COBRE
Discovery of Chemical Probes and Therapeutic Leads

An NIH Center of Biomedical Research Excellence

Facilities and Instrumentation

NIH-COBRE, Design of Chemical Probes and Therapeutic Leads (PI Joseph Fox, P20-GM104316) has developed core facilities consisting of instrumentation and infrastructure for small molecule synthesis, high throughput catalyst discovery, computation, microscopy, mass spectroscopy, and a suite of instruments that compose our Kinetics Laboratory.  Equipment for mass spectrometry was purchased in collaboration with the COBRE on Biomaterials .

Access to mass spectrometry equipment is available by contacting the MS facility https://sites.udel.edu/mslab/

To inquire about access to other instruments contact Dr. Olga Dmytrenko, odmitr@udel.edu

Core instrumentation supported by P20-GM104316 and P30 GM110758 includes:

1. Waters Autopur LC/MS. Prep scale MS-directed LC system Optimized separation and automated mass directed fraction collection on prep scale. Configured for at-column dilution and high-throughput auto purification with 25–50 mg/injection.

2. Waters SQD2 with UPLC. Routine LC-MS for small molecules Low-resolution, single quadrupole MS, range up to 3000 Da.  Rapid (2.5 min) UPLC-MS analysis of small molecules and peptides.

3. Waters QDa with UPLC. Routine LC-MS for small molecules. Low-resolution, single quadrupole MS, range up to 1250 Da. Rapid (2.5 min) UPLC-MS analysis of small molecules and peptides.

4. Waters Xevo G2-S QTof with UPLC. High Resolution of intact proteins, small molecules High resolution/sensitivity instrument for qualitative and quantitative analysis of proteins, peptides, small molecules over a large dynamic range. Equipped for LC-MS/MS analysis with an ESI source.

5. Agilent Intuvo GC-MS Routine analysis for small molecules. It utilizes ferrule-free, click-and-run connections that enables easy leak-free connections. It is equipped with a head space sampler that allows analysis of samples from a variety of matrices including solids.

6. Bruker MicroFlex MALDI-TOF. Polymer and Protein MS Versatile instrument with reflectron mode (HRMS peptide and lower MW polymers); linear mode (proteins and other macromolecules) and tandem MALDI-MS (peptide/protein sequencing and ID)

 

Additional Core instrumentation supported by P20- GM104316 includes:

7. Malvern Panalytical MicroCal VP-DSC Isothermal Titration Calorimeter (ITC). ITC is a quantitative technique for determining the binding affinity, enthalpy changes, and binding stoichiometry of samples in solution. ITC measures protein and nucleic acid stability and the intermolecular stability of complexes.

8. Mettler-Toledo IC10 React IR in situ Spectrometer. This instrument uses a flexible fiber optic conduit, coupled with 6 mm diameter Diamond ATR probe, to monitor reaction kinetics based on infrared spectroscopy.

9. GE Biacore 3000 Surface Plasmon Resonance (SPR) Instrument. SPR is an optical biosensing technology used to measure molecular and biomolecular interactions on a sensor surface. Measurements are made under continuous flow over the sensor surface.

10. Applied Photophysics Stopped-flow Spectrophotometer. This instrument is used to measure the kinetics of reactions in aqueous solutions with the ability to capture data within 3 milliseconds of mixing. The instrument can monitor dual wavelengths through fluorescence or UV-vis monitoring.

11. Hi-Tech Stopped-flow Spectrophotometer.  Similar description to #4. This instrument is generally used for reactions with organic solvents, whereas instrument 4 is used for aqueous solutions only.

12. JASCO J1500 Circular Dichroism (CD) Spectrometer. CD is a spectroscopic technique for structural, kinetic and thermodynamic study of chiral molecules, especially for the study of protein secondary structure and aggregation state. The system can record CD up to 950 nm, has a Peltier temperature control system (-40 to 130 °C) and can hold both standard and capillary cells.

13. JASCO 810 Circular Dichroism (CD) Spectrometer. Similar description to #6. The system can record CD up to 650 nm and can hold standard cells. 

14. JASCO P2000 Polarimeter Instrument for the characterization of chiral molecules by optical rotation; used by COBRE researchers to characterize optically active small molecules and oligosaccharides.

15. CH Instruments CHI440B Time-Resolved Electrochemical Quartz Crystal Microbalance. This versatile instrument is used for ion-transport studies at electrode surfaces, protein biosensor development and kinetic analysis of small-molecule adsorption/desorption phenomena.

16. High Throughput Experimentation (HTE) center. The HTE center houses the equipment needed to setup and analyze organic reactions in parallel format. It includes an 8 port glovebox equipped with SpeedVac. The glove box allows for 24-well and 96-well microscale experiment screening. It supports rapid identification of catalysts for new reactions, and optimization of reaction conditions. 

glove box

Center for High Throughput Experimentation includes an 8 port glovebox equipped with SpeedVac. The glove box allows for 24-well and 96-well microscale experiment screening. It supports rapid identification of catalysts for new reactions, and optimization of reaction conditions.

17. Biotage Microwave Synthesis Units (2 systems). The Biotage Initiator is an automated unit for high throughput and automated heating of chemical reactions. The Biotage Initiator can run reactions on 0.2 to 20 mL without system modifications, allowing direct scale-up of milligrams to grams.  The Initiator systems are configured with eight-vial autosamplers.   

18. Shimadzu Semi-preparative HPLC system. This LC-2010 HPLC system is configured with an autosampler, diode array detector, fraction collector and semiprep scale pumps capable of delivering binary gradients at 25 mL/min. The fraction collector is located in a ventilated cabinet.

19. Biotage V-10 Evaporator. This solvent evaporation system rapidly dries samples directly in vials in organic solvents up to 20 times faster than traditional rotary evaporators. For aqueous samples, concentration takes minutes as opposed to hours through concentration on a lyopholyzer.

20. Karl-Fischer Titrator. Used to quantify the water content in anhydrous solvents, to ensure that the solvents are suitable for moisture sensitive reactions.

21. Shared Computational Resources. Our center has developed shared computational resources that can facilitate highly parallel molecular dynamics for protein calculations as well as DFT and ab initio calculations for research in synthetic and inorganic chemistry. This computational computer cluster currently contains 518 3.2 GHz Intel Haswell based Xeon processor cores inter-connected with 40GB Ethernet, with a total of 3.5 TB of RAM.  The cluster is well suited for highly parallel molecular dynamics, density functional theory calculations, and high throughput virtual screening.  The cluster has 34 compute nodes, 2 high memory nodes, a 1GB switch for installation, and 40GB ethernet and RAID cards for the cluster frontend to connect to the storage devices. 

computer lab

22. Zeiss Laser Scanning Confocal Microscope 800 with incubation chamber. This confocal microscope is used for cell culture and materials characterization efforts. Samples can be imaged within multiwell plates or chamber slides with temporal and 3D spatial resolution, providing a method for evaluating time-course responses of cells to chemical probe molecules.  Continuous imaging provides for real-time examination of rapid or complex cell responses.  Throughput for this confocal microscopy system is further enabled by an independent image analysis workstation for quantifying cell responses in 2D or 3D with Volocity software.  

23. Evos FL fluorescence microscope located in the COBRE cell culture facility in Brown Labs. The Evos FL has a fully computer controlled stage/Z/filters.  The Evos FL has a fully integrated Onstage incubator that can control CO2, O2, and provide 80% humidity. 

24. Shared Resources for Cell Culture and Microscopy. The COBRE supports small instruments in the central cell culture facility, including an Olympus CK40 Inverted Microscope, cell culture incubators, and Sorvall RC5 centrifuge.