This readme.txt file was generated on <20210813> by Recommended citation for the data: Ma, Zixue; Dorfman, Kevin D. (2021). Data for: Interactions between two knots in nanochannel-confined DNA molecules. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/kv7q-fw92. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data for: Interactions between two knots in nanochannel-confined DNA molecules 2. Author Information Principal Investigator Contact Information Name:Zixue Ma Institution:University of Minnesota Address:Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email:ma000052@umn.edu Associate or Co-investigator Contact Information Name: Kevin D. Dorfman Institution: University of Minnesota Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email: dorfman@umn.edu 3. Date of data collection: 2019-08 to 2021-05 4. Geographic location of data collection: N/A 5. Information about funding sources that supported the collection of the data: NSF (CBET-2016879) 6. Published Date: 2021-08-14 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Ma, Zixue, & Dorfman, Kevin D. (2021). Interactions between two knots in nanochannel-confined DNA molecules. J. Chem. Phys. 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): --------------------- DATA & FILE OVERVIEW --------------------- 1. File List\ A. Filename: Image_Analysis.zip Short description: This file contains all the MATLAB codes to process the DNA knot data. Two_Knot_Analysis.m is used to analyze knot-knot interactions in nanochannels and generate knot position data. MATLAB codes in choose_DNA_molecules folder are used to process DNA images to generate DNA intensity data. Extension_Analysis.m is used to analyze DNA extension. After running the codes, there will be files under the 13 folders. B. Filename: Videos.zip (39 .tif files) Short description: This file contains all the DNA image data File name includes device number, DNA used, the concentration of DNA, the buffer solution, the laser power, the location of DNA, the date and the image number. C. Filename: Figure_Data.zip Short description: This file contains the figures, data and MATLAB code used to generated those figures. 2. Relationship between files: MATLAB codes in Image_Analysis.zip are used to process DNA images in Videos.zip. 3. Additional related data collected that was not included in the current data package: No 4. Are there multiple versions of the dataset? no -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: The nanofluidic device was designed based on the knot factory concept. The images of the DNA were recorded by an EMCCD camera (Photometrics, Cascade II:512). To obtain data for knot-knot interactions, the two-knotted DNA were imaged at 2 fps with a 200 ms exposure time with the experiment ending when one of the knots unravels at the chain end. After each experiment, which consists of multiple loading and compression cycles, the device was cleaned and dried to be reused for the next experiment. Additional information can be found in the associated publication. 2. Methods for processing the data: The videos were processed using a customwritten MATLAB script that outputs the time evolution of each DNA molecule's intensity profile. File name contains the experimental conditions and please see the main text of the paper for additional details. 3. Instrument- or software-specific information needed to interpret the data: MATLAB_R2019b was used to analyze the data 4. Standards and calibration information, if appropriate: Please see the main text of the paper for additional information. 5. Environmental/experimental conditions: Please see the main text of the paper for additional information. 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: Kevin D. Dorfman ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Image_Analysis ----------------------------------------- Instructions on how to run image analysis codes Software: MATLAB Part A: Process DNA images to generate DNA intensity data and DNA extension Step 1: Change the directory that MATLAB uses to find DNA image data and MATLAB codes in DNAAnalyze_one.m, DNANanoStretch.m, ExtensionFluct21_one.m, and Extension_Analysis.m under the Image_Analysis folder. Step 2: Open DNANanoStretch.m Change the DNA image file name (line 23 and 29 in the code) and the number of frames of the DNA images (line 212 in the code). Select DNA by creating first a large box and then a small box around the analyzed DNA molecule. Run the code. Step 3: Open Extension_Analysis.m Change the DNA image file name (line 27). Change the number of frames (line 28, 30 and 31). Run the code. Part B: Analyze knot-knot interaction in a nanochannel Step 1: Open Two_Knot_Analysis.m and change the directory that MATLAB uses to find the DNA intensity, edge and extension data. Step 2: Change the DNA image file name (line 19). Run the code.