Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes
<div>##################################################################################################</div> <div> </div> <div>The simulation dataset used for the analysis reported in the manuscript titled -</div> <div> </div> <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> <div> </div> <div> </div> <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> <div> </div> <div>##################################################################################################</div> <div> </div> <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> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <div>Contents:</div> <div> </div> <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> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <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> <div> </div> <div> </div> <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> <div> </div> <div>(b)Results: --folder contains simulation data and analysis scripts for Protonated PNA-DNA-PNA triplexes -----</div> <div> </div> <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> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <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> <div> </div> <div> </div> <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> <div> </div> <div>(b)Results --folder contains simulation data and analysis scripts for-----</div> <div> </div> <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> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <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> <div> </div> <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> <div> </div> <div> </div> <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> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <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> <div> </div> <div> </div> <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> <div> </div> <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>
ShareScore
32/100
Overall dataset sharing score
Score breakdown
These five areas show where the dataset supports — or may limit — practical reuse.
- Stewardship
- 4
- Harmonization
- 4
- Access
- 16
- Reuse readiness
- 8
- Engagement
- 0