DOI: 10.5281/zenodo.11222188
title: 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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The simulation dataset used for the analysis reported in the manuscript titled -

 

            "Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes."

             by Sandip Mandal, Krishna N. Ganesh, and Prabal K. Maiti*

 

 

*E-mail: maiti@iisc.ac.in

Center for Condensed Matter Theory, Department of Physics,

Indian Institute of Science, Bangalore 560012, India

 

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Packages required:

                Visual Molecular Dynamics (VMD)

                xmgrace

                numpy

                matplotlib

                scipy

                tleap/xleap

                AMBER

                CPPTRAJ

                MMGBSA

                Gaussian09 for partial charge calculation of the PNA protonated cytosine residues

 

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Contents:

 

The First main directory contains three folders and a README file--

(1)PNA_DNA_PNA_Triplex

        (2)DNA_DNA_DNA_Triplex

(3)Sequence_Dependence

(4)README file

 

 

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1. PNA_DNA_PNA_Triplex directory contains sub-directory for Protonated PNA-DNA-PNA triplexes simulation data, such as ---

(a) Setup_files

(b) Results

 

 

(a)Setup_files:

It contains input coordinates (PDP_18bp_PP.pdb, Protonated_PNA_DNA_PNA.inpcrd ..), topology files, and files required to build to complete 

system for simulation including library files for non-standard PNA residues and tleap script for the system setup.

 

(b)Results: --folder contains simulation data and analysis scripts for Protonated PNA-DNA-PNA triplexes -----

 

(a)Simulation Trajectories ( It contains simualtion trajectories for three independent trial runs named run1, run2, and run3)

(b)RMSD

(c)Hbond (hydrogen bonding)

(d)Stiffness 

(e)Free Energy Landscape (FEL)

(f)PCA (Principal Component Analysis)

(g)Simulation Movies for the Protonated PNA-DNA-PNA triplex

 

 

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2. DNA_DNA_DNA_Triplex directory contains sub-directory for Protonated DNA-DNA-DNA triplexes simulation data, such as ---

                (a) Setup_files

                (b) Results

 

 

(a)Setup_files :

It contains input coordinates (DDD_18bp_Protonated_NAB.pdb, 18bp_Protonated_NAB.inpcrd ...) and files required to build to complete

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.

 

(b)Results --folder contains simulation data and analysis scripts for-----

 

                (a)Simulation Trajectories ( It contains simulation trajectory for three independent trial runs named run1, run2, and run3)

                (b)RMSD

                (c)Hydrogen bonding

                (d)Stiffness

                (e)Free Energy Landscape

                (f)PCA

                (g)Simulation Movies for the Protonated DNA-DNA-DNA triplex

 

 

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3. Sequence_Dependence  directory contains sub-directory for triplexes with all TAT base triples simualtion data, such as ---

                (A) DNA_DNA_DNA_with_all_TAT_sequence

                (B) PNA_DNA_PNA_with_all_TAT_sequence

 

(A)Sub-directory contains simulation data for DNA-DNA-DNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---

(a)Set_up_files

(b)Trajectory

(c)RMSD

(d)Hbond

 

 

(B)Sub-directory contains simulation data for PNA-DNA-PNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---

                                (a)Set_up_files

                                (b)Trajectory

                                (c)RMSD

                                (d)Hbond

 

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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:

(a)The first frame corresponds to the structure immediately after 5 ns NPT equilibriation.

(b)The next 200 frames are from the production run, at 1 to 200 ns.

 

 

References:

The DNA-DNA-DNA and PNA-DNA-PNA models were constructed using NAB code [1].

System preparation with water and ions are done with the help of tleap/xleap [2].

All simulation runs are conducted in AMBER2020 [3].

For visualization we have used VMD [4].

 

[1] T. J. Macke and D. A. Case, Modeling unusual nucleic acid structures, 1998

[2] D. R. Roe and T. E. Cheatham III, Journal of chemical theory and computation, 2013, 9, 3084–3095

[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

[4] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14(1), 33-38 (1996).