The long term goal of this proposal is the development of tools enabling high throughput single-molecule fluorescence spectroscopy.
The specific aims of this proposal are: (1) Develop an optical setup for 3 color, 48 spot excitation and detection. (2) Develop a 48 pixel custom single-photon avalanche photodiode array (48p-SPADA). (3) Develop field-programmable-gate-array (FPGA) data reduction algorithms for up to 144 channels single-molecule burst analysis. (4) Develop high-throughput fluorescence (cross)-correlation spectroscopy data analysis algorithms in graphical processing unit (GPU). (5) Study fast and transient events in transcription initiation and elongation, focusing on the conformation and interactions of ?70 with the bacterial RNAP holoenzyme. The expected outcome of this proposal is an increase in throughput for single molecule fluorescence techniques of a factor 48. This will include most single-molecule fluorescence techniques such as single-molecule fluorescence resonant energy transfer (smFRET) and microsecond alternating laser excitation (?s-ALEX) as well as fluorescence correlation spectroscopy (FCS). The impact of these developments will be twofold. First, single-molecule fluorescence spectroscopy methods will become attractive to a larger research community, which will be able to use is as an efficient discovery and analytical tool. Additionally, it will give access to new temporal regimes that are unattainable with the current technology. Second, the leap in throughput (by a factor 48) will render this technology attractive for point-of-care diagnostics and large scale screening assays used by the biotechnology and pharmaceutical industry. For these reasons, this proposal is very likely to significantly impact the progresses of many areas of biological research including drug discovery and development as well as diagnostics, thus helping increase our understanding of life processes and lays the foundation for advances in disease diagnosis, treatment, and prevention.

Public Health Relevance

The development of new detectors for high-throughput single-fluorescence molecule spectroscopy will result in accelerated measurements and enable highly parallel studies. This will allow mainstream researchers to take advantage of this powerful technology, thus accelerating the pace of discovery. It will also make high-throughput diagnostics and drug screening applications of single-molecule a practical reality, therefore permitting advances in disease diagnosis, treatment, and prevention.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Deatherage, James F
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University of California Los Angeles
Schools of Arts and Sciences
Los Angeles
United States
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Gulinatti, Angelo; Ceccarelli, Francesco; Rech, Ivan et al. (2016) Silicon technologies for arrays of Single Photon Avalanche Diodes. Proc SPIE Int Soc Opt Eng 9858:
Ingargiola, Antonino; Lerner, Eitan; Chung, SangYoon et al. (2016) FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET. PLoS One 11:e0160716
Ceccarelli, Francesco; Gulinatti, Angelo; Labanca, Ivan et al. (2016) Gigacount/second Photon Detection Module Based on an 8 × 8 Single-Photon Avalanche Diode Array. IEEE Photonics Technol Lett 28:1002-1005
Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert et al. (2016) Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments. Biophys J 110:26-33
Lerner, Eitan; Chung, SangYoon; Allen, Benjamin L et al. (2016) Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 113:E6562-E6571
Peronio, P; Acconcia, G; Rech, I et al. (2015) Improving the counting efficiency in time-correlated single photon counting experiments by dead-time optimization. Rev Sci Instrum 86:113101
Michalet, Xavier; Ingargiola, Antonino; Colyer, Ryan A et al. (2014) Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy. IEEE J Sel Top Quantum Electron 20:38044201-380442020
Burri, Samuel; Maruyama, Yuki; Michalet, Xavier et al. (2014) Architecture and applications of a high resolution gated SPAD image sensor. Opt Express 22:17573-89
Gong, S; Labanca, I; Rech, I et al. (2014) A 32-channel photon counting module with embedded auto/cross-correlators for real-time parallel fluorescence correlation spectroscopy. Rev Sci Instrum 85:103101
Panzeri, Francesco; Ingargiola, Antonino; Lin, Ron R et al. (2013) Single-molecule FRET experiments with a red-enhanced custom technology SPAD. Proc SPIE Int Soc Opt Eng 8590:

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