Rational design and studies of excimer forming novel dual probes to target RNA

O. A. Krasheninina, A. A. Lomzov, V. S. Fishman, D. S. Novopashina, A. G. Venyaminova

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

Abstract

In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2′-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480 nm) of RNA-bound probes; particularly, the length of the linker arm of the 3′-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.

Original languageEnglish
Pages (from-to)2244-2250
Number of pages7
JournalBioorganic and Medicinal Chemistry
Volume25
Issue number7
DOIs
Publication statusPublished - 1 Apr 2017

Keywords

  • Drug Design
  • Oligonucleotide Probes/chemistry
  • RNA/chemistry
  • Spectrometry, Fluorescence
  • Structure-Activity Relationship
  • VISUALIZATION
  • PYRENE
  • BINARY PROBES
  • HYBRIDIZATION
  • NUCLEOSIDE
  • DNA
  • FLUORESCENT-PROBES
  • DERIVATIVES

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