Equipment in the Biomolecular Research Facility

Instruments in DNA Sciences

 Illumina Genome Analyzer II

for:

  • whole chromosomes
  • targeted studies of genomic regions
  • whole genomes
  • BACs

 

 picture of Illumina genome sequencer

 ABI 3730 DNA Analyzer

DNA sequencing

 picture of ABI 3730 DNA sequencer

 ABI Prism® 7900HT Sequence Detection System

for real time PCR measurements

  • quantitation of gene expression
  • mutation detection
  • allelic discrimination
  • single nucleotide polmorphisms (SNP) characterization and screening
  • microRNA quantitation
  • DNA copy number determination
  • viral titration
    		•

    rpicture of real time PCR machine 

    Affymetrix Gene Chip System for studying changes in gene expression

    fluidics station for washing chips 

    		 picture of Affymetrix fluidics station
     hybridization oven used for hybridization of cDNA to gene chip   picture of hybridization oven for microarrays
     laser GeneArray scanner for measuring amounts of bound probes  picture of gene array scanner
      

    Agilent BioAnalyzer 

    This microfluidics based instrument uses electrophoresis for rapid quality control on small samples of DNA and RNA. Minimum concentration is about 0.1 ng/µL, and 1.5 µL is loaded. Separation is by size, similar to a conventional gel 

    		picture of Agilent Bioanalyzer 

     Nanovue spectrophotometer

    for absorbance readings of small volumes, often used to quantitate DNA

    		picture of Nanovue spectrohotometer 

    Molecular Devices Gemini fluorescent plate reader

    can quantitate DNA with PicoGreen
    More information in Shared Instrumentation section

    Equipment in the Mass Spectrometry Core

    Thermo Fourier transform mass spectrometer with Finnigan LTQ front end 

    Electrospray ionization for sample introduction. Linear ion trap and Fourier transform ICR mass analyzers.
    This instrument has very high accuracy and a wide dynamic range and thus gives better quantitation than the LTQ alone.

     

    		picture of Thermo Electron FT-ICR high resolution mass spectrometer

     Thermo Electron LTQ Orbitrap Velos Mass Spectrometer

    equipped with Collision Induced Dissociation (CID), Electron Transfer Dissociation (ETD), Higher-Energy Collision Dissociation (HCD) and a microspray ion source for complex mixture and PTM analysis as well as relative quantification. Operation will start in secnd half December 2009.

    		picture of Orbitrap mass spectrometer 

    Thermo Electron TSQ Quantum Access MAX

    Equipped with Quantitation-Enhanced Data-Dependent MS/MS (QED-MS/MS) and Highly Selective Reaction Monitoring (H-SRM) to provide accurate quantification at low levels for specific molecules of interest.
    Adapting this instrument to perform Selective Reaction Monitoring (SRM)/Multiple Reaction Monitoring on small samples started in December 2009 

    		 picture of Thermo Electron TSQ mass spectrometer
      

    Bruker MicroFlex MALDI

     This instrument measures masses of intact molecules. Sample preparation is usually relatively simple so this instrument is the first choice to obtain the mass of peptides, proteins and some other molecules.

    		picture of Bruker MALDI mass spectrometer 
    Thermo and Agilent HPLC systems coupled to above mass spectrometers

    Equipment in Shared Instrumentation Core

    The Biomolecular Research Facility has equipment which is either not commonly found in individual laboratories or is needed only occasionally by some laboratories. Some equipment is operated by facility personnel, and some is used by individual researchers. Contact John Shannon ph. 3-9399 about use of the equipment listed below.

      Molecular Dynamics Gemini EM Spectramax Fluorescent plate reader

    For fluorescence readings of plates with 384, 96, 24, 12, 6 well microtiter plates.
    Dual monochromator optics.
    Can perform some luminescence readings.
    Does not perform absorbance readings.
    Operated by researcher. Fee for use.

    		picture of fluorescent plate reader 

    High performance liquid chromatography.

    • ABI 140 for 1 and 2 mm diameter columns
    • Beckman System Gold for 4.6, 10, 22 mm diameter columns.
    • Dionex Ultimate for 0.3 mm diameter columns. Detection by variable wavelength UV detector.

    Used for separation of peptides, proteins and some other molecules,  usually with  reverse phase columns.

    Medium pressure chromatography using FPLC

    • Amersham AKTA FPLC, detection at 280 nm (or 260 nm), with a Frac-100 fraction collector.
    • gel filtration, ion exchange, for separation of proteins and peptides

     

    AVIV 410 Circular dichroism spectropolarimeter 

    For studies on tertiary structure of proteins.
    Operated by researcher. Fee for use.
    Brief background on operation here.

    		 picture of circular dichroism spectropolarimeter

     

    Gel scanners

    • Bio-Rad GS800 for absorbance readings on gels or blots at visible wavelengths.  Three wavelength filters for different stains.
    • Bio-Rad FX fluorescent scanner. Three lasers and five filters to cover common fluorescent stains. Multiple stains can be scanned and overlaid. 
    • Both scanners produce files which can be converted to 8 or 16 bit tiff files.

    Bio-Rad Proteome Works Spot Cutter

    allows automated cutting of gel plugs and cutting of gel plugs from gels stained with Sypro Ruby dye or visible dyes.

     Biacore 3000 for biomolecule interactions

    Used to determine kinetics of binding between biological molecules

    		 picture of Biacore 3000

    Isoelectric Focusing apparatus

    • Amersham apparatus for 18 cm strips
    • Bio-Rad Protean IEF cell for 11, 17, 25 cm strips
    • user operated

    Protein Solutions DynaPro dynamic light scattering

    Estimates size of proteins in solution