Optical Tweezers: Methods and Applications
Padgett, Molloy, and McGloin
Handbook of Molecular Biophysics
Bohr
Principles of fluorescence spectroscopy
Lakowicz
Searchable protocols from Springer publications (requires university subscription and authentication)
Cold Spring Harbor Protocols
Searchable protocol and recipes from Cold Spring Harbor (requires university subscription and authentication)
Nature Protocols
Nature's peer-reviewed protocols (requires university subscription and authentication)
OpenWetWare Protocols
Biology and biological engineering protocols from OpenWetWare, Idea Lab members contribute to this resource
Protein Chemist
An award-winning site for the convenience and use of industrial and
academic protein chemists around the world that includes purification,
modification, antibody, and gel protocols, as well as calculators
Where to Find Funding (Fellowships and Grants)
David N. Breslauer's Fellowships and Grants Page
A Berkeley graduate student shares where graduate students in the fields of science and engineering can apply for funding
Handy Online Tools and Databases
RCSB Protein Data Bank
Provides information about experimentally-determined structures of proteins,
nucleic acids, and complex assemblies, performs simple and advanced
searches based on annotations relating to sequence, structure and function
Expert Protein Analysis System (ExPASy) Proteomics Server
Dedicated to the analysis of protein sequences and structures as well as 2-D PAGE, including tools and software packages
Chang Bioscience SDS Page Calculator
Bionumbers
The database of useful biological numbers (volume occupied by a protein, force required to package DNA into a capsid, etc.)
Fluorescence SpectraViewer
A handy site from Invitrogen that lets you plot and compare the spectra for many fluorophores
New England Biolabs (NEB) bring us a neat tool that maps out restriction enzyme sites on a given DNA sequence
Research Groups in the Field
These are some of our "favorites" - the groups performing research of interest to the Idea Lab. Many of these sites have great "useful links" sections of their own! For quick reference, brief descriptions of select research areas are quoted from each group's website.
Berkeley
Ahmet Yildiz's Lab
Understanding the molecular basis of intracellular cargo transportation using single molecule fluorescence and force microscopy. Projects include molecular mechanism of cytoplasmic dynein, control of intraflagellar transport, and telomere loop formation. Microscopy techniques include Total Internal Reflection (TIRF), Forster Resonance Energy Transfer (FRET), Fluorescence Imaging with One Nanometer Accuracy (FIONA), and polarization microscopy.
Haw Yang's Lab
Dynamical Fluctuations in Complex Systems, Single-Molecule Spectroscopy and Advanced Imaging, Protein Structure-Function Dynamics
Novel
methods of single-molecule manipulation and detection: optical
tweezers, single-molecule fluorescence microscopy, Scanning Force Microscopy (SFM)
Xiang Zhang's Lab
Neurobiology, cell biology and tissue engineering, bio-sensing
Biophysics and synthetic biology, understanding and controlling energy and information fluxes in biological systems. Design and synthesis of light-powered forms of E. coli, plasmon rulers: a new tool for measuring molecular distances, optical trapping and manipulation of nanowires, mechanical properties of RNA, forces inside DNA loops.
UCSF
Ron Vale's Lab
Cell biological and biophysical approaches to understanding the cytoskeleton, microtubule-based
"motor proteins",
and more general issues on spatial organization and movement within cells. Technologies include single molecule fluorescence, optical traps, and high throughput microscopy.
Stanford
Probing local
environments using single-molecule spectroscopy and microscopy,
superresolution imaging, biophysics, fluorescent labeling, and imaging
of single molecules in vitro and in vivo, trapping nanoscale objects in
solution, nanophotonics, and quantum optics.
Single molecule biophysics research includes precision measurements on single molecules, time resolved force spectroscopy, topology of knotted polymers, and single molecule DNA sequencing. Other areas include single cell analysis, chemical synthesis on a chip, systems biology, structural biology, in-vitro proteomic biology and medical diagnostics.
Eric Shaqfeh's Lab
DNA dynamics in mixed flows and in micro- and macro- devices, DNA dynamics in microfluidic devices, polymer dynamics in concentrated solutions, polymer conformational hysteresis in mixed flows (experiment and simulations).
Steven Block's Lab
Single-molecule biophysics of motor proteins and nucleic acids. Tools include optical tweezers and fluorescence techniques to measure nm displacements and pN forces.
Assay and single-molecule studies of the structure and function of molecular motors. Tools include laser traps, total internal reflection fluorescence microscopy (TIRF), and gold nanoparticle tracking.
University of Michigan, Ann Arbor
Polymer physics and rheology, surfactant and lipid simulation, micro-fabricated devices for virus identification, fluid mechanics and brownian dynamics.
Mark A. Burns's LabIntegrated microfluidic devices for influenza and other genetic analyses, multiphase droplet bioreaction systems, microfluidic assembly blocks, acoustic microfluidic flow control.
