Work Description

README for: Single-molecule microscopy data files for "An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch." Authors: Rajeev Yadav, Julia R Widom, Adrien Chauvier & Nils G Walter Contact: yadavraj@msu.edu and nwalter@umich.edu Citation to related material: Yadav, R., Widom, J. R., Chauvier, A. & Walter, N.G. (2021). An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch. Nat. Commun. DOI: TBA. Citation for this dataset: Yadav, R., Widom, J., Chauvier, A., Walter, N. Single-molecule microscopy data for "An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/pa6y-fb55 Data Analysis: For all the analysis custom written Matlab codes are used and are given here as �Matlab scripts.zip�. First the �.traces� file was extracted for each movie separately (from the raw movies in .mj2 format). Further, individual single-molecule time traces were extracted from �.traces� file and analyzed using custom Matlab scripts and the QuB software suite (State University of New York at Buffalo). The kinetic analyses were performed using hidden-Markov modeling with a segmental k-means algorithm as implemented in the program QuB. File Organization: This work contains multiple zip files, each of which represents one of the principal experimental conditions presented in the publication. [Name of the zip file Contents] MATLAB scripts.zip This folder contains all the MATLAB codes used for single-molecule FRET analysis and kinetic analysis. 1. beads_mapper.m : To run this script we need a (move file for beads.mj2), it generally depends on instrument to instrument. 2. Generate_time_traces from mj2 file.m : This script generates .traces file (attached here for each dataset). It needs the output of beads_mapper.m script to run this script. 3. Save onebyone time traces.m : This script uses .traces file with .img file for viewing purpose (these files are given in the detaset). The following scripts are for kinetic analysis; 4. RemoveNegOutlier.m : It uses each molecule data (output of step 3 script) as input file and removes negative outlier from each time trace data. 5. IsolateDonorAcceptorSegStitch3QUB_inputFileList.m : This script separate the donor and acceptor signal data and combines in one saperately. **Further use QUB for hmm fitting- no matlab script 6. ParseDTW: It uses the output of QUB hmm fitting and as output we got separate data for each molecule having all information (frames, donor, acceptor, FRET, hmm-Fit). 7. FindTransvbFRETDiagonal_Modified.m or FindTransvbFRETnew2.m : These scripts are used to generate density plots. RNA64 with 0 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for RNA of length 64 nucleotides (RNA64) in absence of both magnesium and fluoride. RNA64 with 0 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 0 mM magnesium and 1 mM fluoride. RNA64 with 1 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 1 mM magnesium and 0 mM fluoride. RNA64 with 1 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 1 mM magnesium and 1mM fluoride. RNA64 with 2 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 2 mM magnesium and 0 mM fluoride. RNA64 with 2 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 2 mM magnesium and 1mM fluoride. RNA64 with 5 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 5 mM magnesium and 0 mM fluoride. RNA64 with 5 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 5 mM magnesium and 1 mM fluoride. RNA64 with 10 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for RNA64 in presence of 10 mM magnesium and 0 mM fluoride. RNA64-U48A with 0 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for the mutation U48A of RNA64 in presence of 0 mM magnesium and 0 mM fluoride. RNA64-U48A with 2 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for the mutation U48A of RNA64 in presence of 2 mM magnesium and 0 mM fluoride. RNA64-U48A with 2 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for the mutation U48A of RNA64 in presence of 2 mM magnesium and 1 mM fluoride. RNA64 with LNA sequence complementary to A39toU48.zip Single molecule time traces and associated files in absence and presence of magnesium and fluoride, where the sequence from A39 to U48 of RNA64 is blocked with a complementary LNA oligonucleotide and prevents pseudoknot formation. EC64 with 2 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 64 nucleotides (EC64) in presence of 2 mM magnesium and 0 mM fluoride. EC64 with 2 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 64 nucleotides (EC64) in presence of 2 mM magnesium and 1 mM fluoride. RNA58 in absence and presence of 5 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for the RNA of length 58 (RNA58) in absence and presence of 5 mM magnesium and 1 mM fluoride. EC58 with 0 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides (EC58) in absence of both magnesium and fluoride. EC58 with 5 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides (EC58) in presence of 5 mM magnesium and 0 mM fluoride. EC58 with 5 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides (EC58) in presence of 5 mM magnesium and 1 mM fluoride. EC58 with 0.4s exposureTime.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides (EC58) with 0.4 sec exposure time in absence and presence of magnesium and fluoride. EC48 with 0 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 48 nucleotides (EC48) in absence of both magnesium and fluoride. EC48 with 5 mM Mg2+ and 0 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 48 nucleotides (EC48) in presence of 5 mM magnesium and 0 mM fluoride. EC48 with 5 mM Mg2+ and 1 mM F-.zip Single molecule time traces and associated files for elongation complex at transcript lengths of 48 nucleotides (EC48) in presence of 5 mM magnesium and 1 mM fluoride. EC58_RNA58 with altered donor labeling position.zip Single molecule time traces and associated files for isolated RNA and elongation complex at transcript lengths of 58 nucleotides (RNA58n and EC58n), where the donor labeling position is altered (A39 instead of U33). The data in all the sub-folders is associated with this altered donor labeling position. EC58n_Mg0F0: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in absence of magnesium and fluoride. EC58n_Mg0F0.1: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in presence of 0 mM magnesium and 0.1 mM fluoride. EC58n_Mg0F0.5: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in presence of 0 mM magnesium and 0.5 mM fluoride. EC58n_Mg5F0: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in presence of 5 mM magnesium and 0 mM fluoride. EC58n_Mg5F0.1: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in presence of 5 mM magnesium and 0.1 mM fluoride. EC58n_Mg5F0.5: Single molecule time traces and associated files for elongation complex at transcript lengths of 58 nucleotides in presence of 5 mM magnesium and 0.5 mM fluoride. EC58n_U45AC46U mutation: Single molecule time traces and associated files for U45A, C46U mutation of EC58 in absence and presence of magnesium and fluoride. EC58n with L1 block seq: Single molecule time traces and associated files in absence and presence of magnesium and fluoride for EC58, where L1 loop is blocked by the complementary LNA oligonucleotide. RNA58n with DNA template: Single molecule time traces and associated files for the RNA of length 58 with DNA template in absence and presence of magnesium and fluoride.