Synthesis and Solvatochromic Fluorescence of Biaryl Pyrimidine Nucleosides

Isomorphic Fluorescent Nucleosides

In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.

Alkoxy-Substituted Quadrupolar Fluorescent Dyes

Polar and polarizable π-conjugated organic molecules containing push-pull chromophores have been investigated extensively in the past. Identifying unique backbones and building blocks for fluorescent dyes is a timely exercise. Here, we report the synthesis and characterization of a series of fluorescent dyes containing quadrupolar A-D-A constitutions (where A = acceptor and D = donor), which exhibit fluorescence emission at a variety of different wavelengths. We have investigated the effects of different electron-withdrawing groups, located at both termini of a para-terphenylene backbone, by steady-state UV/vis and fluorescence spectroscopy. Pyridine and substituted pyridinium units are also introduced during the construction of the quadrupolar backbones. Depending on the quadrupolarity, fluorescence emission wavelengths cover from 380 to 557 nm. Time-resolved absorption and emission spectroscopy reveal that the photophysical properties of those quadrupolar dyes result from intramolecular charge transfer. One of the dyes we have investigated is a symmetrical box-like tetracationic cyclophane. Its water-soluble tetrachloride, which is non-cytotoxic to cells up to a loading concentration of 1 μM, has been employed in live-cell imaging. When taken up by cells, the tetrachloride emits a green fluorescence emission without any hint of photobleaching or disruption of normal cell behavior. We envision that our design strategy of modifying molecules through the functionalization of the quadrupolar building blocks as chromophores will lead to future generations of fluorescent dyes in which these A-D-A constitutional fragments are incorporated into more complex molecules and polymers for broader photophysical and biological applications.

Enhancing fluorescence of benzimidazole derivative via solvent-regulated ESIPT and TICT process: A TDDFT study

In this work, we use density functional theory and time dependent density functional theory to explore the ESIPT and TICT process of 6-(1H-Benzoimidazol-2-yl)-2,3-dimethoxy-phenol (BIDOP) in cyclohexane (CHX) and tetrahydrofuran (THF) solvent, respectively. It reveals that ESIPT process of BIDOP can occur in both CHX and THF solvent at the first excited state with similar reaction barrier. Remarkably, compared to barrierless from keto (K*) to TICT state of BIDOP in THF solvent, the reaction barrier between K* and TICT state is up to 20.28 kcal/mol for in CHX that TICT process is inhibited in CHX solvent. The absence of nonradiative decay TICT state of BIDOP in CHX solvent induces higher fluorescence in CHX compared to in THF solvent. These findings indicate that CHX solvent can effectively enhance fluorescence of BIDOP. Our study highlights a convenient approach for enhancing fluorescence and is significant for photophysics and photobiology field.

Acetophenyl-thienyl-aniline-Linked Nucleotide for Construction of Solvatochromic Fluorescence Light-Up DNA Probes Sensing Protein-DNA Interactions

The synthesis of 2'-deoxycytidine and its 5'-O-triphosphate bearing solvatochromic acetophenyl-thienyl-aniline fluorophore was developed using the Sonogashira cross-coupling reaction as the key step. The triphosphate was used for polymerase synthesis of labelled DNA. The labelled nucleotide or DNA exerted weak red fluorescence when excited at 405 nm, but a significant colour change (to yellow or green) and light-up (up to 20 times) was observed when the DNA probes interacted with proteins or lipids.

Preparation and photophysical properties of quinazoline-based fluorophores

The donor-acceptor design is a classic method of synthesizing new fluorescent molecules. In this study, a series of new fluorescent compounds (1-10) were synthesized based on 2-(3,5-bis(trifluoromethyl)phenyl)-quinazoline acceptor and various amino donors. The fluorescent emissions of 1-10 cover the spectrum from 414 nm to 597 nm in cyclohexane solutions with various amino donors on 4- or 7-positions of quinazoline. Ultimately, compounds 1 and 2 presented the highest photoluminescence quantum yield (QY) over 80%, while compound 10 provided the largest Stokes shift (161 nm) in cyclohexane. Most of them have strong emissions in aggregated states such as in nanoparticles, in powders, in crystals and in films. Mechanochromic properties were observed for compounds 1, 2, 4 and 7. Furthermore, blue OLEDs were fabricated by using compound 2 or 7 as the active layer.

Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels

Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).