Harvard
Biophysics of cells including biofilm formation, cell and cytoskeletal mechanics, and quantifying three-diimensional traction forces exerted by cells in a collagen matrix. Biology in microfluidic devices including using microfluidics to to encapsulate cells in drops, detect antibodies, perform biochemical screening, and study how gene expression changes in response to environmental stimuli.
Single-molecule enzymology, protein-DNA interactions, real-time imaging gene expression, and stimulated raman scattering microscopy (SRS): a label-free and noninvasive imaging method capable of examining living cells and organisms in real time via vibrational spectroscopy.
Development of optical imaging techniques to study individual biological molecules: super-resolution optical microscopy for cell and tissue imaging, single-molecule fluorescence imaging and spectroscopy to study protein-DNA interactions, live-cell imaging techniques for studying virus-cell interactions.
Investigations include the binding energy landscape of binding systems such as biotin/streptavidin and dig/anti-dig, the unzipping of DNA in the presence of proteins, dsDNA homologue binding in real time using an optical force trap, cell differentiation in response to stress, the mechanical properties of DNA, the manipulation of cells by incorporating magnetic particles, magnetic field separation techniques.
Building new tools to study biomolecules: manipulating single molecules in solution, sculpting electromagnetic fields to induce forbidden transitions in molecules, mechanisms of microbial and molecular motions in mucus, ultrasensitive probes of photoactive membrane proteins, dynamics of single molecules of DNA, control of nanoparticles with arbitrary 2-D force fields.
University of Illinois at Urbana-Champaign
Molecular biophysics including protein engineering and DNA replication. Biotechnology including integrated microdevices for medicine, high-throughput analysis of single DNA molecules and proteins in microdevices for disease diagnostics and prediction of drug response. Polymer physics including fluorescence microscopy of novel biopolymers in flow.
DNA-protein and protein-protein interactions, protein and RNA folding, membrane biophysics, fluorescence microscopy of biological systems, single molecule spectroscopy and manipulations, biologically inspired nano-mechanical devices.
Structure and dynamics of biological macromolecules, molecular motors, FRET, and LRET.
Design and construction of instrumentation, development of biological systems for single-molecule manipulation, and quantitiative analysis and modeling of data. Ultrahigh-resolution optical traps resolving angstrom length scale motions, protein-DNA interactions, bacterial chemotaxis.
Columbia University
Single protein mechanics and engineering. Research topics include capturing the role of solvent molecules in transition states of proteins, chair-boat transitions in single polysaccharide molecules, enzyme catalysis under force, chemical reactions under a stretching force, the mechanical design of titin, studies of protein folding from highly extended states, and the mechanical architecture of proteins.
Single-molecule optical microscopy to study fundamental interactions between proteins and nucleic acids. Projects include using TIRF microscopy to study biology, homologous DNA recombination, post-replicative mismatch repair, and designer DNA arrays for "high-throughput" single molecule bioscience (DNA curtains).
Far Away
Nanometer spatial resolution light microscopy, structure and dynamics of cell organelles, single fluorescent molecules, optical system and instrument design, image processing.
Dynamics of DNA and RNA as well as their interaction with proteins. Projects include the torque-dependence of DNA and DNA-protein interactions, nanoscale volumes to study polymerization on DNA, unravelling RNA and RNA-protein interactions, and probing RNA in solid-state nanopores. Techniques include magnetic and optical tweezers, fluorescence detection, and nanopores.
Development of a nano-positioning system (NPS), molecular mechanisms underlying the biological activity of proteins, mechanical properties of polymer molecules. Fluorescence spectroscopy and force spectroscopy with Atomic Force Microscopy (AFM).
Learning Online
Optics and fluorescence
A free digital book download from Chroma
Olympus and Florida State bring you this clear, concise overview of microscopy topics
Nikon's microscope education site offers tutorials and more
Melles Griot offers great resources for learning about open table optics
Steve Smith and Claudio Rivetti explain everything you need to know to build your very own instrument
Biology
DNA from the beginning - An animated primer on the basics of DNA, genes, and heredity from Cold Spring Harbor
A handy online magazine and community for molecular and cell
biology researchers featuring technical tips, career advice and news
This handbook is excellent for understanding molecular biology techniques
A visual guide to x-ray crystallography including movies illustrating the concepts of x-ray diffraction, resolution, R-factor, phase, data completeness, model refinement and more
Fluid mechanics
Some instructive and classic videos from the National Committee for Fluid Mechanics films
Blogs and Online Community Resources
David Breslauer from the Lee Lab at Berkeley shares advice on graduate
school, learning from failure (including excellent microfluidics tips),
and fellowships
A weblog about "biology through the eyes of physicists"
Berkeley-Specific Resources
Biomolecular Structure and Mechanism at Berkeley
A
collection of Faculty, Seminars, Graduate Programs, Resources, and
Facilities for Biomolecular Structure and Mechanism at Berkeley
Berkeley Molecular Imaging Center
Berkeley Academic Services from the Graduate Division
Academic Services including writing resources and workshops
Berkeley Nanosciences and Nanoengineering Seminar Series Calendar
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Thanks to CharISMA Idea Lab members for contributing content!
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