Molecular biology

The Agilent Bioanalyzer permits the rapid separation (as quick as 90 seconds per well), visualization and quantification of DNA, RNA or protein samples. Available kits (provided by the user): DNA 1000 (25 to 1000 bp resolution), DNA 7500 (100 - 7500 bp resolution), DNA 12000 (100 to 12000 bp resolution), RNA 6000 Nano (qualitative range of 5 to 500 ng/µl total RNA, 25 to 250 ng/µl mRNA), RNA 6000 Pico (qualitative range of 50 to 5000 pg/µl total RNA, 250 to 5000 pg/µl mRNA), Protein 230 (14 to 230 kDa resolution), Protein 80 (5 to 80 kDa resolution).

Location: GE S110.04, GE 200.01.

The Implen Nanophotometer allows spectrophotometric analysis of DNA, RNA, proteins and cell cultures samples in standard cuvettes as well as in the LabelGuard Microliter Cell, which can read 0.7 to 5 μL samples. Depending on the lid used, one can use volumes from 3 to 5 ul (Lid 10) or 0.7 to 4 ul (Lid 50). Various methods can be used, including reading single or multiple wavelengths, kinetic colorimetric assays or detecting the level of incorporation of a variety of dyes. The absorbance value limits are 0.010 to 1.06 A with very high reproducibility. For nucleic acids, this allows the detection of concentrations of dsDNA from 5 to 4000 ng/uL and, RNA from 4 to 3200 ng/uL. The samples can be excited in the 190 to 1100 nm range and scanned within the 200 to 950 range.

Location: GE S110.04.

The Cary 60 spectrophotometers are used for quantification of light-absorbing materials. The scanning range of these instruments spans from 190 nm to 1100 nm, therefore UV-absorbing molecules such as DNA and proteins, as well colored materials can be easily be quantified. Absorbance readings can be taken from 0.001 (just above the noise level) to 3 absorbance units. These spectrophotometers use single source full spectrum Xenon flash lamps. One of the units at the CSFG is dedicated for use with plastic or quartz cuvettes, while the other is dedicated for use with a fibre-optic probe, which can be directly dipped into the solution of interest.

Location: GE 200.01, GE 330.00.

The CSFG has numerous options for gradient PCR. The Eppendorf Mastercycler Gradient Thermal Cycler is capable of establishing a temperature gradient across its functional surface (midpoint +/- 1° C to 10° C, or a 2° C to 20° C gradient, with the lowest temperature of a gradient being 4° C and the highest 99° C), allowing a quick determination of the optimal annealing temperature for PCR reactions. It can accomodate 96 x 0.2 ml or 77 x 0.5 ml PCR reaction tubes or one 96-well microtiter plate.

We have several ABI Veriti thermocyclers, whose temperature can range from 4.0ºC to 99.9º C with ±0.25º C accuracy in the 35º C – 99.9º C range and the maximal ramp rate is 3.9º C/sec. The 96 well block is separated into 6 block zones, whose temperature can be controlled independantly. The Veriti can accomodate 96 x 0.2 ml PCR reaction tubes or one 96-well microtiter plate (reaction volume 10-80 ul).

Finally, the Techne Touchgene Gradient Thermal Cycler also establishes a gradient across its temperature block, but has a slightly more linear and larger maximum gradient (midpoint +/- 0.5° C to 15° C, or a 1° C to 30° C gradient, with the gradient range being from 20° C to 70° C and operating temperatures from 4° C to 99° C) than the Eppendorf model. It can accomodate 96 x 0.2 ml microtubes or one 96-well microtiter plate.

Location: GE S110.04, GE 200.00.

The CSFG possesses a number of different PCR machines, each with unique capabilities. We have four Applied Biosystems GeneAmp PCR System 9700 units primarily used for PCR-based DNA sequencing and for amplifying high throughput PCR reactions in 96-well microtiter plates (capacity of 96 x 0.2 ml microtubes or one 96-well microtiter plate). The CSFG has an additional interchangeable block for the GeneAmp 9700 that can accomodate two 384-well (25 µl capacity) microtiter plates.

Location: GE S110.04, GE 200.00, SP444.00 (Biology).

The Eco real-time PCR instrument can be used for quantitative PCR (absolute quantification or relative quantification) using SYBR green/EvaGreen or fluorescent probes (FAM, HEX, VIC, ROX, and Cy5 dyes), allelic discrimination by end-point fluorescence using probes and finally SNP genotyping, mutation screening and methylation analysis by High-Resolution Melt curve analysis uusing fluorescent probes and EvaGreen (in High Resolution Melt experiments). Many features make this instrument stand out from other qPCR instruments: 1) fast ramp rate makes typical experiments last 40-60 minutes; 2) reaction volume is 5 to 10 ul, drastically reducing the cost of reagents; 3) tight temperature control leads to very small standard deviations in Ct between replicates on the same plate, between two plates, or even between two instruments; 3) software is easy to use to design your experiments and analyze your results (can download for free here). The Eco has to be used with custom 48 well plate and plastic film and we recommend using 5X master mixes. For High Resolution Melt genotyping, we recommend EvaGreen master mixes made specifically for this purpose. Its optics are based on LED excitation (452–486 nm, 542–582 nm), emission filters (505–545 nm, 562–596 nm, 604–644 nm, and 665–705 nm) and a CCD camera.

