Thiophene-linked tetramethylbodipy-labeled nucleotide for viscosity-sensitive oligonucleotide probes of hybridization and protein-DNA interactions

0522408 - ÚOCHB 2021 RIV GB eng J - Journal Article
Güixens-Gallardo, Pedro - Humpolíčková, Jana - Miclea, Sebastian Paul - Pohl, Radek - Kraus, Tomáš - Jurkiewicz, Piotr - Hof, Martin - Hocek, Michal
Thiophene-linked tetramethylbodipy-labeled nucleotide for viscosity-sensitive oligonucleotide probes of hybridization and protein-DNA interactions.
Organic & Biomolecular Chemistry. Roč. 18, č. 5 (2020), s. 912-919. ISSN 1477-0520. E-ISSN 1477-0539
R&D Projects: GA ČR(CZ) GA17-14791S; GA MŠMT(CZ) EF16_019/0000729; GA ČR(CZ) GX19-26854X
Grant - others:AV ČR(CZ) AP1501
Program: Akademická prémie - Praemium Academiae
Institutional support: RVO:61388963 ; RVO:61388955
Keywords : polymerase synthesis * molecular rotors * fluorescent probes
OECD category: Organic chemistry; Physical chemistry (UFCH-W)
Impact factor: 3.876, year: 2020
Method of publishing: Limited access
https://pubs.rsc.org/en/content/articlelanding/2020/OB/C9OB02634G#!divAbstract

Cytosine 2′-deoxyribonucleoside dCTBdp and its triphosphate (dCTBdpTP) bearing tetramethylated thiophene-bodipy fluorophore attached at position 5 were designed and synthesized. The green fluorescent nucleoside dCTBdp showed a perfect dependence of fluorescence lifetime on the viscosity. The modified triphosphate dCTBdpTP was substrate to several DNA polymerases and was used for in vitro enzymatic synthesis of labeled oligonucleotides (ONs) or DNA by primer extension. The labeled single-stranded ONs showed a significant decrease in mean fluorescence lifetime when hybridized to the complementary strand of DNA or RNA and were also sensitive to mismatches. The labeled dsDNA sensed protein binding (p53), which resulted in the increase of its fluorescence lifetime. The triphosphate dCTBdpTP was transported to live cells where its interactions could be detected by FLIM but it did not show incorporation to genomic DNA in cellulo.
Permanent Link: http://hdl.handle.net/11104/0306910