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“siRNA traffic lights”: arabino-configured 2′-anchors for fluorescent dyes are key for dual color readout in cell imaging

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Abstract

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.

Graphical abstract: “siRNA traffic lights”: arabino-configured 2′-anchors for fluorescent dyes are key for dual color readout in cell imaging

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Publication details

The article was received on 16 Feb 2018, accepted on 13 Mar 2018 and first published on 13 Mar 2018


Article type: Paper
DOI: 10.1039/C8OB00417J
Citation: Org. Biomol. Chem., 2018, Advance Article
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    “siRNA traffic lights”: arabino-configured 2′-anchors for fluorescent dyes are key for dual color readout in cell imaging

    J. Steinmeyer, H. Walter, M. A. Bichelberger, V. Schneider, T. Kubař, F. Rönicke, B. Olshausen, K. Nienhaus, G. U. Nienhaus, U. Schepers, M. Elstner and H. Wagenknecht, Org. Biomol. Chem., 2018, Advance Article , DOI: 10.1039/C8OB00417J

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