Abstract

Single-molecule FRET (smFRET) spectroscopy is a powerful tool for studying inhomogeneous dynamics in biological systems. However, because of the intrinsic variations that accompany the sample sizes, massive data sets are essential to extract statistically reliable information. In this aspect, a simple motorized stage and autofocusing modification can save time without the expense of a high-end automated microscope. In this report, we describe a simple and economical modification of a commercial inverted microscope with a manual stage to automate the data acquisition and measurement process. We collected 8000 images with a 100 ms exposure time in 1000 fields of view in approximately 13 min, where it would take more than 8 h by manual collection. We demonstrated the method with a DNA oligo quantification experiment. In this experiment, the measurement platform is a FRET signal from a dye-labeled DNA duplex containing unmatched base pairs. The target DNA replaces one of the strands because of the formation of a perfect duplex. This thermodynamically driven exchange reaction causes FRET to disappear, which correlated with the DNA concentration. The data are batch processed with the freeware ImageJ. These modifications are feasible and economical for general smFRET experiments.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Full Article  |  PDF Article
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  5. A. Tufman, F. Tian, and R. M. Huber, “Can microRNAs improve the management of lung cancer patients? a clinician’s perspective,” Theranostics 3(12), 953–963 (2013).
    [Crossref] [PubMed]
  6. C. G. Liu, G. A. Calin, S. Volinia, and C. M. Croce, “MicroRNA expression profiling using microarrays,” Nat. Protoc. 3(4), 563–578 (2008).
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  7. P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  11. P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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    [Crossref] [PubMed]
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    [Crossref] [PubMed]
  16. B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
    [Crossref] [PubMed]
  17. C. Joo and T. Ha, “Single-molecule FRET with total internal reflection microscopy,” Cold Spring Harb. Protoc. 2012(12), 072058 (2012).
    [Crossref]
  18. M. E. Altuntop, C. T. Ly, and Y. Wang, “Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center,” Biophys. J. 99(9), 3002–3009 (2010).
    [Crossref] [PubMed]
  19. L. W. Lee, S. Zhang, A. Etheridge, L. Ma, D. Martin, D. Galas, and K. Wang, “Complexity of the microRNA repertoire revealed by next-generation sequencing,” RNA 16(11), 2170–2180 (2010).
    [Crossref] [PubMed]
  20. C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
    [Crossref] [PubMed]
  21. L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
    [Crossref] [PubMed]

2018 (2)

E. Lerner, T. Cordes, A. Ingargiola, Y. Alhadid, S. Chung, X. Michalet, and S. Weiss, “Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer,” Science 359(6373), eaan1133 (2018).
[Crossref] [PubMed]

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

2015 (1)

Z. Jin, D. Geißler, X. Qiu, K. D. Wegner, and N. Hildebrandt, “a rapid, amplification-free, and sensitive diagnostic assay for single-step multiplexed fluorescence detection of MicroRNA,” Angew. Chem. Int. Ed. Engl. 54(34), 10024–10029 (2015).
[Crossref] [PubMed]

2014 (1)

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

2013 (5)

V. Del Vescovo, T. Meier, A. Inga, M. A. Denti, and J. Borlak, “A cross-platform comparison of affymetrix and Agilent microarrays reveals discordant miRNA expression in lung tumors of c-Raf transgenic mice,” PLoS One 8(11), e78870 (2013).
[Crossref] [PubMed]

L. Yao, Y. Wang, and S. Xu, “Label-free microRNA detection based on exchange-induced remnant magnetization,” Chem. Commun. (Camb.) 49(45), 5183–5185 (2013).
[Crossref] [PubMed]

S. Zadran, F. Remacle, and R. D. Levine, “miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients,” Proc. Natl. Acad. Sci. U.S.A. 110(47), 19160–19165 (2013).
[Crossref] [PubMed]

G. Di Leva and C. M. Croce, “miRNA profiling of cancer,” Curr. Opin. Genet. Dev. 23(1), 3–11 (2013).
[Crossref] [PubMed]

A. Tufman, F. Tian, and R. M. Huber, “Can microRNAs improve the management of lung cancer patients? a clinician’s perspective,” Theranostics 3(12), 953–963 (2013).
[Crossref] [PubMed]

2012 (1)

