"siRNA traffic lights": arabino-configured 2'-anchors for fluorescent dyes are key for dual color readout in cell imaging.
Jeannine SteinmeyerHeidi-Kristin WalterMathilde A BichelbergerVioletta SchneiderTomáš KubařFranziska RönickeBettina OlshausenKarin NienhausGerd Ulrich NienhausUte SchepersMarcus ElstnerHans-Achim WagenknechtPublished in: Organic & biomolecular chemistry (2019)
Two fluorescent dyes covalently attached in diagonal interstrand orientation to siRNA undergo energy transfer and thereby enable a dual color fluorescence readout (red/green) for hybridization. Three different structural variations were carried out and compared by their optical properties, including (i) the base surrogate approach with an acyclic linker as a substitute of the 2-deoxyriboside between the phosphodiester bridges, (ii) the 2'-modification of conventional ribofuranosides and (iii) the arabino-configured 2'-modification. The double stranded siRNA with the latter type of modification delivered the best energy transfer efficiency, which was explained by molecular dynamics simulations that showed that the two dyes are more flexible at the arabino-configured sugars compared to the completely stacked situation at the ribo-configured ones. Single molecule fluorescence lifetime measurements indicate their application in fluorescence cell imaging, which reveals a red/green fluorescence contrast in particular for the arabino-configured 2'-modification by the two dyes, which is key for tracking of siRNA transport into HeLa cells.
Keyphrases
- energy transfer
- single molecule
- quantum dots
- molecular dynamics simulations
- living cells
- cancer therapy
- single cell
- high resolution
- cell therapy
- aqueous solution
- cell cycle arrest
- induced apoptosis
- atomic force microscopy
- hyaluronic acid
- air pollution
- molecular docking
- stem cells
- binding protein
- mesenchymal stem cells
- photodynamic therapy
- fluorescent probe
- nucleic acid