fish probes targeting tmprss2 and erg flanking sequences tmp erg del-tecttm  (CymoGenDx LLC)

Journal: bioRxiv

Article Title: Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling

doi: 10.1101/2024.07.29.605618

Figure Lengend Snippet: Experimental and modelled ECD spectrum of the TMPRSS2 mRNA G4 in solution.

Article Snippet: For this experiment we used the TMPRSS2 sequence 5’-GGGCGGGCGGCCUGCAGGGACAUGGG-3’ (IDT Technologies).

Techniques:

Journal: bioRxiv

Article Title: Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling

doi: 10.1101/2024.07.29.605618

Figure Lengend Snippet:

Article Snippet: For this experiment we used the TMPRSS2 sequence 5’-GGGCGGGCGGCCUGCAGGGACAUGGG-3’ (IDT Technologies).

Techniques:

Journal: Virology

Article Title: An engineered A549 cell line expressing CD13 and TMPRSS2 is permissive to clinical isolate of human coronavirus 229E.

doi: 10.1016/j.virol.2023.109889

Figure Lengend Snippet: Fig. 1. Expression of CD13 and TMPRSS2 in engineered A549 cells. 30 μg of protein from cell lysates was loaded onto a 4%–12% Bis-Tris gel and sepa rated by SDS-PAGE before expressions of (A) CD13 and (B) TMPRSS2 were analyzed by Western Blot. GAPDH detection is included as the loading control. WT A549 cells are included as a negative control, whereas HAE lysates are included as a positive control for TMPRSS2.

Article Snippet: The mix consisted of 27 μg of PEI (Sigma-Aldrich), 9 μg of a vector carrying either the CD13/aminopeptidase N sequence (pLEX307-APN-G418 was a gift from Alejandro Chavez & Sho Iketani; Addgene plasmid #158456) or the TMPRSS2 sequence (pLEX307-TMPRSS2-blast was a gift from Alejandro Chavez & Sho Iketani; Addgene plasmid #158458).

Techniques: Expressing, SDS Page, Western Blot, Control, Negative Control, Positive Control

Journal: Scientific Reports

Article Title: In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis

doi: 10.1038/s41598-020-77602-0

Figure Lengend Snippet: Binding energy of top ranked plant secondary metabolites against four targets of SARS-CoV-2 pathogenesis and their physicochemical properties.

Article Snippet: The TMPRSS2 sequence (NP_001128571.1) was retrieved from the National Center for Biotechnology Information (NCBI) protein database.

Techniques: Binding Assay

Journal: Scientific Reports

Article Title: In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis

doi: 10.1038/s41598-020-77602-0

Figure Lengend Snippet: ( a ) Structural activity relationship: Correlation of canonical SMILES structure similarity (data points are joined by colored lines) and binding energy (represented in different color shades of data point) of selected plant secondary metabolites (PSM) evaluated against SARS-CoV-2 TMPRSS2 using Data Warrior software. Structurally similar molecules are grouped in dotted lines and a representative molecule with low binding energy (kcal/mol) (values in parenthesis) is represented in box. Among top ranked PSM studied, > 32% found belonging to Flavonoid glucoside and other major groups are ellagitannins and triterpenoids. ( b ) Data analysis of selected PSM against SARS-CoV-2 TMPRSS2. ( A ) Bioavailability radar chart representing lipophilicity (LIPO), Molecular weight (SIZE), Topological polar surface area (POLAR), Solubility (INSOLU), Flexibility (FLEX) and Saturation (INSATU) along with Bioavailability score (BAS) of selected molecules, ( B ) 3D visualization of protein–ligand interaction using PyMOL (selected amino acid residue of target site of protein are colored in cyan, and ( C ) 2D visualization of different types of interactions between ligand and target site of protein using Discovery Studio software (different types of interactions are represented in color codes).

Article Snippet: The TMPRSS2 sequence (NP_001128571.1) was retrieved from the National Center for Biotechnology Information (NCBI) protein database.

Techniques: Activity Assay, Binding Assay, Software, Molecular Weight, Solubility, Residue