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Peak Finding Algorithm Matlab 2010, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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A, Use of unnatural-amino-acid mutagenesis, Staudinger ligation with Cy3B-phosphine and Alexa647-phosphine, and total-internal-reflection <t>fluorescence</t> microscopy with alternating-laser excitation microscopy (TIRF-ALEX) to obtain FRET data for single molecules of RNAP having fluorescent probes at the tips of the walls of the RNAP active-center cleft (see STAR Methods). Green, fluorescence donor probe Cy3B; red, fluorescent acceptor probe Alexa647; black square, hexahistidine tag. B, Surface-immobilization of fluorescent-probe-labelled RNAP for TIRF-ALEX. C, Time trace of donor emission intensity (green) and acceptor emission intensity (red) (top) and corresponding time trace of donor-acceptor FRET efficiency (bottom). D, Single-molecule FRET data for RNAP holoenzyme in absence of Lpm. Left, histogram. Gray, all states; colors, Hidden Markov Model (HMM)-assigned open, partly closed, and closed states (red, yellow, and green). Right, time trace with HMM-assigned open, partly closed, and closed states (red, yellow, and green). E, Single-molecule FRET data for RNAP holoenzyme in presence of Lpm (histogram and time trace as in D). F, Summary of RNAP clamp angles and dwell times for open, partly closed, and closed clamp states in absence and presence of Lpm. G, Time trace for RNAP holoenzyme before and after addition of Lpm.
Matlab Software, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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program matlab 2010  (MathWorks Inc)
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A, Use of unnatural-amino-acid mutagenesis, Staudinger ligation with Cy3B-phosphine and Alexa647-phosphine, and total-internal-reflection <t>fluorescence</t> microscopy with alternating-laser excitation microscopy (TIRF-ALEX) to obtain FRET data for single molecules of RNAP having fluorescent probes at the tips of the walls of the RNAP active-center cleft (see STAR Methods). Green, fluorescence donor probe Cy3B; red, fluorescent acceptor probe Alexa647; black square, hexahistidine tag. B, Surface-immobilization of fluorescent-probe-labelled RNAP for TIRF-ALEX. C, Time trace of donor emission intensity (green) and acceptor emission intensity (red) (top) and corresponding time trace of donor-acceptor FRET efficiency (bottom). D, Single-molecule FRET data for RNAP holoenzyme in absence of Lpm. Left, histogram. Gray, all states; colors, Hidden Markov Model (HMM)-assigned open, partly closed, and closed states (red, yellow, and green). Right, time trace with HMM-assigned open, partly closed, and closed states (red, yellow, and green). E, Single-molecule FRET data for RNAP holoenzyme in presence of Lpm (histogram and time trace as in D). F, Summary of RNAP clamp angles and dwell times for open, partly closed, and closed clamp states in absence and presence of Lpm. G, Time trace for RNAP holoenzyme before and after addition of Lpm.
Program Matlab 2010, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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A, Use of unnatural-amino-acid mutagenesis, Staudinger ligation with Cy3B-phosphine and Alexa647-phosphine, and total-internal-reflection fluorescence microscopy with alternating-laser excitation microscopy (TIRF-ALEX) to obtain FRET data for single molecules of RNAP having fluorescent probes at the tips of the walls of the RNAP active-center cleft (see STAR Methods). Green, fluorescence donor probe Cy3B; red, fluorescent acceptor probe Alexa647; black square, hexahistidine tag. B, Surface-immobilization of fluorescent-probe-labelled RNAP for TIRF-ALEX. C, Time trace of donor emission intensity (green) and acceptor emission intensity (red) (top) and corresponding time trace of donor-acceptor FRET efficiency (bottom). D, Single-molecule FRET data for RNAP holoenzyme in absence of Lpm. Left, histogram. Gray, all states; colors, Hidden Markov Model (HMM)-assigned open, partly closed, and closed states (red, yellow, and green). Right, time trace with HMM-assigned open, partly closed, and closed states (red, yellow, and green). E, Single-molecule FRET data for RNAP holoenzyme in presence of Lpm (histogram and time trace as in D). F, Summary of RNAP clamp angles and dwell times for open, partly closed, and closed clamp states in absence and presence of Lpm. G, Time trace for RNAP holoenzyme before and after addition of Lpm.

Journal: Molecular cell

Article Title: STRUCTURAL BASIS OF TRANSCRIPTION INHIBITION BY FIDAXOMICIN (LIPIARMYCIN A3)

doi: 10.1016/j.molcel.2018.02.026

Figure Lengend Snippet: A, Use of unnatural-amino-acid mutagenesis, Staudinger ligation with Cy3B-phosphine and Alexa647-phosphine, and total-internal-reflection fluorescence microscopy with alternating-laser excitation microscopy (TIRF-ALEX) to obtain FRET data for single molecules of RNAP having fluorescent probes at the tips of the walls of the RNAP active-center cleft (see STAR Methods). Green, fluorescence donor probe Cy3B; red, fluorescent acceptor probe Alexa647; black square, hexahistidine tag. B, Surface-immobilization of fluorescent-probe-labelled RNAP for TIRF-ALEX. C, Time trace of donor emission intensity (green) and acceptor emission intensity (red) (top) and corresponding time trace of donor-acceptor FRET efficiency (bottom). D, Single-molecule FRET data for RNAP holoenzyme in absence of Lpm. Left, histogram. Gray, all states; colors, Hidden Markov Model (HMM)-assigned open, partly closed, and closed states (red, yellow, and green). Right, time trace with HMM-assigned open, partly closed, and closed states (red, yellow, and green). E, Single-molecule FRET data for RNAP holoenzyme in presence of Lpm (histogram and time trace as in D). F, Summary of RNAP clamp angles and dwell times for open, partly closed, and closed clamp states in absence and presence of Lpm. G, Time trace for RNAP holoenzyme before and after addition of Lpm.

Article Snippet: For experiments in , laser powers were 3.5 mW (532 nm laser) and 0.7 mW (635 nm laser), and data were collected for 20 s using a frame rate of 1 frame per 20 ms. For experiments in , laser powers were 0.5 mW (532 nm laser) and 0.15 mW (635 nm laser), and data were collected for 50 s using a frame rate of 200 ms. Fluorescence emission intensities in donor (green) and acceptor (red) emission channels were detected using the peak-finding algorithm of the MATLAB (MathWorks) software package TwoTone-ALEX ( Holden et al., 2010 ), as in Holden et al., 2010 .

Techniques: Mutagenesis, Ligation, Fluorescence, Microscopy