C. Joo and T. Ha, “Single-molecule FRET with total internal reflection microscopy,” Cold Spring Harb. Protoc. 2012(12), 072058 (2012).
[Crossref]

2011 (3)

H. Schwarzenbach, D. S. Hoon, and K. Pantel, “Cell-free nucleic acids as biomarkers in cancer patients,” Nat. Rev. Cancer 11(6), 426–437 (2011).
[Crossref] [PubMed]

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
[Crossref] [PubMed]

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

2010 (2)

M. E. Altuntop, C. T. Ly, and Y. Wang, “Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center,” Biophys. J. 99(9), 3002–3009 (2010).
[Crossref] [PubMed]

L. W. Lee, S. Zhang, A. Etheridge, L. Ma, D. Martin, D. Galas, and K. Wang, “Complexity of the microRNA repertoire revealed by next-generation sequencing,” RNA 16(11), 2170–2180 (2010).
[Crossref] [PubMed]

2009 (1)

B. T. Wilhelm and J. R. Landry, “RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing,” Methods 48(3), 249–257 (2009).
[Crossref] [PubMed]

2008 (3)

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nat. Methods 5(6), 507–516 (2008).
[Crossref] [PubMed]

C. G. Liu, G. A. Calin, S. Volinia, and C. M. Croce, “MicroRNA expression profiling using microarrays,” Nat. Protoc. 3(4), 563–578 (2008).
[Crossref] [PubMed]

P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
[Crossref] [PubMed]

2006 (1)

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
[Crossref] [PubMed]

2005 (1)

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
[Crossref] [PubMed]

Alhadid, Y.

E. Lerner, T. Cordes, A. Ingargiola, Y. Alhadid, S. Chung, X. Michalet, and S. Weiss, “Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer,” Science 359(6373), eaan1133 (2018).
[Crossref] [PubMed]

Alon, S.

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

Altuntop, M. E.

M. E. Altuntop, C. T. Ly, and Y. Wang, “Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center,” Biophys. J. 99(9), 3002–3009 (2010).
[Crossref] [PubMed]

Ambrose, B.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Andersen, M. R.

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
[Crossref] [PubMed]

Andreasen, D.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Aznauryan, M.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Baeriswyl, L.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Barbisin, M.

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
[Crossref] [PubMed]

Barth, A.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Bernard, N.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
[Crossref] [PubMed]

Birkedal, V.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Borlak, J.

V. Del Vescovo, T. Meier, A. Inga, M. A. Denti, and J. Borlak, “A cross-platform comparison of affymetrix and Agilent microarrays reveals discordant miRNA expression in lung tumors of c-Raf transgenic mice,” PLoS One 8(11), e78870 (2013).
[Crossref] [PubMed]

Bowen, M. E.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Broomer, A. J.

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
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Brown, M.

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
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Calin, G. A.

C. G. Liu, G. A. Calin, S. Volinia, and C. M. Croce, “MicroRNA expression profiling using microarrays,” Nat. Protoc. 3(4), 563–578 (2008).
[Crossref] [PubMed]

Chen, C.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
[Crossref] [PubMed]

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
[Crossref] [PubMed]

Chen, H.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Cheo, D.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Christodoulou, D. C.

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

Chung, S.

E. Lerner, T. Cordes, A. Ingargiola, Y. Alhadid, S. Chung, X. Michalet, and S. Weiss, “Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer,” Science 359(6373), eaan1133 (2018).
[Crossref] [PubMed]

Church, G. M.

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

Cordes, T.

E. Lerner, T. Cordes, A. Ingargiola, Y. Alhadid, S. Chung, X. Michalet, and S. Weiss, “Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer,” Science 359(6373), eaan1133 (2018).
[Crossref] [PubMed]

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Craggs, T. D.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Croce, C. M.

G. Di Leva and C. M. Croce, “miRNA profiling of cancer,” Curr. Opin. Genet. Dev. 23(1), 3–11 (2013).
[Crossref] [PubMed]

C. G. Liu, G. A. Calin, S. Volinia, and C. M. Croce, “MicroRNA expression profiling using microarrays,” Nat. Protoc. 3(4), 563–578 (2008).
[Crossref] [PubMed]

D’Andrade, P.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Del Vescovo, V.

