DOI: 10.6084/m9.figshare.13116890
title: Atomic force microscopy and atomistic molecular dynamics simulation data to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution.

description: This data record consists 2 zipped folders: <b>Full AFM raw data set.zip</b>, and <b>Source data .zip</b>.<br>The zipped folder <b>Full AFM raw data set.zip</b> contains all raw AFM data including repeats and experiments carried out in alternative conditionsThe primary subfolder names correspond to the method of DNA immobilisation:Nickel - use of 3 mM NiCl2 in Ph7.4 20 mM HEPES bufferPLLNaOAc - use of PLL and pH 5.4 50 mM NaOAc bufferHR images - high resolution images, obtained also using the nickel conditions.The secondary subfolder names correspond to the superhelical density as shown in figure 3 in the article, and these contain the raw AFM images as .spm isles, the sub folders within those are created by the program TopoStats, and are processed data from the raw AFM images. File formats included in the zipped folder: .<b>spm, .tiff, .json, .txt </b>and<b> .pdf.</b><br>The zipped folder <b>Source data .zip </b>comprises all relevant data, pdbs of all the structures depicted in the paper obtained from simulations and AFM. See below for details on each sub folder within Source data 2.zip. Each folder contains the data used to generate each figure ad supplementary figure in the article. <br><b>Figure 1</b>: AFM data: the AFM raw files for the high-resolution images shown in figure 1, and calculations of their aspect ratios as aspectratiomanual.xlsxAFM movie: the AFM raw files for the time-lapse images shown in figure 1.MD data: the MD images used for the high-resolution images shown in figure 1 and .tar files - the MD files used to generate the snapshots MD movie: the MD snapshots files for the time-lapse images shown in figure 1 and .tar files - the MD files used to generate the snapshotsFile formats included in the Figure 1 sub folder: <b>0## files where ## represent numbers, .gwy, .txt, .eps, .mpg </b>and<b> .xlsx.</b><br><b>Figure 2</b>: Kink and defect measurements - the measured bend angles shown in Fig 2 and an AFM image showing how the FAM bends were measuredMD Radgyr Writhe - measurements of radius of gyrations and writhe for each topoisomer.tar files - the MD files used to generate the snapshots in 2a.txt file - the profile shown in fig 2bFile formats included in the Figure 2 sub folder: <b>.tiff, .txt </b>and<b> .dat</b><br><b>Figure 3</b>: The subfolder names correspond to the superhelical density as shown in figure 3, and these contain the raw AFM images as '.spm' isles, the sub folders within those are created by the program TopoStats, and are processed data from the raw AFM images. The '.json' file contains the data used to make the plots shown in Figure 3File formats included in the Figure 3 sub folder: <b>.spm, .tiff, .txt, .json </b>and<b> .pdf</b><br><b>Figure 4:</b> '.dat' files contain information from MD simulations used to create the subfigure they are labelled with.The '.spm' and '.037' files are the raw AFM images used in this figure.The .tar files are MD simulations data used to generate the snapshots shown in figure 4.File formats included in the Figure 4 sub folder: .<b>spm, .txt, .pdf </b>and<b> .dat</b><br><b>Figure S1</b>: Simulations data generated using the SerraLine program, showing the average and maximum deviations from planarity in relative and absolute numbers.Data were plotted suing the distributions_plot.py script.File formats included in the Figure S1 sub folder: <b>.csv, .pdf, </b>and<b> .txt</b><br><b>Figure S2a</b>: MD measurement of the writhe over time as a '.dat file' and snapshots as '.pdb' files. File formats included in the Figure S2a sub folder: .<b>pdb</b> and <b>.dat.</b><br><b>Figure S2b</b>: MD measurement of the writhe over time as a '.dat file' and snapshots as '.pdb' files.File formats included in the Figure S2b sub folder: .<b>pdb </b>and<b> .dat.</b><br><b>Figure S3</b>: The AFM and MD measurements of bending angles including all profiles for MD simulations, generated using Serraline A, FM images and measurements in the form '251angles' '339 angles'.File formats included in the Figure S3 sub folder: <b>.tiff, .txt </b>and<b> .pdb.</b><br><b>Figure S4</b>: AFM length analysis of the position of the triplex on linearised minicircles. 'Csv' file contains the length data measured by hand using the IMOD software.Plots: plots of the data raw AFM data: AFM data files used in the analysisFile formats included in the Figure S4 sub folder: .<b>csv, .xlsx, .pdf and 0## files </b>where ## represent numbers.<br><b>Figure S5</b>: Surface plasmon resonance (SPR) data show the effect of ions on the affinity of the triplex for varying superhelical densities of DNA minicircles, plotted using the script 'sprplot'. '.pdf' files are the plots of the various excel files.File formats included in the Figure S5 sub folder: .<b>json, .pdf </b>and<b> .xlsx.</b><br><b>Figure S6</b>: SPR data in showing the affinity of the triplex for varying superhelical densities of DNA minicircles, plotted using the script 'sprplot'. '.pdf' files are the plots of the various excel files.File formats included in the Figure S6 sub folder: .<b>json, .pdf, .xlsx </b>and<b> .pdf.</b><br><b>Figure S7:</b> An MS '.tar' file containing the snapshots shown in figure S7File formats included in the Figure S7 sub folder: <b>.pdb</b><br><b>Figure S8:</b> AFM data used in figure s8, the '.gwy' files are AFM images of the wide view, and each of the time-lapse images. The '.txt' files are the profiles taken in those images and plotted in the figure.File formats included in the Figure S8 sub folder: .<b>gwy </b>and<b> .txt.</b><br><b>Figure S9:</b> Simulations data showing the difference between the OL$ and BSC1 forcefields.File formats included in the Figure S9 sub folder: .<b>dat</b><br><b>Simulations</b>: The simulations data File formats included in the Simulations sub folder: .<b>gro </b>and<b> .xtc</b><br><b>Supp videos</b>: The supplementary videosFile formats included in the SuppVideods sub folder: .<b>pdb </b>and<b> .mpg</b><br><b>Software needed to access data: </b>20151103_251_NAT_17ng_Ni_20mm_052DX.058 or AFM_339_TFO_HR_cs.037, spm files & all files included in the “Raw AFM data” sub folder - Gwyddion, Nanoscope Analysiseps files - illustrator/ pdf software.mpg - any movie player.gro - gromacs files- GRO files may be viewed on a computer using a supporting HP calculator emulator, such as Emu48.xtc files - gromacs files- a suitable software like XTrkCADsee http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html for more information on gromacs files.<br><b>Study aims and methodology:</b> In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. In this study, the authors combined high-resolution atomic force microscopy (AFM) with molecular dynamics (MD) simulations to reveal how supercoiling affects global and local DNA conformation, structure and dynamics in DNA minicircles of length 250-340 bp. The following procedures are described in more detail in the related article: generation and purification of small DNA circles, preparation and analysis of different topological species of minicircles, S1 nuclease digestions, atomic force microscopy, atomistic simulations and surface plasmon resonance.<br>