Nucleotides bearing aminophenyl- or aminonaphthyl-3-methoxychromone solvatochromic fluorophores for the enzymatic construction of DNA probes for the detection of protein–DNA binding

Abstract

Two new 2'-deoxyribonucleoside triphosphates bearing solvatochromic fluorophores were prepared and used for enzymatic synthesis of DNA probes that light-up and change colour upon interactions with proteins.

trans-Cyclooctene- and Bicyclononyne-Linked Nucleotides for Click Modification of DNA with Fluorogenic Tetrazines and Live Cell Metabolic Labeling and Imaging

“…Although two-step labeling protocols are more complex compared to direct labeling using SNTT1 with FL-dNTP, there are cases where they can serve as first choice methods: when the fluorophore moiety prevents efficient incorporation of FL-dNTP into DNA by cellular DNA polymerases. In the course of testing a wide range of commercially available FL-dNTPs (data not shown) as well as new FL-dNTPs developed in our lab, we observed that while all tested FL-dNTPs were transported into cells by SNTT1 , only some of them were efficiently incorporated into genomic DNA, − and others were incorporated either inefficiently or not at all. − In such cases, fluorescent labeling could, in principle, be achieved by SNTT1 -assisted delivery of dNTPs equipped with a “clickable handle”. These dNTPs need to be good substrates for intracellular DNA polymerases, and after their incorporation into DNA, the clickable handles of the nucleotides must be able to undergo a chemical post-labeling performed with suitably modified fluorophores in live cells.…”

Acyclic 2-Ethynylnaphthalene-Modified 8-Aza-3,7-dideaza-2′-deoxyadenosine Allows Thymine Discrimination by Probing the DNA Minor Groove Environment

“…3c Hocek et al have reported the use of solvatochromic nucleosides containing aminophenyl-3-methoxychromone or aminonaphthyl-3-methoxychromone fluorophores in the enzymatic construction of DNA probes and demonstrated the detection of DNA–protein interactions. 3b Viscosity-sensitive nucleotides containing the dimethoxy-BODIPY fluorophore have also been reported for applications in enzymatic incorporation and as tools for DNA staining and DNA synthesis imaging. 3e Moreover, numerous base-modified fluorescent nucleosides have been developed that are being used for the detection of target DNA or RNA sequences.…”

Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid – protein interactions: molecular design and biosensing applications

“…Nevertheless, one of the obtained dC ATA -labeled probes showed a 9-20 fold increase of emission intensity with a concomitant 33 nm blue shift of the maxima upon interaction with the histone 3.1 and p53. A subsequent work from the same group reported FNAs based on solvatochromic 7-aryl-3hydroxy chromone fluorophores [184]. Nucleoside analogues dC AC and dT NC (figure 8) were prepared, bearing 7-aminophenyl and 7-aminonaphthyl methoxychromones conjugated to position 5 of deoxycytidine and deoxythymidine, respectively.…”