Benzothiazole-based cyanines as fluorescent "light-up" probes for duplex and quadruplex DNA

Anton V Turaev; Vladimir B Tsvetkov; Maria V Tankevich; Igor P Smirnov; Andrey V Aralov; Galina E Pozmogova; Anna M Varizhuk

doi:10.1016/j.biochi.2019.04.018

Benzothiazole-based cyanines as fluorescent "light-up" probes for duplex and quadruplex DNA

Biochimie. 2019 Jul:162:216-228. doi: 10.1016/j.biochi.2019.04.018. Epub 2019 Apr 22.

Authors

Anton V Turaev¹, Vladimir B Tsvetkov², Maria V Tankevich³, Igor P Smirnov³, Andrey V Aralov⁴, Galina E Pozmogova⁵, Anna M Varizhuk⁶

Affiliations

¹ Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, 141700, Russia.
² Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of Russian Federation, Prof. Popov Str. 15/17, Saint-Petersburg, 197376, Russia; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Bolshaya Pirogovskaya Str. 19/1, Moscow, 119146, Russia.
³ Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia.
⁴ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia. Electronic address: baruh238@mail.ru.
⁵ Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow, 119071, Russia. Electronic address: pozmge@gmail.com.
⁶ Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow, 119991, Russia.

PMID: 31022429
DOI: 10.1016/j.biochi.2019.04.018

Abstract

Analogs of benzothiazole orange (BO) with one, two or three methylbenzothiazolylmethylidene substituents in the 1-methylpyridinium ring were obtained from the respective picolinium, lutidinium or collidinium salts. Fluorescence parameters of the known and new dyes in complexes with various DNA structures, including G-quadruplexes (G4s) and i-motifs (IMs), were analyzed. All dyes efficiently distinguished G4s and ss-DNA. The bi- and tri-substituted derivatives had basically similar distributions of relative fluorescence intensities. The mono-substituted derivatives exhibited enhanced sensitivity to parallel G4s. All dyes were particularly sensitive to a G4 structure with an additional duplex module (the thrombin-binding aptamer TBA31), presumably due to a distinctive binding mode (interaction with the junction between the two modules). In particular, BO showed a strong (160-fold) enhancement in fluorescence quantum yield in complex with TBA31 compared to the free dye. The fluorescence quantum yields of the 2,4-bisubstituted derivative in complex with well-characterized G4s from oncogene promoters were in the range of 0.04-0.28, i.e. comparable to those of ThT. The mono/bi-substituted derivatives should be considered as possible light-up probes for G4 formation.

Keywords: Cyanine dyes; G-quadruplex; I-motif; Light-up probe.

MeSH terms

Benzothiazoles / chemistry*
Circular Dichroism / methods
DNA / chemistry*
Fluorescence
Fluorescent Dyes / chemistry*
G-Quadruplexes*
Molecular Docking Simulation / methods
Molecular Dynamics Simulation
Nucleotide Motifs*
Spectrometry, Fluorescence / methods*

Substances

Benzothiazoles
Fluorescent Dyes
DNA