Instrumentation and Services

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Associated instrument: Beckman Coulter XL-I

Analytical ultracentrifugation characterizes macromolecules and complexes in free solution by measuring sedimentation under high centrifugal force. The method can evaluate sample composition, oligomerization, aggregation, and complex formation.

Applications and capabilities

• Solution-state sedimentation analysis
• Heterogeneity, purity, and aggregation assessment
• Oligomerization and reversible association analysis
• Complex formation and condition-dependent comparisons

Sample requirements and instrument details

• Typical sample volume: 400 µL per sample, with additional matching buffer for reference cells and handling.
• Detection: UV/visible absorbance and Rayleigh interference optics.
• Cell windows: quartz and sapphire options are available.
• Preferred absorbance range: approximately 0.1-1.0 OD when expressed for a 1 cm path length at the measurement wavelength.
• Runs are typically performed overnight.
• Simple analysis is performed by the Core; more complex global or mechanistic analysis should be discussed during consultation.

Access and support: Consultation and instrument setup are provided by Core staff. Independent operation may be approved by the Facility Manager after appropriate training, based on the user, project, and instrument requirements.

Associated instrument: MicroCal iTC200

ITC directly measures heat released or absorbed during molecular interactions. A single titration can provide affinity, stoichiometry, enthalpy, and entropy without labeling or immobilization.

Applications and capabilities

• Protein-protein, protein-ligand, and nucleic-acid interaction thermodynamics
• Affinity and binding stoichiometry
• Comparison of mutants, ligands, formulations, or buffer conditions

Sample requirements and instrument details

• A typical starting experiment uses approximately 300 µL of the macromolecule at 10 µM and 50 µL of the ligand at 100 µM. Final concentrations should be designed for the expected affinity and stoichiometry.
• The most informative direct-binding experiments generally satisfy an appropriate c-value; in practice, ITC commonly measures interactions from low-nanomolar to micromolar affinity, while very tight or very weak interactions may require competition designs or another method.
• Samples should be exhaustively buffer-matched. Recommended controls include buffer into buffer, ligand into buffer, and buffer into macromolecule.
• Standard outputs include Kd, stoichiometry (n), enthalpy change (ΔH), and entropy change (ΔS).

Access and support: Training includes an assisted experiment and review of sample preparation, instrument loading, controls, and data fitting. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: JASCO J-815

The JASCO J-815 measures absorbance, circular dichroism, and optical rotary dispersion to characterize biomolecular secondary structure, conformation, stability, and structural transitions.

Applications and capabilities

• Far-UV and near-UV CD spectra
• Absorbance spectra
• Optical rotary dispersion
• Thermal and chemical denaturation
• Conformational and ligand-induced structural comparisons

Sample requirements and instrument details

• Quartz cuvettes with path lengths from 0.02 mm to 1 cm are available.
• The appropriate path length and concentration depend on wavelength range and sample absorbance.
• Users should discuss strongly absorbing buffers, high salt, detergents, or low-wavelength measurements with the Core before sample preparation.

Access and support: Training covers cuvette selection, setup, baseline collection, acquisition, temperature control, and data export. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: Horiba FluoroMax-3/FM3 and Horiba Fluorolog 2

The two fluorometers support conventional excitation and emission measurements and fluorescence anisotropy. The instruments are grouped as one fluorescence spectroscopy service, with instrument selection based on the required temperature control and automation.

Applications and capabilities

• Excitation and emission spectra
• Fluorescence intensity and kinetic measurements
• Polarization and anisotropy
• Binding, conformational, and stability assays
• Temperature-dependent fluorescence measurements and automated titrations on the Fluorolog 2

Sample requirements and instrument details

• Fluorolog 2: Peltier temperature control for temperature ramps, an automated titrator, and anisotropy capability.
• FluoroMax-3/FM3: excitation/emission and anisotropy measurements.
• The FluoroMax plate-reader accessory is non-functional and should not be advertised.
• Cuvette type, volume, wavelength range, and concentration depend on fluorophore brightness, absorbance, and expected signal. Users may bring compatible cuvettes.

Access and support: Training covers wavelength selection, excitation/emission scans, anisotropy, temperature-dependent measurements, automated titration where applicable, and data export. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: NanoTemper Monolith NT.115 Pico

MST quantifies interactions in solution by detecting binding-dependent changes in thermophoretic motion and fluorescence.

Applications and capabilities

• Affinity measurements across protein, nucleic-acid, and small-molecule systems
• Interaction screening and assay optimization
• Measurements in a range of solution conditions with low sample consumption

Sample requirements and instrument details

• The instrument has the standard RED and BLUE detection options for the Monolith NT.115 Pico.
• RED channel: excitation approximately 600-645 nm; commonly used with Cy5, NT647, and Alexa Fluor 647-type labels.
• BLUE channel: excitation approximately 460-490 nm; commonly used with fluorescein, GFP, Alexa Fluor 488-type labels, and compatible dyes.
• Standard and premium capillaries are stocked. Assay planning should address capillary type, fluorescence level, titration range, adsorption, aggregation, and ligand fluorescence.

Access and support: Training includes dilution-series design, capillary handling, instrument setup, signal-quality review, and binding analysis. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: Wyatt DynaPro Plate Reader III

DLS measures particle-size distributions from Brownian-motion-dependent fluctuations in scattered light. The plate format is useful for screening samples and conditions efficiently.

