Development of functionalized SYBR green II related cyanine dyes for viral RNA detection
Journal article, 2020

Fluorescent probes for sensing nucleic acids have found widespread use in the field of cell and molecular biology. However, probes combined with potential for post-synthetic conjugation, e.g. for intra-endosomal measurements of RNA, are unavailable. Herein we developed cyanine dyes that can be conjugated to viral capsid or other targets. First, we solved the crystal structure of SYBR Green II. The structural elucidation of this commonly used RNA probe provided the basis for synthesizing similar molecules with much desired function for post-synthetic conjugation. To address this need, cyanine dyes were prepared using an alternative synthesis protocol. All studied compounds showed considerable brightness upon binding to nucleic acids. However, regardless of the common chromophore on the dyes, the observed fluorescence emission intensities varied significantly, where methyl-substituted dye 1 gave values higher than SYBR Green II, whereas compounds 2–5 containing undecyl spacers had lower values. Studying the structure-activity relationship revealed the longer alkyl chains to induce slight perturbation in dye intercalation, as well as demand larger binding area on the nucleic acid lattice, explaining these differences. To study the potential biological use of the dyes, the RNA genome of enterovirus echovirus 1 was studied in vitro with the probes. A novel method employing the low binding space requirement of 1 was developed to determine the single-to-double-stranded RNA ratio of a sample, whereas compound 4 was covalently bound to the viral capsid and used successfully to monitor the viral RNA release from within the capsid. The presented results open new possibilities for preparation and use of SYBR Green-based nucleic acid probes to further apply these compounds for increasingly demanding targeting in biological contexts.

Host-guest systems



Fluorescent probes

RNA recognition

Nucleic acids


Ville K. Saarnio

Nanoscience Center

Kirsi Salorinne

Nanoscience Center

Visa P. Ruokolainen

University of Jyväskylä

Jesper Nilsson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Tiia Riikka Tero

Nanoscience Center

Sami Oikarinen

University of Tampere

Marcus Wilhelmsson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Tanja M. Lahtinen

Nanoscience Center

Varpu S. Marjomäki

University of Jyväskylä

Dyes and Pigments

0143-7208 (ISSN) 18733743 (eISSN)

Vol. 177 108282

Areas of Advance

Nanoscience and Nanotechnology

Subject Categories

Biochemistry and Molecular Biology

Structural Biology

Organic Chemistry



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