Biophysics & Biochemistry Core
About the Core
The Biophysics & Biochemistry (B2) Core is home to a variety of equipment, as well as a skilled staff who can offer services, training and support. Research applications include measurement of hydrodynamic properties of macromolecules, determination of molecular oligomerization and stoichiometry, secondary structure analysis of proteins, peptides, and RNA, molecular size and shape measurements, fluorescence signal, molecular interaction measurements, gel and western-blot imaging and analysis, and much more.
The core offers access to state-of-the-art instrumentation for characterizing protein, nucleic acid, and small molecule structures and their interactions. We support researchers by studying spectroscopic and biophysical traits of molecules, identifying structures and interactions that are essential to the drug discovery process, and elucidating biological mechanisms. We also train researchers to design and perform the experiments. We’re always looking to expand our instrument inventory; please contact us if you think you have equipment that would make a good addition to this core.
Services
B2 core equipment is available to access at a per-hour or per-half hour rate. Some equipment may be rented by the day to save on cost. All equipment requires training by skilled core personnel. Some limited theory training may also be available. Equipment rental services are currently only offered to Scripps Research personnel.
The B2 core offers direct measurements of submitted samples by skilled personnel. Because of the dynamic nature of these experiments, there is no set fee for each measurement. Direct experimentation is available to both scientists at Scripps Research and outside institutions. Please inquire for details.
Instruments: Measuring Biomolecular Interactions
SPR is a well-established technique for observing and measuring the association and dissociation of molecular complexes. The Biacore S200 is specifically manufactured for studying the interactions of large macromolecules with their small molecule counterparts. Results may include:
- Binding kinetic constants (ka kd)
- Binding dissociation/association constants (Ka/Kd)
- Concentration determination
- Inhibitor Binding Concentrations (IC50)
| Biacore S200
$360/day (internal pricing, rental fee includes daily consumable usage, excluding chips) |
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BLI is a new and revolutionary technology for observing and measuring the association and dissociation of molecular complexes. Results are like those measured using SPR and may include:
- Binding kinetic constants (ka kd)
- Binding dissociation/association constants (Ka/Kd)
- Concentration determination
- Inhibitor Binding Concentrations (IC50)
| OctetR8 and OctetRED96
$47/hr and $42/hr (internal pricing, rental fee includes daily consumable usage, excluding biosensors) |
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GCI is a well-established technique for observing and measuring the association and dissociation of molecular complexes. The Malvern Panalytical – Wave instrument is specifically manufactured for studying the interactions of large macromolecules with their small molecule counterparts. The Rapid Kinetics function allows for screening of hundreds of small molecules in a 24 hr period. Results may include:
- Binding kinetic constants (ka, kd)
- Binding dissociation/association constants (Ka/Kd)
- Concentration determination
- Inhibitor Binding Concentrations (IC50)
| Malvern – Wave
Full-service only (internal pricing) |
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MicroITC is a technique that measures the association of molecular complexes indirectly by measuring the enthalpic change. ITC is a powerful tool for determining thermodynamic components, and results may include:
- Binding enthalpy (∆H)
- Binding entropy (∆S)
- Binding dissociation/association constants (Ka/Kd)
- Inhibitory Concentrations (IC50)
| PEAQ-ITC
$35/hr (internal pricing only) |
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MST is a new technique for observing and measuring the molecular interaction of molecules. MST is revolutionizing the field of fluorescence-based binding technology as it does not experience the same size restrictions as fluorescence polarization/anisotropy. Results may include:
- Binding dissociation/association constants (Ka/Kd)
- Inhibitory Concentrations (IC50)
| Monolith NT.115
$45/hr (internal pricing only) |
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Mass Photometry is a new technology capable of analyzing molecules in solution and giving the molecular weights and relative distributions. This is a single-molecule technique and so requires samples to be between 100 pM-100 nM for best results.
| Mass Photometry Refeyen TwoMP (MP)
$50/hr (internal pricing, rental fee includes daily consumable usage) |
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The B2 core is equipped with high-throughput qPCR (384 well). Customers are expected to supply their own reagents and consumables. A short training session is required before use of the equipment. The Quantstudio Pro 6 qPCR instrument operates with 384 well plates and plate seals. The instrument operates with either low ROX or no ROXin any qPCR amplification mix. ThermoFisher plates to be used with the instrument are; MicroAmp™ EnduraPlate™ Optical 384-Well Clear Reaction Plates Barcode, 20 plates cat. no. 4483285 or MicroAmp™ Optical 384-Well Reaction Plate with Barcode, 50 plates cat. no. 4309849, and Optical Adhesive Covers cat. no. 4360954.
| QuantStudio 6 Pro
$60/hr (internal pricing only) |
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Instruments: Liquid Handling
The Mosquito HV is a 384-well plate high-throughput liquid pipettor for small volumes (less than 5 µL). We are available for any collaborative projects where high throughput liquid handling may be considered essential.