Location: one in GE S101 (belongs to Biology) and the other in GE 301.00 (belongs to Walsh lab).

The Beadbeater can homogenize tissue or cell samples in order to isolate proteins, DNA or RNA. It can process samples in 1 to 3 minutes in 0.1 ml to 1 ml of buffer containing glass or ceramic beads. Up to eight 1.5 ml microcentrifuge tubes can be accomodated in the sample chamber. The timer can be set from 1 to 5 minutes (or on hold) and the speed can be varied from 100 to 3200 rpm.

Location: GE S110.04.

The Powerwave HT plate reader can measure optical densities of samples in 96-well or 384-well microtiter plates. A monochromator with a xenon flash lamp is used to allow selection of wavelenghts from 200 - 999 nm in 1 nm increments without the use of filters. The instrument has a dynamic range of 0 - 4.0 OD units. Temperature can be set from 4° C above ambient to 50° C and plate shaking can be programmed if necessary. Microtiter plates can be read in endpoint, kinetic, spectral scanning and well scanning modes. Using the normal reading speed, a 96-well plate can be read in 20 sec (a 384-well plate in 66 sec); using the rapid reading speed, a 96-well plate can be read in 11 sec (384-well plate in 23 sec); using the sweep reading speed, a 96-well plate can be read in 5 sec (384-well plate in 11 sec).

Location: GE S101

The J-20I, J-26XP and J-30I are high speed centrifuges designed to meet the standard requirements of most laboratories, such as spinning down cells, purifying DNA, or separating macromolecules. Rotors: JA-10 (6 x 500 ml bottles), JA-14 (6 x 250 ml bottles), JA-30.50 Ti (8 x 50 ml tubes), JS-24.15 (6 x 15 ml tubes; swinging bucket), JS-4.3 with adapters for 4 x 750 ml bottles, 4 x 500 ml bottles, 4 x 250 ml bottles, 8 x 50 ml conical tubes, 28 x 15 ml conical tubes, 4 x microtiter plates (stackable up to 3 shallow-well plates per carrier).

The Beckman Allegra X12-R refrigerated tabletop centrifuge has a SX4750A Aries swinging bucket with holders for 15 ml conical tubes (up to 56), 50 ml conical tubes (up to 16) or four 250 ml bottles as well as microplate carriers for 96 well plates.

Location: GE 330.00 and GE 230.00. Biology also has one in SP 380.01

The Speed Vac is primarily used for concentrating dilute solutions of proteins or DNA or completely evaporating the solvent from these solutions. Acceptable solvents include water, ethanol, methanol and acetonitrile. The Speed Vac can process up to 40 x 1.5 ml or 96 x 0.2 ml microcentrifuge tubes or two microtiter plates. The unit can either be operated at room temperature or from 35° C to 80° C, in 5° C increments. An oil-free (therefore, low-maintenance) pump provides the vacuum.

Location: GE S110.04.

The Thermo ModulyoD freeze dryer is used to remove moisture from samples. It has a condenser chamber capacity of 5 liters (maximum ice capacity of 4.5 kg) and can remove 1.2 kg of ice from frozen samples in 24 hours. The instrument operates at -50° C and about 30 ubar. A 24-port drum has neoprene valves that can accomodate flasks of up to 4 liters each. Small volume samples can be placed inside the drum in trays, beakers, vials or microtubes.

Location: GE S110.04.

The CHEF-DR III Pulsed Field Electrophoresis System allows very large (chromosome-sized, or millions of base pairs) DNA molecules to be efficiently separated. DNA resolved in such a manner can be used for karyotype analysis, chromosomes can be probed to map the locations of genes of interest and DNA digested with restriction endonucleases can be probed to detect restriction fragment length polymorphisms. The 14 cm x 12.7 cm pulsed field certified agarose gel can be loaded with up to 15 samples (6 mm x 1.5 mm well) and the Cooling Module is used to set the buffer temperature to the operational 14° C.

Location: GE 200.04.

The Bio-Rad electroporator permits the introduction of exogenous DNA into prokaryotic or eukaryotic cells at high efficiencies. It can be used for the standard introduction of plasmid DNA during cloning applications or for other experiments, such as the insertion of DNA for gene replacement through recombination. Resistance can be set from 50 to 400 ohms (low range) or 500 to 1000 (or "infinite") ohms (high range); capacitance from 1.0 to 50 µF (or user selectable high capacitance); and voltage from 0.2 to 2.5 kV.

Location: GE S110.04.

Location: GE 109

The uFill can dispense reagents into standard 96- or 384-well microtiter plates and into 96- or 384-well deepwell plates. Volumes of 10 to 3000 ul can be added per well of a 96-well plate and 5 to 1500 ul can be added per well of a 384-well plate. Dispense rates depend on the selected dispense volume. Typically, a 96-well plate can be filled with 100 ul of reagent in about 10-15 sec.

Location: GE 109.

Location: GE S126.00