title: Rational design and studies of excimer forming novel dual probes to target RNA.
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 ∼480nm) 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.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia. Electronic address: OKrasheninina@gmail.com.
authors.forename: O A
authors.initials: OA
authors.lastname: Krasheninina
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
authors.forename: A A
authors.initials: AA
authors.lastname: Lomzov
authors.affiliation: Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave., Novosibirsk 630090, Russia.
authors.forename: V S
authors.initials: VS
authors.lastname: Fishman
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
authors.forename: D S
authors.initials: DS
authors.lastname: Novopashina
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia.
authors.forename: A G
authors.initials: AG
authors.lastname: Venyaminova
mesh_terms: D015195:Drug Design; D015345:Oligonucleotide Probes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013329:Structure-Activity Relationship
chemical_list: D015345:Oligonucleotide Probes; D012313:RNA