DOI: 10.5281/zenodo.6588769
title: Gold Nanoparticles Synthesized in the Presence of Peptides - UV-Vis Spectra, Fluorescence, USAXS, Electron Microscopy

description: Content Summary: Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, fluorescence emission, USAXS, TEM, and SEM. Notebooks for loading and plotting data Code for synthesizing samples using an OT2 Opentrons liquid-handling robot. README: <strong>/Data</strong> Contains all UV-Vis, electron microscopy, fluorescence, and SAXS data for gold nanoparticles synthesized in the presence of peptides and HEPES. <strong>/Data/2021_12_30_Prepared_UV_Vis_Data</strong> The primary portion of the experimental dataset. UV-Vis spectroscopy data collected on a Biotek Epoch 2 microplate spectrophotometer 24 hours after samples were synthesized using a liquid handling robot (Opentrons OT2). The <strong>4x4x4_SI.csv </strong>file is the compilation of all sample information: Concentrations (M) of peptide, HAuCl4, and HEPES UID – unique ID based on date of synthesis, sample position, and peptide which was used to synthesize the sample. Peptide names: Z2: RMRMKMK; MZ2: myristoylated - RMRMKMK; MZ2R: myristoylated - KMKMRMR; PZ2: palmitoylated – RMRMKMK; Z2M6I: RMRMKIK; Z2M246I: RIRIKIK; AG3: AYSSGAPPMPPF. Each sample’s UID is a key to match with UV-Vis measurement result stored in the {<strong>UID}.txt </strong>files. Each of these files contains the wavelength, absorbance, and absorbance after subtraction of a water measurement. <strong>/Data/2022_02_13_AuPeptide_Kinetics</strong> <strong>Measurement_Data.xlsx</strong> and <strong>Measurement_Times.xlsx </strong>contain UV-Vis spectra at several time points for each well measured, and the time corresponding to each time step, respectively. See <strong>/Notebooks/UV_Vis_Kinetics.ipynb</strong> for data plotting and sample concentration information. <strong>/Data/ElectronMicroscopy</strong> Scanning electron microscopy and transmission electron microscopy results of gold nanoparticles formed from the reduction of HAuCl4 in the presence or absence of different peptides. Fig A, B, C, D, E/F were prepared in the presence of Z2, Z2M6I, Z2M246I, no peptide, and MZ2R, respectively. <strong>/Data/Fluorescence</strong> Pyrene fluorescence data collected in the presence of different concentrations of lipidated peptides (MZ2, MZ2R, and PZ2) for estimation of the peptide critical micelle concentration. <strong>/Data/SAXS</strong> SAXS data of a high concentration of MZ2 which was fit using a cylindrical model form factor. The evaluated model is also shared in this directory. <strong>/Data/USAXS</strong> Similarly to the UV-Vis data directory, the <strong>USAXS_SI.csv</strong> file contains sample information for all of the USAXS measurements. The <strong>dsm_rg.csv</strong> file contains the output of AUTORG evaluated on the desmeared data after subtraction of a flat background at high-q. <strong>/DSM_Nexus, DSM_sub_AUTORG, </strong>and <strong>SMR_Nexus</strong> contain the desmeared, desmeared with background subtraction, and smeared versions of the USAXS data, respectively. <strong>/Notebooks</strong> Notebooks for plotting the shared data and estimating the CMC from the fluorescence data. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. We recommend installing this environment by using: conda env create -f /environment.yml Refer to https://github.com/SasView/sasmodels and the first cell of <strong>/Notebooks/USAXS.ipynb</strong> for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file). <strong>/Figures</strong> Figures generated from <strong>/Notebooks</strong>. <strong>/Synthesis_Protocol</strong> Please read the instructions within <strong>/Synthesis_Procol/Example.ipynb</strong>. In short, this folder contains the code used to synthesize the samples in this dataset using an OT2 Opentrons liquid handling robot.