V. Del Vescovo, T. Meier, A. Inga, M. A. Denti, and J. Borlak, “A cross-platform comparison of affymetrix and Agilent microarrays reveals discordant miRNA expression in lung tumors of c-Raf transgenic mice,” PLoS One 8(11), e78870 (2013).
[Crossref] [PubMed]

DeMayo, M.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Dennis, L.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Denti, M. A.

V. Del Vescovo, T. Meier, A. Inga, M. A. Denti, and J. Borlak, “A cross-platform comparison of affymetrix and Agilent microarrays reveals discordant miRNA expression in lung tumors of c-Raf transgenic mice,” PLoS One 8(11), e78870 (2013).
[Crossref] [PubMed]

Derveaux, S.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Di Leva, G.

G. Di Leva and C. M. Croce, “miRNA profiling of cancer,” Curr. Opin. Genet. Dev. 23(1), 3–11 (2013).
[Crossref] [PubMed]

Doroshenko, O.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Eilert, T.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Eisenberg, E.

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

Eminaga, S.

S. Alon, F. Vigneault, S. Eminaga, D. C. Christodoulou, J. G. Seidman, G. M. Church, and E. Eisenberg, “Barcoding bias in high-throughput multiplex sequencing of miRNA,” Genome Res. 21(9), 1506–1511 (2011).
[Crossref] [PubMed]

Etheridge, A.

L. W. Lee, S. Zhang, A. Etheridge, L. Ma, D. Martin, D. Galas, and K. Wang, “Complexity of the microRNA repertoire revealed by next-generation sequencing,” RNA 16(11), 2170–2180 (2010).
[Crossref] [PubMed]

Feng, Y.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Feys, T.

P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
[Crossref] [PubMed]

Fijen, C.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Fulmer-Smentek, S.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Galas, D.

L. W. Lee, S. Zhang, A. Etheridge, L. Ma, D. Martin, D. Galas, and K. Wang, “Complexity of the microRNA repertoire revealed by next-generation sequencing,” RNA 16(11), 2170–2180 (2010).
[Crossref] [PubMed]

Gallo, M.

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
[Crossref] [PubMed]

Garver, J.

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
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Gebhardt, C.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Geißler, D.

Z. Jin, D. Geißler, X. Qiu, K. D. Wegner, and N. Hildebrandt, “a rapid, amplification-free, and sensitive diagnostic assay for single-step multiplexed fluorescence detection of MicroRNA,” Angew. Chem. Int. Ed. Engl. 54(34), 10024–10029 (2015).
[Crossref] [PubMed]

Gerstmayer, B.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Götz, M.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Gouffon, J.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Gouridis, G.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Gratton, E.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Grimley, C.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Guegler, K. J.

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
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Guenther, S.

P. Mestdagh, T. Feys, N. Bernard, S. Guenther, C. Chen, F. Speleman, and J. Vandesompele, “High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA,” Nucleic Acids Res. 36(21), e143 (2008).
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Guettouche, T.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Gullans, S.

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
[Crossref] [PubMed]

Ha, T.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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C. Joo and T. Ha, “Single-molecule FRET with total internal reflection microscopy,” Cold Spring Harb. Protoc. 2012(12), 072058 (2012).
[Crossref]

R. Roy, S. Hohng, and T. Ha, “A practical guide to single-molecule FRET,” Nat. Methods 5(6), 507–516 (2008).
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Hackett, M.

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
[Crossref] [PubMed]

Hafner, M.

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
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Hanke, C. A.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Hao, P.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Harris, J.

L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
[Crossref] [PubMed]

Hartmann, A.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Hartmann, N.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
[Crossref] [PubMed]

Hellenkamp, B.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Hendrix, J.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Hildebrandt, L. L.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
[Crossref] [PubMed]

Hildebrandt, N.

Z. Jin, D. Geißler, X. Qiu, K. D. Wegner, and N. Hildebrandt, “a rapid, amplification-free, and sensitive diagnostic assay for single-step multiplexed fluorescence detection of MicroRNA,” Angew. Chem. Int. Ed. Engl. 54(34), 10024–10029 (2015).
[Crossref] [PubMed]

Hirschfeld, V.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Hohlbein, J.

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Morozov, P.

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
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P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Nguyen, J. T.

C. Chen, D. A. Ridzon, A. J. Broomer, Z. Zhou, D. H. Lee, J. T. Nguyen, M. Barbisin, N. L. Xu, V. R. Mahuvakar, M. R. Andersen, K. Q. Lao, K. J. Livak, and K. J. Guegler, “Real-time quantification of microRNAs by stem-loop RT-PCR,” Nucleic Acids Res. 33(20), e179 (2005).
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Nusbaum, J. D.

