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Experimental and molecular modelling data from the study of 46mer DNAzyme

Version 2 2023-11-20, 15:52
Version 1 2023-06-19, 08:34
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posted on 2023-06-19, 08:34 authored by Sarath DantuSarath Dantu, Giuseppe Sicoli

Here we are providing access to experimental and molecular dynamics (MD) simulation data from the study of 46mer DNAzyme.


Experimental data:

  1. NMR experiments for the determination of the diffusion coefficients of the c4, s4, c4s4 without and with Copper(II). (NMR.zip)
  2. EPR/ESR experiments, both 1D and 2D, for the determination of g-factors and hyperfine couplings with Cu2+
  3. Mass spectroscopy for the analysis of DNA fragments before and after the cleavage reactions


Molecular dynamics data:

  1. Atomic pdb models of 46mer DNAzyme with (46m_WithCU.pdb) and without Cu2+ ions (46m_WithoutCU.pdb)
  2. Ten trajectories/replicas of 46mer DNAzyme with Cu2+ ions (1-10 46m-WithCU-500ns_dt100ps.xtc)
  3. Three trajectories/replicas of 46mer DNAzyme without Cu2+ ions (1-3 46m-WithoutCU-500ns_dt100ps.xtc)


Each replica contains 500 nanaoseconds of simulation data sampled at 100 picosecond intervals. Simulations were done using GROMACS2020 package using parmbsc1 forcefield on JADE2 cluster.


This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1). EPR experiments were supported by financial support from the IR INFRANALYTICS FR2054.

Funding

The UK High-End Computing Consortium for Biomolecular Simulation

Engineering and Physical Sciences Research Council

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IR INFRANALYTICS FR2054

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