2. Academic Validation
  3. Phenoxazine pseudonucleotides in DNA i-motifs allow precise profiling of small molecule binders by fluorescence monitoring

Phenoxazine pseudonucleotides in DNA i-motifs allow precise profiling of small molecule binders by fluorescence monitoring

  • Analyst. 2021 Jul 21;146(14):4436-4440. doi: 10.1039/d1an00660f.
Vladimir B Tsvetkov 1,  Anton V Turaev 2,  Nataliia A Petrunina 3,  Denis M Melnik 4,  Yuriy M Khodarovich 5,  Galina E Pozmogova 2,  Timofei S Zatsepin 6,  Anna M Varizhuk 7,  Andrey V Aralov 8
Affiliations

Affiliations

  • 1 Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, 8/2 Trubetskaya Str., Moscow, 119146, Russia and A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, 119071, Russia.
  • 2 Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
  • 3 Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia.
  • 4 Center for Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy boulevard 30b1, Moscow, 121205, Russia.
  • 5 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia. [email protected].
  • 6 Center for Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy boulevard 30b1, Moscow, 121205, Russia and Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory Str. 1-3, 119992 Moscow, Russia.
  • 7 Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia and Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia. [email protected].
  • 8 Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia. [email protected].
PMID: 34132709 DOI: 10.1039/d1an00660f
Abstract

The lack of high throughput screening (HTS) techniques for small molecules that stabilize DNA iMs limits their development as perspective drug candidates. Here we showed that fluorescence monitoring for probing the effects of ligands on the iM stability using the FAM-BHQ1 pair provides incorrect results due to additional dye-related interactions. We developed an alternative system with fluorescent phenoxazine pseudonucleotides in loops that do not alter iM unfolding. At the same time, the fluorescence of phenoxazine residues is sensitive to iM unfolding that enables accurate evaluation of ligand-induced changes of iM stability. Our results provide the basis for new approaches for HTS of iM ligands.

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