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
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L. A. Neely, S. Patel, J. Garver, M. Gallo, M. Hackett, S. McLaughlin, M. Nadel, J. Harris, S. Gullans, and J. Rooke, “A single-molecule method for the quantitation of microRNA gene expression,” Nat. Methods 3(1), 41–46 (2006).
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Peiffer, S.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Pena, J. T.

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
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Peters, T.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Qiu, R.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Qiu, X.

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Rezaei Adariani, S.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Röcker, C.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Sanabria, H.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Schlierf, M.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Schmid, S.

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Schröder, T.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Schroth, G.

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Schuler, B.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Schuster, D.

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Seidel, C. A. M.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Seidel, H.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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Seidman, J. G.

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Shaffer, J. M.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Shelton, E. J.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Silveria, S.

P. Mestdagh, N. Hartmann, L. Baeriswyl, D. Andreasen, N. Bernard, C. Chen, D. Cheo, P. D’Andrade, M. DeMayo, L. Dennis, S. Derveaux, Y. Feng, S. Fulmer-Smentek, B. Gerstmayer, J. Gouffon, C. Grimley, E. Lader, K. Y. Lee, S. Luo, P. Mouritzen, A. Narayanan, S. Patel, S. Peiffer, S. Rüberg, G. Schroth, D. Schuster, J. M. Shaffer, E. J. Shelton, S. Silveria, U. Ulmanella, V. Veeramachaneni, F. Staedtler, T. Peters, T. Guettouche, L. Wong, and J. Vandesompele, “Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study,” Nat. Methods 11(8), 809–815 (2014).
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Staedtler, F.

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Streit, L.

B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. E. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. A. Hanke, A. Hartmann, J. Hendrix, L. L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. G. Hübner, E. Kallis, A. N. Kapanidis, J. Y. Kim, G. Krainer, D. C. Lamb, N. K. Lee, E. A. Lemke, B. Levesque, M. Levitus, J. J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. C. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. M. Vera, K. R. Weninger, B. Wünsch, I. S. Yanez-Orozco, J. Michaelis, C. A. M. Seidel, T. D. Craggs, and T. Hugel, “Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study,” Nat. Methods 15(9), 669–676 (2018).
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L. Yao, Y. Wang, and S. Xu, “Label-free microRNA detection based on exchange-induced remnant magnetization,” Chem. Commun. (Camb.) 49(45), 5183–5185 (2013).
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Angew. Chem. Int. Ed. Engl. (1)

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C. G. Liu, G. A. Calin, S. Volinia, and C. M. Croce, “MicroRNA expression profiling using microarrays,” Nat. Protoc. 3(4), 563–578 (2008).
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PLoS One (1)

V. Del Vescovo, T. Meier, A. Inga, M. A. Denti, and J. Borlak, “A cross-platform comparison of affymetrix and Agilent microarrays reveals discordant miRNA expression in lung tumors of c-Raf transgenic mice,” PLoS One 8(11), e78870 (2013).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (1)

S. Zadran, F. Remacle, and R. D. Levine, “miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients,” Proc. Natl. Acad. Sci. U.S.A. 110(47), 19160–19165 (2013).
[Crossref] [PubMed]

RNA (2)

M. Hafner, N. Renwick, M. Brown, A. Mihailović, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, and T. Tuschl, “RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries,” RNA 17(9), 1697–1712 (2011).
[Crossref] [PubMed]

L. W. Lee, S. Zhang, A. Etheridge, L. Ma, D. Martin, D. Galas, and K. Wang, “Complexity of the microRNA repertoire revealed by next-generation sequencing,” RNA 16(11), 2170–2180 (2010).
[Crossref] [PubMed]

Science (1)

E. Lerner, T. Cordes, A. Ingargiola, Y. Alhadid, S. Chung, X. Michalet, and S. Weiss, “Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer,” Science 359(6373), eaan1133 (2018).
[Crossref] [PubMed]

Theranostics (1)

A. Tufman, F. Tian, and R. M. Huber, “Can microRNAs improve the management of lung cancer patients? a clinician’s perspective,” Theranostics 3(12), 953–963 (2013).
[Crossref] [PubMed]

