Author: Varpu S. Marjomäki

Development of functionalized SYBR green II related cyanine dyes for viral RNA detection

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 considerabl…

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Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization

In recent years, the studies of RNA and its use for the development of RNA based vaccines have increased drastically. Although cyanine dyes are commonly used probes for studying nucleic acids, in a wide range of applications, there is still a growing need for better and brighter dyes. To meet this demand, we have systematically studied the structure of SYBR green-related cyanine dyes to gain a deeper understanding of their interactions with biomolecules especially how they interact with nucleic acids and the structural components which makes them strongly fluorescent. Herein, five new dyes were synthesized, and their photophysical properties were evaluated. Observations of photophysical cha…

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Inspired by nature: Fiber networks functionalized with tannic acid and condensed tannin-rich extracts of Norway spruce bark show antimicrobial efficacy

This study demonstrated the antibacterial and antiviral potential of condensed tannins and tannic acid when incorporated into fiber networks tested for functional material purposes. Condensed tannins were extracted from industrial bark of Norway spruce by using pressurized hot water extraction (PHWE), followed by purification of extracts by using XADHP7 treatment to obtain sugar-free extract. The chemical composition of the extracts was analyzed by using HPLC, GC‒MS and UHPLC after thiolytic degradation. The test matrices, i.e., lignocellulosic handsheets, were produced and impregnated with tannin-rich extracts, and tannic acid was used as a commercial reference. The antibacterial and antiv…

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CCDC 1482405: Experimental Crystal Structure Determination

Related Article: Ville K. Saarnio, Kirsi Salorinne, Visa P. Ruokolainen, Jesper R. Nilsson, Tiia-Riikka Tero, Sami Oikarinen, L. Marcus Wilhelmsson, Tanja M. Lahtinen, Varpu S. Marjomäki|2020|Dyes Pigm.|177|108282|doi:10.1016/j.dyepig.2020.108282

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