Facilities

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The RNA Institute Facilities

The RNA Institute is housed in the University at Albany's Life Sciences Research Building which includes four core facilities available for all trainees and faculty: Molecular Biology, Tissue Culture, Biological Imaging, and Structural Chemistry. We have an outstanding environment for research with state of the art equipment to perform analytical, biochemical, biophysical, cellular, chemical computational, and biological experiments. We are powered by the next generation of tools to push the limits of RNA science and technology.

 

    RNA Institute Facilities Virtual Tour

    Computational Facility

    • Six multi-CPU workstations with NVDIA Tesla GPUs from Dell
    • 600-core xeon HPC Linux cluster with 10TB storage, dedicated for RNA Institute research.
    • Access to the university’s general purpose cluster
    • Christie Mirage 6000 3D projector
    • Computational software for molecular modeling, visualization, and simulations including licensed software- Molecular Operating Environment (MOE), PyMOL, Q-Chem, GOLD, Material Studio
    • Access to the Cambridge Structural Database (CSD)


    Instrumentation Facility

    • Automated liquid handlers (2), including capabilities for 96 and 384 well plates- PerkinElmer – Janus Varispan + MDT Automated Workstation, Perkin Elmer
    • Multilabel Microplate reader – including fluorescence, ultra-sensitive luminescence, absorbance, time-resolved fluorescence (TRF) and TR-FRET, – Envision, PerkinElmer
    • Liquid Scintillation Counter-  Tri-Carb, Perkin Elmer
    • Nano Isothermal Titration Calorimeters (2)  (low volume)– TA Instruments
    • Differential Scanning Calirometer – TA Instruments
    • Ultra Performance Liquid Chromatography/ Mass Spectrometry Triple Quadrupole – Acquity I-Class/XevoTQ-S, Waters Corp.
    • Ultra Performance Liquid Chromatography/ Photodiode Array detector – Acquity I-Class/PDA Waters Corp.
    • High Performance Liquid Chromatography /UV detectors (2) – Waters Co.
    • High Performance Liquid Chromatography /UV detector – Prominence, Shimadzu.
    • UV-Vis Spectrophotometers (3) with automated cell changers and thermal ramping – Cary 100, Agilent
    • Oligo Synthesizer – MerMade 4, Bioautomation
    • Sigma RNA libraries, Mission Series including mouse lentiviral shRNA, siRNA Human, and rat druggable genome,  Human and mouse esiRNA and human and mouse pooled shRNA and target ID library which enables bench-top transcriptome-wide human miRNA and ncRNA gene target identification.


    Mass Spectrometry Center

    The RNA Institute Mass Spectrometry (MS) Center is dedicated to the development of MS-based technologies for investigating the structure-function relationships of natural and synthetic RNA as tools for drug discovery.
     

    Novel Mass spectrometry technologies and state of the art instruments

    Consistent with the mission of The RNA Institute, the unique collection of modern instruments, and enabling technologies developed by Dan Fabris at the Mass Spectrometry Center, will be utilized in full-fledged collaborations with colleagues who have projects aimed at reaching a greater understanding of the role of non-coding RNA in gene regulation and viral replication. These insights will lead to the identification of possible targets for early drug discovery operations that could produce new treatments for orphan diseases and alternative drugs for resistant strains responsible for infectious diseases. Mass Spectrometry (MS) has the versatility necessary to accomplish the elucidation of the structure-function relationships of biologically relevant RNA and associated proteins. New methods for evaluating the ability of small molecule ligands to affect the structure of RNA substrates, to modulate their binding properties, and ultimately to influence their biological and pharmacologic activities are currently under development. Strategies combining footprinting and crosslinking reagents with MS detection, collectively known as MS3D, have been devised to pursue the 3D structure determination of RNA and ribonucleoprotein complexes that are not readily amenable to traditional high-resolution techniques. New technologies are being developed for sensitive analysis of RNA adducts with extremely low-copy-number to enable discovery of rare modifications and for in vivo structural determination of targets immersed in their natural cellular environment. These efforts are supported by state of the art instrumentation at The RNA Institute’s Center for Mass Spectrometry. 

    • A 12 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer for ultra high-resolution characterization of large protein-RNA complexes involved in gene regulation and viral replication processes
    • An Orbitrap mass spectrometer for high-resolution determination of protein-RNA crosslinks capable of revealing the identity of cellular factors involved in RNA-mediated functions
    • An ion mobility spectroscopy (IMS) mass spectrometer for investigating the effects of small molecule ligands as possible drug candidates on the conformation of target protein-RNA complexes
    • A quadrupole-time of flight (Q-TOF) instrument interfaced with a nanoflow high-performance liquid chromatography (nanoLC) system for sensitive detection of low copy number RNA modifications