Laboratory of artificial antibodies

Scientific interests and research areas

Our group has a long-standing interest in DNA/RNA aptamers as functional analogs of antibodies.

Current research areas include the dynamics and biological roles of non-canonical nucleic acid structures (ncDNA), such as G-quadruplexes (G4s) or i-motifs (iMs).

To clarify the interplay between ncDNA formation, chromatin packaging, and gene expression regulation, we investigate G4/iM-protein interactions and optimize ligands/light-up probes for selective targeting/visualization of genomic ncDNA. Using in silico modeling and biophysical methods, we study the recruitment of transcription factors or chromatin remodelers to G4 sites in the human genome.

Other ongoing projects include the design of selective small-molecule G4 binders and the development of iM-based tools for monitoring intracellular pH changes.

Collaborators

• Lomonosov Moscow State University,
• Lomonosov Moscow State University of Fine Chemical Technology,
• Engelhardt Institute of Molecular Biology,
• D. Mendeleev University of Chemical Technology of Russia

List of selected publications

• Tsvetkov et al. EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. Biochimie 2021
• Tikhonova et al. DNA G-Quadruplexes Contribute to CTCF Recruitment. International Journal of Molecular Sciences 2021
• Tsvetkov et al. Phenoxazine pseudonucleotides in DNA i-motifs allow precise profiling of small molecule binders by fluorescence monitoring. Analyst 2021
• Turaev et al. Genomic DNA i-motifs as fast sensors responsive to near-physiological pH microchanges. Biosensors and Bioelectronics 2021
• Pavlova et al. Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures.  International Journal of Biological Macromolecules 2020
• Tsvetkov et al. Phenoxazine-based scaffold for designing G4-interacting agents. Organic & Biomolecular Chemistry 2020
• Turaev et al. Benzothiazole-based cyanines as fluorescent "light-up" probes for duplex and quadruplex DNA. Biochimie 2021
• Turaev et al. DNA i-Motifs with Guanidino-i-Clamp Residues: The Counterplay Between Kinetics and Thermodynamics and Implications for the Design of pH Sensors. Computational and Structural Biotechnology Journal 2019
• Varizhuk et al. DNA G-Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling. BioEssays 2019
• Tsvetkov et al. i-Clamp phenoxazine for the fine tuning of DNA i-motif stability. Nucleic Acids Research  2018
• Varizhuk et al. Polymorphism of G4 associates: from stacks to wires via interlocks. Nucleic Acids Research 2018
• Varizhuk et al. The expanding repertoire of G4 DNA structures. Biochimie 2017

Phones:
+7 (499) 246-4570,
+7 (499) 246-9646

E-mail:
annavarizhuk@rcpcm.org