Macromolecular Analysis Shared Resource
Contact Information
Directors:
Christopher Albanese ,
PhD
Habtom Ressom, PhD
Phone: (202) 687-3305 or (202) 687-2283
Postal Address:
E401, The Research Building
3970 Reservoir Rd, NW
Washington, DC 20007
Description
The Lombardi Macromolecular Analysis Shared
Resource (MASR) provides service for microarray
analysis and DNA sequencing. The resource also
houses, supervises, and maintains instruments
including a densitometer, molecular
modeling workstations, luminometer, fluorescence
polarization, glass slide scanner, real time RT-PCR,
bioanalyzer, and spectrophotometers.
Services
- Microarray Analysis
- DNA Sequencing
- Densitometry and Image Analysis
- Molecular Modeling
- Fluorescent Spectrophotometry
- UV Spectrophotometry
- Plate Readers (Fluorescence, Absorbance, Luminescence)
- NanoDrop ND-1000 Spectrophotometer
1. Microarray Analysis:
The Macromolecular Analysis Shared Resource (MASR) at Lombardi Comprehensive Cancer Center (LCCC) provides microarray services. MASR houses the following instruments: (1) Affymetrix GeneChip analysis system with fluidic station, hybridization oven, GeneChip scanner, and computer workstations for Affymetrix data acquisition, storage, and analysis; (2) Agilent system that includes a hybridization oven, Agilent DNA microarray scanner (G2565AA), and Feature Extraction software; (3) GenePix 4000A glass slide scanner (Axon Instruments) and GenePix Pro software; (4) Agilent Bioanalyzer 2100 (lab-on-a-chip) for RNA analysis in nanogram concentrations; and (5) ABI sequence analyzer HT7900 for real-time polymerase chain reaction (Real-Time PCR) experiments.
In collaboration with the LCCC Biostatistics and Bioinformatics Shared Resource, MASR
provides state of the art bioinformatics and statistical tools for pre-processing and
analysis of microarray data. For more information, contact
Habtom Ressom or visit our homepage.
For information on wet lab procedures and assays, contact
Xiaojun Zou.
To complete an online sample submission form,
click here.
2. DNA Sequencing:
DNA sequencing uses ABI 3100 Genetic Analyzer, a fluorescence based DNA analysis system utilizing capillary electrophoresis. This service provides high quality results, fast turn-around times and no minimum number of reactions. ABI 3100 Genetic Analyzer is housed in Dr Hamilton’s Lab, Biology Dept, 703 Reiss Science. MASR runs DNA sequencing in conjunction with Dr. Hamilton’s Lab. Click here for more information, or contact M.D. Islam.
MASR also provides reagents and supplies as listed below.
DNA sequencing/Fragment analysis related products:
Primers:
| 21M13 Primer |
5' tgt aaa
acg acg gcc agt 3' |
| M13 Reverse
Primer |
5' cag gaa
aca gct atg acc 3' |
| T7 Primer |
5' taa tac
gac tca cta tag gg 3' |
| T3 Primer |
5' att aac
cct cac taa agg ga 3' |
| SP6 Primer |
5' att tag
gtg aca cta tag 3' |
Columns:
| Spin Columns (Fluorescent labeling
reaction purification) |
| Microcon-100
Columns |
Kits:
| ABI PRISM Dye Terminator Cycle Sequencing
Reaction Kit with AmpliTaq, FS |
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3. Densitometry and Image Analysis:
The Alpha Innotech Chemiimager is equipped with a 12-bit peltier cooled CCD detection camera with filters with wavelengths of 595, 500, 460, and 630. It has light sources for transillumination and epiillumination of both visible and fluorescent samples. Images are captured as digital image files and are stored on the attached computer. The computer has a Zip drive and rewriteable CD for data storage. The images can also be quantified using the software on the attached computer. Images can be printed using the attached thermal printer.
For more information, contact
M.D. Islam or X. Zou.
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4. Molecular Modeling:
As a part of molecular modeling services, MASR provides latest computational tools and expertise in various areas of drug discovery such as protein structure/property prediction and analysis, sequence analysis, homology modeling, molecular docking, molecular dynamics simulations, and QSAR analysis.
MASR hosts various tools for molecular analysis. For example, sequence analysis tools allow display, editing, transforming, and analysis of protein and nucleic acid sequences including homology search and multiple sequence alignment. Macromolecular analysis can be performed by molecular mechanics, molecular dynamics, and quantum-mechanical methods to obtain optimum structure, molecular properties, and description of electrostatic interactions. Macromolecular analysis also provides theoretical estimates of optimum molecular geometries, energies of reactions that can be useful in evaluating spectroscopic data.
