READ ME File For 'Data from Targeting the IRES structure of mRNA for modulating gene translation'

Dataset DOI: 10.5258/SOTON/D3510

ReadMe Author: Albert Ferriol Monjo, University of Southampton ORCID ID 0000-0003-0754-4716

This dataset supports the thesis entitled Targeting the IRES structure of mRNA for modulating gene translation
AWARDED BY: University of Southampton
DATE OF AWARD: 2025


Licence: CC BY

Related projects/Funders: 
Project: OLIGOMED: Oligonucleotides for Medicinal Applications
PI: Eugen Stulz
Funder: H2020 
Website: https://www.oligomed.eu/

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DATA & FILE OVERVIEW
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This dataset contains:

Data corresponding to the synthesis and analysis of the synthesized oligonucleotide sequences, along with their subsequent characterization. This includes assessments of purity, yield, and structural integrity using techniques such as HPLC (High-Performance Liquid Chromatography) and mass spectrometry to ensure quality control.

Data corresponding to the synthesis and analysis of gold and silver nanoparticles, as well as their subsequent functionalization with polyethylene glycol (PEG). These processes were characterized by various analytical techniques to confirm nanoparticle formation, size distribution, and successful surface modification with PEG ligands

Data corresponding to the analysis and optimization process carried out to conjugate PEG molecules to the previously synthesized ssDNA sequences. This process included the evaluation of conjugation efficiency, reaction conditions, and product purity using appropriate analytical techniques.

Data corresponding to the synthesis and analysis of gold and silver nanoparticles, as well as their subsequent functionalization with polyethylene glycol (PEG). These processes were characterized by various analytical techniques to confirm nanoparticle formation, size distribution, and successful surface modification with PEG ligands

Data deriving from cell-based assays evaluating the effects of various synthesized ssDNA sequences in HeLa cells, transfected using Lipofectamine® 3000 and gold nanoparticles (AuNPs). The results are organized into separate folders, each corresponding to a specific assay:

Cell Cytotoxicity

Cell Viability

Confocal Microscopy

Flow Cytometry

Fluorescence Microscopy

qPCR (quantitative Polymerase Chain Reaction)

Western Blot


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METHODOLOGICAL INFORMATION
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Oligosynthesis folder contains the results of the analysis and characterization performed using a different technique, including Liquid Chromatography-Mass Spectrometry (LC-MS), High-Performance Liquid Chromatography (HPLC), Nanodrop UV-Vis spectroscopy, and m-Fold computational analysis for DNA and RNA secondary structure prediction.

Nanoparticles folder corresponds to the analysis and characterization of a specific step in the functionalization process, during which various techniques were employed—including UV-Vis spectroscopy, TEM (Transmission Electron Microscopy), DLS (Dynamic Light Scattering), and Zetasizer measurements—to fully characterize the different nanosystems.

PEG-DNA folder contains the results of the analysis and characterization performed on the reaction between each specific oligonucleotide sequence and the PEG molecules. The efficiency of the coupling assay was characterized using Liquid Chromatography-Mass Spectrometry (LC-MS) and High-Performance Liquid Chromatography (HPLC).

AUNPs to PEG-DNA coupling folder corresponds to the analysis and characterization of a specific step in the functionalization process, during which various techniques were employed—including UV-Vis spectroscopy, TEM (Transmission Electron Microscopy), DLS (Dynamic Light Scattering), and Zetasizer measurements—to fully characterize the different nanosystems.

The "cell Assays" data correspond to various measurements and analyses from different assays conducted to evaluate the effects of transfecting the sequences into cells. To properly open and analyze the associated documents, it is recommended to use specialized software such as ImageJ for image analysis, FlowJo for flow cytometry data, and GraphPad Prism for statistical analysis and graphing.

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File created: June 2025