| Mosquito HV
Inquire for pricing. |
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Instruments: Measuring Enzyme Kinetics
This instrument measures the excitation and emission of fluorophores in a cuvette. Because of the larger sample size, and the strong light source, this instrument is more sensitive than most plate-readers. Accessories include a polarizer and temperature control cell. Resulting data may include:
- Absolute Fluorescence Signal
- Quantification
- Enzymatic assays
- FRET
| Cary Eclipse
$20/hr (internal pricing only) |
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Plate readers are dynamic instruments that may measure absorbance, fluorescence, and luminescence in 96-well and other plate formats. This plate reader is monochromator based, and is capable of the following results:
- Measurement of absolute fluorescence, luminescence, and OD signal of wavelengths that have an associated filter for:
- Quantification
- Enzymatic assays
- FRET
- Growth curves
| NanoQuant Cuvette and Plate Reader
$20/hr (internal pricing only) |
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Powerful UV spectrophotometer which measuring sample absorbance in standard cuvettes. Applications may include:
- Absorbance determination and quantification
- Growth curves
- Enzymatic assays
| Cary 100 UV Spectrophotometer
$20/hr (internal pricing only) |
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This instrument measures the excitation and emission of fluorophores in a cuvette. Because of the larger sample size, and the strong light source, this instrument is more sensitive than most plate-readers. Accessories include a polarizer and temperature control cell. Resulting data may include:
- Absolute Fluorescence Signal
- Quantification
- Enzymatic assays
- FRET
| Cary Eclipse
$20/hr (internal pricing only) |
|
Plate readers are dynamic instruments that may measure absorbance, fluorescence, and luminescence in 96-well and other plate formats. This plate reader is monochromator based, and is capable of the following results:
- Measurement of absolute fluorescence, luminescence, and OD signal of wavelengths that have an associated filter for:
- Quantification
- Enzymatic assays
- FRET
- Growth curves
| NanoQuant Cuvette and Plate Reader
$20/hr (internal pricing only) |
|
Instruments: Imaging Gels and Blots
For imaging of phosphor-screens, and compatible with both magnetic-receptive and standard phosphoscreens.
| Typhoon IP
$10/0.5 hours (internal pricing only) |
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This documentation system images blots and gels using a variety of white, UV, and single wavelength light sources. Light sources include:
- White light for imaging of SDS PAGE and other gel formats.
- UV Trans imaging of agarose and other gel formats.
- Fluorescence for imaging of gels and blots. Wavelengths include:
- Trans-UV, 302 nm excitation
- Trans-blue, 450−490 nm
- Epi-blue, 460−490 nm excitation
- Epi-green, 520−545 nm excitation
- Epi-red, 625−650 nm excitation
- Epi-far red, 650−675 nm excitation
- Epi-near IR, 755−777 nm excitation
- Chemiluminescence for imaging blots
| Chemidoc MP
$10/0.5 hours (internal pricing only) |
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This high-resolution documentation system images blots and gels for fluorescence and chemiluminescence.
- >6 log dynamic range
- 5, 10, 20, 50, or 100 um resolution
| Odyssey M Imager
$10/0.5 hours (internal pricing only) |
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Instruments: Biophysical Characterization of Macromolecules
Analytical ultracentrifugation is a technique for measuring a molecule’s (or molecular complex’s) hydrodynamic properties. This can lead to the determination of general molecular shape changes and molecular weight determination. The Optima XL-I offers both absorbance and interference detection systems. Experimental methods include:
- Sedimentation velocity
- Sedimentation equilibrium
| Optima XL-I – analytical ultracentrifuge
Full-service only (internal pricing) |
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| Jasco J815 Spectrometer/Spectropolarimeter
$45/hr (internal pricing) |
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| MP: Refeyn TwoMP
$50/hr (internal pricing, rental fee includes daily consumable usage) |
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This instrument measures the excitation and emission of fluorophores in a cuvette. Because of the larger sample size, and the strong light source, this instrument is more sensitive than most plate-readers. Accessories include a polarizer and temperature control cell. Resulting data may include:
- Absolute Fluorescence Signal
- Quantification
- Enzymatic assays
- FRET
| Cary Eclipse
$20/hr (internal pricing only) |
|
Plate readers are dynamic instruments that may measure absorbance, fluorescence, and luminescence in 96-well and other plate formats. This plate reader is monochromator based, and is capable of the following results:
- Measurement of absolute fluorescence, luminescence, and OD signal of wavelengths that have an associated filter for:
- Quantification
- Enzymatic assays
- FRET
- Growth curves
| NanoQuant Cuvette and Plate Reader
$20/hr (internal pricing only) |
|
Powerful UV spectrophotometer which measuring sample absorbance in standard cuvettes. Applications may include:
- Absorbance determination and quantification
- Growth curves
- Enzymatic assays
| Cary 100 UV Spectrophotometer
$20/hr (internal pricing only) |
|
This instrument measures the excitation and emission of fluorophores in a cuvette. Because of the larger sample size, and the strong light source, this instrument is more sensitive than most plate-readers. Accessories include a polarizer and temperature control cell. Resulting data may include:
- Absolute Fluorescence Signal
- Quantification
- Enzymatic assays
- FRET
| Cary Eclipse
$20/hr (internal pricing only) |
|
Plate readers are dynamic instruments that may measure absorbance, fluorescence, and luminescence in 96-well and other plate formats. This plate reader is monochromator based, and is capable of the following results:
- Measurement of absolute fluorescence, luminescence, and OD signal of wavelengths that have an associated filter for:
- Quantification
- Enzymatic assays
- FRET
- Growth curves
| NanoQuant Cuvette and Plate Reader
$20/hr (internal pricing only) |
|