanopore, Solid-State, Size Control, Noise Reduction, Translocation, DNA, High Electric Fields, Nanopore Conditioning
1Department of Chemical and Biomolecular Engineering, University of Akron
Developing biotinylatable fusion proteins has many potential applications in various fields of research. Recombinant protein engineering is a straight forward procedure that is cost-effective, providing high yields of custom-designed proteins.
Published January 22, 2014. Keywords: Bioengineering, protein engineering, recombinant protein production, AviTag, BirA, biotinylation, pET vector system, E. coli, inclusion bodies, Ni-NTA, size exclusion chromatography
1Nanoscale Engineering Graduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 2Nanoscale Science Undergraduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 3Nanobioscience Constellation, College of Nanoscale Science and Engineering, University at Albany, State University of New York, 4The RNA Institute, University at Albany, State University of New York, 5Department of Biological Sciences, University at Albany, State University of New York
Optical tweezers have been used to study RNA folding by stretching individual molecules from their 5’ and 3’ ends. Here common procedures are described to synthesize RNA molecules for tweezing, calibration of the instrument, and methods to manipulate single molecules.
Published August 20, 2014. Keywords: Bioengineering, RNA folding, single-molecule, optical tweezers, nanomanipulation, RNA secondary structure, RNA tertiary structure
JoVE Immunology and Infection
1Department of Biomedical Engineering, Vanderbilt University, 2Vanderbilt Institute for Nanoscale Science & Engineering, Vanderbilt University, 3Interdisciplinary Materials Science Program, Vanderbilt University, 4Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, 5Department of Chemical & Biomolecular Engineering, Vanderbilt University, 6Department of Cancer Biology, Vanderbilt University
A hemolysis assay can be used as a rapid, high-throughput screen of drug delivery systems' cytocompatibility and endosomolytic activity for intracellular cargo delivery. The assay measures the disruption of erythrocyte membranes as a function of environmental pH.
Published March 9, 2013. Keywords: Immunology, Cellular Biology, Medicine, Biomedical Engineering, Bioengineering, Cancer Biology, Molecular Biology, Erythrocytes, Endosomes, Small Interfering RNA, Gene Therapy, Nanomedicine, Gene delivery, Nanoparticles, Endosome Escape, Intracellular Trafficking, Cytosolic Drug Delivery, red blood cells, assay
1Department of Electrical and Computer Engineering, Boston University, 2Department of Biomedical Engineering, Boston University, 3Center for Advanced Genomics Technology, Boston University, 4Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, 5Department of Microbiology, Boston University School of Medicine, 6CNR (National Research Council), Istituto di Chimica del Riconoscimento Molecolare
Quantitative, high-throughput, real-time, and label-free biomolecular detection (DNA, protein, etc.) on SiO2 surfaces can be achieved using a simple interferometric technique which relies on LED illumination, minimal optical components, and a camera. The Interferometric Reflectance Imaging Sensor (IRIS) is inexpensive, simple to use, and amenable to microarray formats.
Published May 3, 2011. Keywords: Bioengineering, Interferometry, label-free, biosensing, microarray, quantification, real-time detection
1Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, 2Biomedical Engineering Program, Ohio University
Dual camera emission splitting systems for two-color fluorescence microscopy generate real-time image sequences with exceptional optical and temporal resolution, a requirement of certain live cell assays including parallel plate flow chamber adhesion assays. When software is employed to merge images from simultaneously acquired emission channels, pseudocolored image sequences are produced.
Published September 4, 2013. Keywords: Bioengineering, Cellular Biology, Biomedical Engineering, Molecular Biology, Biophysics, Biochemistry, Chemical Engineering, Chemistry, Cell Adhesion Molecules, Biological Markers, Antigens, Cell Adhesion Molecules, Microscopy, Fluorescence, Cell Physiological Processes, Cell Adhesion, Cell Physiological Phenomena, Colocalization, cell rolling, two-color fluorescence, cell, imaging
1College of Nursing, Interdisciplinary Life Sciences Research Laboratory, Seattle University, 2College of Science and Engineering, Interdisciplinary Life Sciences Research Laboratory, Seattle University
A tapping mode atomic force microscope (AFM) method for the visualization of plasmid DNA, cytoplasmic proteins, and DNA-protein complexes is described. The method includes alternate approaches for preparing samples for AFM imaging following biochemical manipulation. DNA containing specific protein interacting regions are observed in near-physiologic buffer conditions.
Published July 18, 2011. Keywords: Bioengineering, atomic force microscopy, glucocorticoid receptor, protein-protein interaction, DNA-protein interaction, scanning probe microscopy, immunoadsorption