dGenhancer v2: A software tool for designing oligonucleotides that can trigger gene-specific Enhancement of Protein Translation.

Software tool designed to calculate 5’UTR properties, enabling the creation of oligonucleotides that can trigger gene-specific enhancement of protein translation.
An excel-based calculator - dGenhancer can be used to search for putative 5’UTR cis-acting elements, which functional activity could be determined by Gibbs energy-dependent secondary structure formation.
This version requires pre-calculated total Gibbs energies of the tested sequences. Prediction of total Gibbs energies (ΔG=ΔH–TΔS) of the 5’UTR structures can be performed using RNAstructure version 5.2. ΔGs are input data for final dGenhancer calculations as shown by Master A et al 2016¹

The algorithms of the calculator were constructed to visualize ΔG changes after in silico introduced single nucleotide substitutions (SNPs) of the 5’UTR sequences. These artificial SNPs differently affected overall sequence ΔGs (Gibbs energies) that were drawn by the dGenhancer to show regions where substitution can alter ΔGs the most, indicating putative cis-acting elements with the highest translational regulatory potential.

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S1 supplementary material: https://pmc.ncbi.nlm.nih.gov/articles/instance/4865139/bin/pone.0155359.s001.pdf
dGenhancer - previous localization: http://www.serwer1448847.home.pl/biotechnology/dGenhancer.xlsx

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References:

1. Master A, Wójcicka A, Giżewska K, Popławski P, Williams GR, Nauman A. A Novel Method for Gene-Specific Enhancement of Protein Translation by Targeting 5'UTRs of Selected Tumor Suppressors. PLoS One. 2016 May 12;11(5):e0155359. doi: 10.1371/journal.pone.0155359. PMID: 27171412; PMCID: PMC4865139.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155359

2. Master A, Wojcicka A, Nauman A. The 5’UTR-dependent enhancement of protein translation efficiency triggered by self-transfecting 3’-aminoallyl-containing oligonucleotides (aa-dGoligos) targeting a pool of strongly folded transcript variants of the THRB suppressor gene. Molecular Therapy, Volume 22, Supplement 1, S38, May 2014.
Abstract: https://www.cell.com/molecular-therapy-family/molecular-therapy/pdf/S1525-0016(16)35113-9.pdf

Poster: https://doi.org/10.6084/m9.figshare.27894564.v1

contact: adam.master.science@gmail.com