Convergent Synthesis of N,S-bis Glycosylquinolin-2-ones via a Pd-G3-XantPhos Precatalyst Catalysis

Buchwald-Hartwig-Migita cross-coupling of 1-thiosugars with α- or β-3-iodo-N-glycosylquinolin-2-ones has been accomplished under mild and operationally simple reaction conditions through the use of a Pd-G3 XantPhos palladacycle precatalyst. This new methodology has been successfully applied to a variety of α- or β-mono-, di-, and poly-thiosugar derivatives to efficiently synthesize a series of α- or β-N,S-bis-glycosyl quinolin-2-ones, which are difficult to synthesize by classical methods.

Emissive Synthetic Cofactors: Enzymatic Interconversions of tz A Analogues of ATP, NAD+ , NADH, NADP+ , and NADPH

A series of enzymatic transformations, which generate visibly emissive isofunctional cofactors based on an isothiazolo[4,3-d]pyrimidine analogue of adenosine (tz A), was developed. Nicotinamide adenylyl transferase condenses nicotinamide mononucleotide and tz ATP to yield Ntz AD+ , which can be enzymatically phosphorylated by NAD+ kinase and ATP or tz ATP to the corresponding Ntz ADP+ . The latter can be engaged in NADP-specific coupled enzymatic transformations involving conversion to Ntz ADPH by glucose-6-phosphate dehydrogenase and reoxidation to Ntz ADP+ by glutathione reductase. The Ntz ADP+ /Ntz ADPH cycle can be monitored in real time by fluorescence spectroscopy.

A two-photon fluorescent probe for real-time monitoring of autophagy by ultrasensitive detection of the change in lysosomal polarity

The first two-photon probe, Lyso-OC, was proposed for use in monitoring cell autophagy by detection of the change in the lysosomal polarity during the membrane fusion process.

Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn

We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.

High quantum yield and pH sensitive fluorescence dyes based on coumarin derivatives: fluorescence characteristics and theoretical study

The fluorescence coumarin derivatives were synthesized by an efficient one-pot, three-component reaction in 80–90% yields.

A fluorescent surrogate of thymidine in duplex DNA

DMAT is a new fluorescent thymidine mimic composed of 2′-deoxyuridine fused to dimethylaniline.

An ultrasensitive near-infrared ratiometric fluorescent probe for imaging mitochondrial polarity in live cells and in vivo

We describe a new mitochondria-targeting fluorescent probe MCY-BF₂ that is singularly sensitive and specifically responsive to mitochondrial polarity.

Mitochondrial polarity is a crucial characteristic of these indispensable organelles, and tremendously impacts cellular events. Herein, we describe a new mitochondria-targeting fluorescent probe MCY-BF₂ that is singularly sensitive and specifically responsive to mitochondrial polarity. The pull–push system in the conjugated structure of MCY-BF₂ is responsible for the polarity-ultrasensitivity due to the excited state intramolecular charge transfer (ICT). By combining with cardiolipin, MCY-BF₂ preferentially accumulates in mitochondria. Because the fluorescence emission wavelengths exhibit an obvious red-shift with increasing media polarity, the fluorescence intensity ratio at two different wavelengths versus the solvent dielectric constant can quantify the mitochondrial polarity. Experimental results demonstrate that the fluorescent intensity of MCY-BF₂ in a non-polar solvent, dioxane, is 120 times higher than that in a polar solvent, dimethyl sulfoxide. As the first near-infrared (NIR) and most sensitive fluorescent imaging probe for polarity, MCY-BF₂ can locate exclusively in mitochondria in various cells and discriminate polarity differences between normal and cancer cells. Also, the intrinsic polarity variance at different developmental stages in Caenorhabditis elegans (C. elegans) was reported here for the first time. Interestingly, the embryonic development stage has a more non-polar environment with a dielectric constant of 7.20, and in contrast the polarity at the young adult stage changes to 10.07. In addition, in vivo imaging results suggest that the tumor tissues of mice have an obviously lower polarity than that in normal tissues. Altogether, the merits of the NIR property, high sensitivity and moderate Stokes shift all greatly promote the accuracy of imaging. This probe will be a promising tool for studying biological processes and the pathological mechanism of polarity-related diseases.

Study on the solution and solid-state fluorescence of novel BF2 complexes with (Z)-2-[phenanthridin-6(5H)-ylidene]-1-phenylethanone and its derivatives as ligands

A family of novel N,O-chelated BF₂ complexes with intense solution and solid-state emission were synthesized and their photophysical properties were studied.

Fluorescent chemosensors of carbohydrate triols exhibiting TICT emissions

4-4′-Disubstituted biphenyl boronic acids (BBAs) are push–pull fluorophores with “turn-on” fluorescence properties.