Applications and capabilities

• Hydrodynamic size and polydispersity analysis
• Aggregation and sample-quality screening
• Formulation and crystallization-condition screening
• Temperature ramps and thermal-stability measurements

Sample requirements and instrument details

• The instrument has the standard capabilities of the DynaPro Plate Reader III. The Core stocks 384-well plates.
• A sample volume of at least 30 µL per well is recommended.
• The nominal hydrodynamic-radius range is approximately 0.5-1000 nm, with sensitivity dependent on particle size, concentration, and sample quality.
• DLS is highly sensitive to dust and large particles; plate cleanliness and appropriate sample clarification are important.

Access and support: Training covers plate selection, sample loading, measurement setup, temperature programs, and interpretation of size distributions. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: Cytiva Biacore T200

SPR provides label-free, real-time analysis of biomolecular binding by monitoring refractive-index changes at a sensor surface during association and dissociation.

Applications and capabilities

• Kinetic rate constants and affinity
• Steady-state affinity analysis
• Concentration and activity measurements
• Binding-site, competition, and interaction-screening assays

Sample requirements and instrument details

• The facility has the standard capabilities of a Biacore T200, including multi-channel analysis, temperature control, kinetic and steady-state workflows, and solvent correction.
• The Core supports common sensor-chip formats and immobilization or capture strategies. Users supply project-specific sensor chips and analytes.
• Assay development should consider immobilization level, reference surfaces, blank injections, regeneration, nonspecific binding, mass transport, and DMSO matching for small molecules.
• Sample concentrations and volumes are project-specific and are established during consultation.

Access and support: New projects begin with assay-design consultation. Routine analysis using the Biacore Evaluation software suite is included. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: Refeyn TwoMP

Mass photometry measures the mass distributions of individual biomolecules and complexes in solution without labels, providing rapid information on oligomeric state, heterogeneity, and assembly.

Applications and capabilities

• Native mass and oligomeric-state determination
• Complex formation and stoichiometry
• Heterogeneity and aggregate detection
• Comparative condition screening
• Controlled-mixing mass photometry using the installed MassFluidix capability

Sample requirements and instrument details

• The instrument has the standard capabilities of the Refeyn TwoMP, including controlled-mixing capability.
• The practical mass range is approximately 30 kDa-5 MDa, with performance depending on sample and buffer.
• Typical measurements use low-nanomolar sample concentrations and approximately 10 µL per measurement, although dilution is optimized during setup.
• Clean, aggregate-free samples and compatible buffers are important for reliable measurements.

Access and support: Training covers calibration, coverslip preparation, sample loading, measurement acquisition, and analysis in Refeyn software. Independent operation may be approved by the Facility Manager after appropriate training.

Associated instrument: LUMICKS C-Trap Dymo-400

The C-Trap combines quad optical tweezers, three-color confocal fluorescence, automated microfluidics, and temperature control for simultaneous mechanical manipulation and fluorescence imaging of single biomolecules and mesoscale systems.

Applications and capabilities

• Single-molecule force spectroscopy
• Force-fluorescence measurements
• Nucleic-acid, protein-nucleic-acid, chromatin, membrane, and condensate studies
• Confocal scans, kymographs, and fluorescence tracking
• Automated microfluidic solution exchange

Sample requirements and instrument details

• Up to four independent optical traps; force acquisition up to 78 kHz on two traps.
• Force resolution below 0.1 pN at 100 Hz and force stability below 0.3 pN over two minutes under specified conditions.
• Three confocal excitation colors: 488, 561, and 638 nm; diffraction-limited imaging optimized for single-fluorophore detection.
• Confocal field of view: approximately 50 µm × 35 µm; scanning up to 100 Hz.
• Advanced automated microfluidics and temperature control from room temperature to 45 °C.
• The surface-assay and short-tether packages are installed. A standard flow cell is available, and the Core can construct sample cells for non-flow applications when appropriate. Assays generally require project-specific tether, bead, labeling, and cell design, which is discussed during feasibility consultation.

Access and support: Access is consultation-first and generally staff-assisted during assay development. Independent operation may be approved by the Facility Manager after project-specific training.

Associated instrument: Stratagene Mx3000P

The Mx3000P provides real-time fluorescence detection during PCR amplification and can also be used for fluorescence-based thermal denaturation and melt-curve measurements.

Applications and capabilities

• User-designed real-time PCR assays
• Fluorescence-based thermal denaturation and melt-curve measurements
• Four-color fluorescence detection with the installed filter sets
• Thermal denaturation experiment design support from Core staff

Sample requirements and instrument details

• Standard 96-well real-time PCR format; users should confirm plate and optical-seal compatibility before use.
• Installed filter sets (excitation/emission): FAM 492/516 nm; HEX/JOE 535/555 nm; REX 585/610 nm; Cy5 635/665 nm.
• Users provide assay-specific plates, optical seals, reagents, primers, probes, and standards.

Access and support: Assisted and trained-user operation are both available at the Facility Manager’s discretion. Core experimental-design assistance is limited to thermal denaturation and melt-curve applications; the Core does not provide experimental-design support for other qPCR applications. Training can cover plate loading, run programming, and data export.