The group of molecular tools for living system studies

Department of functioning of living systems

Head: Andrey Aralov, Ph.D.
Baruh238@mail.ru+7(926)6062910

RNA, DNA, G-quadruplex, i-motif, antisense oligonucleotides, probes, pH sensors, modification, fluorescence

The main research areas of the group include:

  • design and synthesis of nucleotide modifications for fine tuning the properties of canonical and non-canonical secondary nucleic acids structures;
  • development of nucleotide modifications suitable for antisense and RNAi technologies for regulating gene expression;
  • synthesis and screening of probes/ligands for detecting and fine tuning physicochemical parameters of noncanonical secondary nucleic acids structures; 
  • development and study of the properties of metal-binding modifications within oligonucleotides;
  • study of the physicochemical properties of modifications that arise in living organisms when exposed to mutagenic factors; 
  • design and synthesis of antiviral compounds.

All publications (show selected)

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Andrey Aralov

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 51, office. 454
  • Phone: +7(926)6062910
  • E-mail: Baruh238@mail.ru

Molecular tools for stabilizing non-canonical nucleic acids secondary structures

Ligands and nucleic base modifications for stabilizing non-canonical nucleic acids secondary structures have been developed.

Publications

  1. Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J (2019). Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine. J Biol Inorg Chem 24 (5), 693–702
  2. (book) Zatsepin TS, Varizhuk AM, Dedkov VG, Shipulin GA, Aralov AV (2019). Oligonucleotide Primers with G8AE-Clamp Modifications for RT-qPCR Detection of the Low-Copy dsRNA. Methods Mol Biol 1973, 281–297
  3. Tsvetkov VB, Zatsepin TS, Turaev AV, Farzan VM, Pozmogova GE, Aralov AV, Varizhuk AM (2019). DNA i-Motifs With Guanidino-i-Clamp Residues: The Counterplay Between Kinetics and Thermodynamics and Implications for the Design of pH Sensors. Comput Struct Biotechnol J 17, 527–536

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

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 quantumyield 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 0.04e0.28, i.e. comparable to those of ThT. The mono/bi-substituted derivatives should be considered as possible light-up probes for G4 formation.

Publications

  1. Turaev AV, Tsvetkov VB, Tankevich MV, Smirnov IP, Aralov AV, Pozmogova GE, Varizhuk AM (2019). Benzothiazole-based cyanines as fluorescent “light-up” probes for duplex and quadruplex DNA. Biochimie 162, 216–228

New antiviral nucleoside derivatives for inhibiting the reproduction of varicella-zoster virus and tick-borne encephalitis virus

In collaboration with Laboratory of molecular design and synthesis

A series of analogues of potent antiviral perylene nucleoside dUY11 with methylthiomethyl (MTM), azidomethyl (AZM) and HO-C1-4-alkyl-1,2,3-triazol-1,4-diyl groups at 3`-O-position as well as the two products of copper-free alkyne-azide cycloaddition of the AZM derivative were prepared and evaluated against tick-borne encephalitis virus (TBEV). Four compounds showed EC50 ≤10 nM, thus appearing the most potent TBEV inhibitors to date. Moreover, these nucleosides have higher lipophilicity (clogP) and increased solubility in aq. DMSO vs. parent compound dUY11.

Phenoxazine scaffold is widely used to stabilize nucleic acid duplexes, as a part of fluorescent probes for the study of nucleic acid structure, recognition, and metabolism etc. We present the synthesis of phenoxazine-based nucleoside derivatives and their antiviral activity against a panel of structurally diverse viruses: enveloped DNA herpesviruses varicella zoster virus (VZV) and human cytomegalovirus, enveloped RNA tick-borne encephalitis virus (TBEV), and non-enveloped RNA enteroviruses. Studied compounds were effective against DNA and RNA viruses reproduction in cell culture. 3-(2’-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenoxazine proved to be a potent inhibitor of VZV replication with superior activity against wild type than thymidine kinase deficient strains (EC50 0.06 and 10 µM, respectively). This compound did not show cytotoxicity on all the studied cell lines. Several compounds showed promising activity against TBEV (EC50 0.35-0.91 µM), but the activity was accompanied with pronounced cytotoxicity. These compounds may be considered as a good starting point for further structure optimization as antiherpesviral or antiflaviviral compounds.

Publications

  1. Proskurin GV, Orlov AA, Brylev VA, Kozlovskaya LI, Chistov AA, Karganova GG, Palyulin VA, Osolodkin DI, Korshun VA, Aralov AV (2018). 3′-O-Substituted 5-(perylen-3-ylethynyl)-2′-deoxyuridines as tick-borne encephalitis virus reproduction inhibitors. Eur J Med Chem 155, 77–83