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High-throughput single-molecule optofluidic analysis


We describe a high-throughput, automated single-molecule measurement system, equipped with microfluidics. The microfluidic mixing device has integrated valves and pumps to accurately accomplish titration of biomolecules with picoliter resolution. We demonstrate that the approach enabled rapid sampling of biomolecule conformational landscape and of enzymatic activity, in the form of transcription by Escherichia coli RNA polymerase, as a function of the chemical environment.

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Figure 1: A microfluidic formulator for high-throughput single-molecule FRET measurements.
Figure 2: RNAP activity measured with smFRET.


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We thank R. Colyer, P. Blainey and other members of the Weiss and Quake laboratories for helpful discussions. This work was supported by US National Science Foundation Frontiers in Integrative Biological Research grant 0623664 and National Institutes of Health grant GM069709. Fluorescence spectroscopy was performed at the University of California, Los Angeles and California NanoSystems Institute Advanced Light Microscopy and Spectroscopy Shared Facility. A.M.S. was supported by the Stanford University Diversifying Academia, Recruiting Excellence fellowship.

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Authors and Affiliations



S.K., A.M.S. and D.S.M. designed experiments, conducted experiments, wrote and implemented data acquisition and analysis software, and analyzed data. R.R.L. analyzed data. S.K., A.M.S., S.R.Q., S.W. and D.S.M. assisted in writing and editing of the manuscript.

Corresponding authors

Correspondence to Shimon Weiss or Devdoot S Majumdar.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10, Supplementary Note 1, Supplementary Table 1 (PDF 918 kb)

Supplementary Software

Software used in this study to control and coordinate microfluidics and optical components. (ZIP 112854 kb)

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Kim, S., Streets, A., Lin, R. et al. High-throughput single-molecule optofluidic analysis. Nat Methods 8, 242–245 (2011).

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