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

Here we are providing access to experimental and molecular dynamics (MD) simulation data from the study of 46mer DNAzyme.<b>Experimental data:</b>NMR experiments for the determination of the diffusion coefficients of the c4, s4, c4s4 without and with Copper(II). (NMR.zip)EPR/ESR experiments, both 1D and 2D, for the determination of g-factors and hyperfine couplings with Cu2+Mass spectroscopy for the analysis of DNA fragments before and after the cleavage reactions<b>Molecular dynamics data:</b>Atomic pdb models of 46mer DNAzyme with (46m_WithCU.pdb) and without Cu2+ ions (46m_WithoutCU.pdb)Ten trajectories/replicas of 46mer DNAzyme with Cu2+ ions (1-10 46m-WithCU-500ns_dt100ps.xtc)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.

本数据集收录了针对46mer脱氧核酶（46mer DNAzyme）的实验与分子动力学（Molecular Dynamics, MD）模拟数据。
**实验数据：**
1. 核磁共振（Nuclear Magnetic Resonance, NMR）实验：用于测定c4、s4、c4s4在不含与含二价铜离子（Copper(II)）条件下的扩散系数，相关数据存储于NMR.zip压缩包中。
2. 电子顺磁共振/电子自旋共振（Electron Paramagnetic Resonance/Electron Spin Resonance, EPR/ESR）实验：涵盖一维（1D）与二维（2D）两种模式，用于测定与二价铜离子（Cu²+）相关的g因子及超精细耦合常数。
3. 质谱（Mass Spectroscopy, MS）实验：用于分析裂解反应前后的DNA片段。
**分子动力学模拟数据：**
1. 46mer脱氧核酶的原子级pdb模型：含二价铜离子的模型文件为46m_WithCU.pdb，不含二价铜离子的模型文件为46m_WithoutCU.pdb。
2. 含二价铜离子的46mer脱氧核酶轨迹/复制品轨迹：共10条，对应数据文件为1-10 46m-WithCU-500ns_dt100ps.xtc。
3. 不含二价铜离子的46mer脱氧核酶轨迹/复制品轨迹：共3条，对应数据文件为1-3 46m-WithoutCU-500ns_dt100ps.xtc。
每条复制品轨迹包含500纳秒的模拟数据，采样间隔为100皮秒。本次模拟工作采用GROMACS2020软件包完成，使用parmbsc1力场，计算集群为JADE2。
本项目使用的高性能计算（High-Performance Computing, HPC）资源由英国生物分子模拟高端计算联盟HECBioSim（http://hecbiosim.ac.uk）提供，该联盟受工程与物理科学研究委员会（EPSRC）资助，资助编号为EP/R029407/1。电子顺磁共振实验得到了IR INFRANALYTICS FR2054的经费支持。