Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes
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<div>The simulation dataset used for the analysis reported in the manuscript titled -</div>
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<div> "Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes."</div>
<div> by Sandip Mandal, Krishna N. Ganesh, and Prabal K. Maiti*</div>
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<div>*E-mail: maiti@iisc.ac.in</div>
<div>Center for Condensed Matter Theory, Department of Physics,</div>
<div>Indian Institute of Science, Bangalore 560012, India</div>
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<div>Packages required:</div>
<div> Visual Molecular Dynamics (VMD)</div>
<div> xmgrace</div>
<div> numpy</div>
<div> matplotlib</div>
<div> scipy</div>
<div> tleap/xleap</div>
<div> AMBER</div>
<div> CPPTRAJ</div>
<div> MMGBSA</div>
<div> Gaussian09 for partial charge calculation of the PNA protonated cytosine residues</div>
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<div>Contents:</div>
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<div>The First main directory contains three folders and a README file--</div>
<div>(1)PNA_DNA_PNA_Triplex</div>
<div> (2)DNA_DNA_DNA_Triplex</div>
<div>(3)Sequence_Dependence</div>
<div>(4)README file</div>
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<div>1. PNA_DNA_PNA_Triplex directory contains sub-directory for Protonated PNA-DNA-PNA triplexes simulation data, such as ---</div>
<div>(a) Setup_files</div>
<div>(b) Results</div>
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<div>(a)Setup_files:</div>
<div>It contains input coordinates (PDP_18bp_PP.pdb, Protonated_PNA_DNA_PNA.inpcrd ..), topology files, and files required to build to complete </div>
<div>system for simulation including library files for non-standard PNA residues and tleap script for the system setup.</div>
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<div>(b)Results: --folder contains simulation data and analysis scripts for Protonated PNA-DNA-PNA triplexes -----</div>
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<div>(a)Simulation Trajectories ( It contains simualtion trajectories for three independent trial runs named run1, run2, and run3)</div>
<div>(b)RMSD</div>
<div>(c)Hbond (hydrogen bonding)</div>
<div>(d)Stiffness </div>
<div>(e)Free Energy Landscape (FEL)</div>
<div>(f)PCA (Principal Component Analysis)</div>
<div>(g)Simulation Movies for the Protonated PNA-DNA-PNA triplex</div>
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<div>2. DNA_DNA_DNA_Triplex directory contains sub-directory for Protonated DNA-DNA-DNA triplexes simulation data, such as ---</div>
<div> (a) Setup_files</div>
<div> (b) Results</div>
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<div>(a)Setup_files :</div>
<div>It contains input coordinates (DDD_18bp_Protonated_NAB.pdb, 18bp_Protonated_NAB.inpcrd ...) and files required to build to complete</div>
<div>system for simulation, including amber input files in the "Sander-Input-files" subdirectory, a script to run the simulation in a GPU clusters, and a leap script for the system setup.</div>
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<div>(b)Results --folder contains simulation data and analysis scripts for-----</div>
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<div> (a)Simulation Trajectories ( It contains simulation trajectory for three independent trial runs named run1, run2, and run3)</div>
<div> (b)RMSD</div>
<div> (c)Hydrogen bonding</div>
<div> (d)Stiffness</div>
<div> (e)Free Energy Landscape</div>
<div> (f)PCA</div>
<div> (g)Simulation Movies for the Protonated DNA-DNA-DNA triplex</div>
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<div>3. Sequence_Dependence directory contains sub-directory for triplexes with all TAT base triples simualtion data, such as ---</div>
<div> (A) DNA_DNA_DNA_with_all_TAT_sequence</div>
<div> (B) PNA_DNA_PNA_with_all_TAT_sequence</div>
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<div>(A)Sub-directory contains simulation data for DNA-DNA-DNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---</div>
<div>(a)Set_up_files</div>
<div>(b)Trajectory</div>
<div>(c)RMSD</div>
<div>(d)Hbond</div>
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<div>(B)Sub-directory contains simulation data for PNA-DNA-PNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---</div>
<div> (a)Set_up_files</div>
<div> (b)Trajectory</div>
<div> (c)RMSD</div>
<div> (d)Hbond</div>
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<div>The trajectories are sampled at 1 ns intervals (since the full trajectory dumped at 10 ps interval, will take huge dataspace) in each trajectory file:</div>
<div>(a)The first frame corresponds to the structure immediately after 5 ns NPT equilibriation.</div>
<div>(b)The next 200 frames are from the production run, at 1 to 200 ns.</div>
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<div>References:</div>
<div>The DNA-DNA-DNA and PNA-DNA-PNA models were constructed using NAB code [1].</div>
<div>System preparation with water and ions are done with the help of tleap/xleap [2].</div>
<div>All simulation runs are conducted in AMBER2020 [3].</div>
<div>For visualization we have used VMD [4].</div>
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<div>[1] T. J. Macke and D. A. Case, Modeling unusual nucleic acid structures, 1998</div>
<div>[2] D. R. Roe and T. E. Cheatham III, Journal of chemical theory and computation, 2013, 9, 3084–3095</div>
<div>[3]D. A. Case, H. M. Aktulga, K. Belfon, I. Ben-Shalom, S. R.Brozell, D. S. Cerutti, T. E. Cheatham III, V. W. D. Cruzeiro,T. A. Darden, R. E. Duke et al., Amber 2021, University of California, San Francisco, 2021</div>
<div>[4] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14(1), 33-38 (1996).</div>
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