Macromolecular associations, e.g., protein-protein, protein-DNA, or protein-ligand interactions can be studied with the aid of a high-resolution graphic display system that can determine optimal interactions and conformational searches. Specialized computational and graphical tools can also be used for the analysis of structural and energetic properties. In addition, methods based on molecular simulation provide useful tools for description of molecular reaction mechanisms and dynamic protein flexibility.
To perform a search for small molecules, MASR has acquired an extensive small molecule database library of structures from ChemNavigatior Inc. MASR is using ChemNavigatior Inc. products on a collaborative basis. MASR has access to ChemNavigator's iResearch Library database of screening compounds, which provides comprehensive tracking of all classes or commercial screening compounds (14.1 million unique structures).
The MASR has access of several molecular modeling programs including Insight II, SYBYL 7.0, and protein-protein and protein-ligand docking software. This software allow visualization, docking, comparative modeling, quantum mechanics (QM), molecular mechanics (MM), molecular dynamics (MD) simulation, and Computer Aided Drug (CADD) designing.
Software modules currently available in MASR can be used for searching, downloading, examining, and analyzing macromolecular structures (e.g., protein structures from the Brookhaven PDB database), and for docking purposes. These software run interactively on Silicon Graphics (SGI) workstations. MASR houses several SGI workstations fully capable of running this software.
In addition to access to hardware and software, MASR provides consultation on collaborations. The MASR staff provides advice in the design of computational study approach, instruction in the use of the software and hardware, and assistance in data interpretation. For more information contact
Sivanesan Dakshanamurthy.
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5. Fluorescent Spectrophotometer:
We have a Hitachi F-4500 Fluorescence Spectrophotometer. This instrument can be used to
measure fluorescence, phosphorescence and luminescence in the ultraviolet and visible
regions of the spectrum. This instrument is also equipped with a Hitachi A-3000
autosampler.
For more information, contact
M.D. Islam or X. Zou.
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6. UV Spectrophotometer:
We have a Beckman DU-640 Spectrophotometer. This can be used to measure the UV or
visible optical density of samples.
For more information, contact
M.D. Islam or X. Zou.
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7. Plate Readers (Fluorescence, Absorbance, Luminescence):
Wallac VICTOR2 96-well plate reader. This instrument
is capable of measuring flash or glow luminescence, fluorescence, high-sensitivity
time-resolved fluorescence, flash absorbance, and photometry. It is connected to a PC
computer for data collection and analysis.
Tecan Ultra fluorescence microplate reader. This plate reader is capable of reading steady state fluorescence, time-resolved fluorescence, fluorescence polarization, and luminescence. The wavelength usable range is 230 to 850 nm. It can read plates with 6 to 1536 wells. The sensitivity for fluorescence (fluorescein) is 1 pM and for time resolved fluorescence (europium) is 3 amols. Precision for fluorescence polarization assays is 3 mP. The instrument is controlled by a computer that can also be used for data analysis.
For more information, contact
M.D. Islam or X. Zou .
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8. NanoDrop ND-1000 Spectrophotometer:
The NanoDrop ND-1000 is a full-spectrum (220-750nm) spectrophotometer that is used to measure samples as small as 1ul with high accuracy and reproducibility. It also has the capability to measure highly concentrated samples without dilution.
The applications of NanoDrop ND-1000 spectrophotometer include for measuring nucleic acid concentration and quality of nucleic acid samples up to 3700 ng/ul (dsDNA) without dilution, fluorescent dye labeling density of nucleic acid microarray samples, purified protein analysis (A280) up to 100 mg/ml (BSA), and etc..
For more information, contact M.D. Islam or X. Zou.
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Personnel
Christopher Albanese, PhD
Phone: (202) 687-3305
E-mail: albanese@georgetown.edu
GD10 Preclinical Science
3970 Reservoir Rd, NW
Washington, DC 20057
Habtom Ressom, PhD
Phone (202) 687-2283
E-mail: hwr@georgetown.edu
Room 174, Building D
4000 Reservoir Rd, NW
Washington, DC 20057
Sivanesan Dakshanamurthy, PhD
Phone: (202) 687-2347
E-mail: sd233@georgetown.edu
Lombardi Comprehensive Cancer Center
E401, The Research Building
3970 Reservoir Rd, NW
Washington, DC 20057
Xiaojun Zou, MS
Phone: (202) 687-7776
E-mail: zoux@georgetown.edu
E401, The Research Building
3970 Reservoir Rd, NW
Washington, DC 20057
M.D. Islam, MD
Phone: (202) 687-7776
E-mail: mni3@georgetown.edu
E401, The Research Building
3970 Reservoir Rd, NW
Washington, DC 20057
Xin (James) Li, MS
Phone (202) 687-8533
E-mail: xl35@georgetown.edu
Room 176, Building D
4000 Reservoir Rd, NW
Washington, DC 20057
Acknowledgements
For funding purposes, it is important to acknowledge the Macromolecular Analysis Shared Resource in all publications that include data derived from the resource.