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Figures (10)

Fig. 1
Fig. 1 Simplified scheme of a TIRF microscope with 2 laser lines. The insert shows a picture of the flow cell with 6 channels. Step motors were connected to the stage and the microscope focus knob for the automation modification.
Fig. 2
Fig. 2 The motor stepping size calibration. For three settings, P50, 100 and 150, consecutive images were taken with a grid on the stage. Because of the distinguishable grid thickness, the stage movements could be deduced by aligning the same grid in different images. To avoid a one-pixel calibration, the alignment was performed by aligning the vertical profile of all the grids (a, b, c). For 7 images, 6 alignments were obtained and averaged to generate the linear line of (d).
Fig. 3
Fig. 3 (a) The scheme of the sample cell ensemble. A physical picture is shown in Fig. 1. Holes were drilled on the glass slide, which is shown as the larger rectangle (25x75 mm). The smaller rectangle that circumvents the channels is the cover slip. These two glass surfaces were glued together via double-faced tape. (b) Illustration of the 2x20 rectangular stage movement pattern.
Fig. 4
Fig. 4 Illustration of electronic signals to synchronize the stage, camera, and the laser shutter.
Fig. 5
Fig. 5 (a) smFRET platform illustration. The exchange reaction between S2 and S3 is thermodynamically driven for perfect duplex formation. (b) An example smFRET image. The left and right panels are the donor (Cy3) and acceptor (Cy5) emissions, respectively. Each channel is half of the camera imaging area with 512x256 pixels. The boxes show the FRET-paired particles. Not all pairs are boxed for clarity. (c) The FRET value distribution of (b). This value is not critical for the quantification of the analyte. (d) An example overlay fluorescence figure. The Cy3 and Cy5 channels were superposed and labeled with green and red colors, respectively. The colocalized spots formed one FRET pair. For illustration, the superposition offset was exaggerated by several pixels to show both spots. Each of the green-red pairs correspond to one pair of spots in (b) in the box of the same number.
Fig. 6
Fig. 6 The FRET% histogram of the reference and exchange channels. The actually exchange efficiency is normalized to the reference.
Fig. 7
Fig. 7 Quantification curve of analyte S3 from 0 to 1000 nM. The insert shows the exchange linear region. The error bars are adapted from the “σ” values of the Gaussian distribution. The errors of the mean are much smaller because of the large sample sizes.
Fig. 8
Fig. 8 Physical photo of the TIRF set up. A thin blue line illustrated one of the laser paths. The most important component was the beam expander (manual available with KT110 of thorlabs). The microscope is at the end of the light path.
Fig. 9
Fig. 9 (Left) Illustration of the auto-focusing set up. The laser reflected light was detected by the quad photodiode PDP90A. Because the very close distance between the in and out laser spots, the rectangular neutral density filter was used and it was placed at the edge of the reflected laser spot. The signals of X- and Y-displacements were sent to the PID controller TPA101. At the perfect focus point, the X- (or Y-) signals fluctuated around the zero, and were amplified to be high or low voltage by the TPA 101. One of these signals was sent out to the I/O input of the motor, which was clamped to the focusing knob of the microscope via its Z-axis kit. The command to the motor caused it to crank the focus knob to opposite directions with H/L signals. For example, when using the command (/4F0S04P200F1S14P200R), the motor will move the Z-position to reach a “low voltage” signal if the focus is giving a “high voltage” signal; and vice versa. During the back and forth adjustment, the laser spot was kept constant on the PDP90A, which was the perfectly focused position. In this command, the first half (F0S04P200) and second half (F1S14P200) cranked the focus-knob at different direction; and (R) looped the commands infinitely. (right) A physical picture of the optics is shown. The totally reflected laser light was directly by a neutral density filter to a mirror, which relayed the light to the quad photodiode, PDP90A.
Fig. 10
Fig. 10 (a) The alternative platform with Cy 5-labeled S2 being tethered on the surface. (b) The images are presented as binary data for display. The FRET pair % were calculated by the ratio of the particles under green laser radiation to those under red laser radiation. Each panel represent half of the camera area of 512x256 pixels.

Tables (1)

Tables Icon

Table 1 DNA sequences (S1-S2 forms the platform, and S3 is the analyte), the shaded part formed a stem loop to specifically recognize short DNAs.

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