A Highly Fluorescent Nucleobase Molecular Rotor

Abstract

Fluorescent base analogs (FBAs) are powerful probes of nucleic acids’ structures and dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore limited sensitivity of detection. Here we report the hitherto brightest FBA that has ideal molecular rotor properties for detecting local dynamic motions associated with base pair mismatches. The new trans-stilbene annulated uracil derivative “tsT” exhibits bright fluorescence emissions in various solvents (ε × Φ = 3400–29 700 cm–1 M–1) and is highly sensitive to mechanical motions in duplex DNA (ε × Φ = 150–4250 cm–1 M–1). tsT is thereby a “smart” thymidine analog, exhibiting a 28-fold brighter fluorescence intensity when base paired with A as compared to T or C. Time-correlated single photon counting revealed that the fluorescence lifetime of tsT (τ = 4–11 ns) was shorter than its anisotropy decay in well-matched duplex DNA (θ = 20 ns), yet longer than the dynamic motions of base pair mismatches (0.1–10 ns). These properties enable unprecedented sensitivity in detecting local dynamics of nucleic acids.

Screening Internal Donor–Acceptor Biaryl Nucleobase Surrogates for Turn-On Fluorescence Affords an Aniline–Carboxythiophene Probe for Protein Detection by G-Quadruplex DNA

“…Within the AXA single strand, the [COOTh]­An surrogate absorbs at 363 nm (ε = 29 189 M –1 cm –1 ) with emission at 480 nm and a fluorescence quantum yield (Φ fl ) of 0.25 for a brightness (ε × Φ fl ) of 7297 cm –1 M –1 . For comparison, the brightest canonical fluorescent base analogs (FBAs) display brightness values ranging from 2000 to 4250 cm –1 M –1 in duplex DNA …”

Fluorescent nucleobase analogs constructed by aldol‐type condensation: Design, properties, and synthetic optimization for fluorogenic labeling of 5‐formyluracil

“…First, 4a can be applied to fluorescent nucleic acid probes based on its high sensitivity to microenvironmental changes. Because various viscosity‐sensitive fluorophores or AIEgens have been conjugated with oligodeoxynucleotides to probe intracellular pH, DNA hybridization, DNA quadruplexes, abasic sites, or protein–DNA interactions, 5a,24 4a can be utilized for designing fluorescent light‐up probes for biomolecules. Second, 4a can be used as a basic structure for the selective fluorescent labeling of 5‐formyluracil.…”

“…To date, many novel fluorescent nucleobases have been designed and utilized to reveal the location, structural changes, environmental changes, 3 and biomolecular interactions of certain nucleic acids with advantageous properties, such as high sensitivity and fast response time 2b,4 . However, the design and environmental sensitivity of fluorescent nucleobases are still limited and insufficient to detect a specific biologically relevant nucleic acid (e.g., single nucleotide polymorphism, epigenetic nucleobases) or biomolecular interaction (e.g., DNA–, RNA–protein binding) with high selectivity 5 . Thus, designing new fluorescent nucleobase analogs with novel or improved functionality appears to be an important challenge to reveal new nucleic acid technologies for biomedical applications.…”

Recent advances in synthesis of quinazoline‐2,4(1H,3H)‐diones: Versatile building blocks in N‐heterocyclic compounds

“…[ 20 ] Quinazoline‐2,4( 1H,3H )‐diones also exhibit a wide variety of biological functions like α 1 ‐antagonist, [ 21 ] bacterial gyrase/topoisomerase inhibitors, [ 22,23 ] AMPA and kainate (KA) receptor antagonists, [ 24 ] PGGTase‐I inhibitors, [ 25 ] NAPE‐PLD inhibitors, [ 26 ] inhibitors of non‐small‐cell lung cancer, [ 27 ] and inhibitors of the growth of multiple human tumor cell lines, [ 28 ] and some of them have acted as nucleoside analogues, [ 29 ] fluorescent bioprobes for visualization of puromycin‐sensitive aminopeptidase in living cells, [ 30 ] and fluorescent base analogue (FBA) probes of nucleic acids' structures. [ 31 ] They also have attracted interest in preparing various pharmacological activities, such as antiviral, [ 32 ] antibacterial, [ 33–35 ] anticonvulsant and antioxidant agents, [ 36 ] and antitumor. [ 37 ]…”