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Environmentally Sensitive Fluorescent Nucleoside Analogues for Surveying Dynamic Interconversions of Nucleic Acid Structures
Author(s) -
Sholokh Marianna,
Sharma Rajhans,
Grytsyk Natalia,
Zaghzi Lyes,
Postupalenko Viktoriia Y.,
Dziuba Dmytro,
Barthes Nicolas P. F.,
Michel Benoît Y.,
Boudier Christian,
Zaporozhets Olga A.,
Tor Yitzhak,
Burger Alain,
Mély Yves
Publication year - 2018
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201802297
Subject(s) - nucleic acid , förster resonance energy transfer , dna , primer binding site , nucleic acid structure , chemistry , nucleobase , biophysics , rna , combinatorial chemistry , fluorescence , biochemistry , reverse transcriptase , biology , gene , physics , quantum mechanics
Nucleic acids are characterized by a variety of dynamically interconverting structures that play a major role in transcriptional and translational regulation as well as recombination and repair. To monitor these interconversions, Förster resonance energy transfer (FRET)‐based techniques can be used, but require two fluorophores that are typically large and can alter the DNA/RNA structure and protein binding. Additionally, events that do not alter the donor/acceptor distance and/or angular relationship are frequently left undetected. A more benign approach relies on fluorescent nucleobases that can substitute their native counterparts with minimal perturbation, such as the recently developed 2‐thienyl‐3‐hydroxychromone (3HCnt) and thienoguanosine ( th G). To demonstrate the potency of 3HCnt and th G in deciphering interconversion mechanisms, we used the conversion of the (−)DNA copy of the HIV‐1 primer binding site (−)PBS stem‐loop into (+)/(−)PBS duplex, as a model system. When incorporated into the (−)PBS loop, the two probes were found to be highly sensitive to the individual steps both in the absence and the presence of a nucleic acid chaperone, providing the first complete mechanistic description of this critical process in HIV‐1 replication. The combination of the two distinct probes appears to be instrumental for characterizing structural transitions of nucleic acids under various stimuli.