Synthesis and characterization of fluorenone-, anthraquinone-, and phenothiazine-labeled oligodeoxynucleotides: 5'-probes for DNA redox chemistry

Phenothiazine-Embedded Hexaphyrins

Unprecedented nonaromatic stable phenothiazine-embedded porphyrinoids were synthesized by incorporating phenothiazine subunits into the hexaphyrin framework. The crystal structure revealed that the macrocycle adopted a twisted conformation wherein the phenothiazine units maintained their planarity, which was an impediment in π-delocalization throughout the macrocyclic core. The macrocycles exhibited distinct absorption bands in the visible-near-infrared region, and electrochemical studies indicated their electron-rich nature. Theoretical studies were consistent with the experimental observations.

Phenothiazine-Biaryl-Containing Fluorescent RGD Peptides

Cyclic RGD peptides are well-known ligands of integrins. The integrins αV β3 and α5 β1 are involved in angiogenesis, and integrin αV β3 is abundantly present on cancer cells, thus representing a therapeutic target. Hence, synthetic and biophysical studies continuously are being directed towards the understanding of ligand-integrin interaction. In this context, the development of versatile synthetic strategies to obtain fluorescent building blocks that can add molecular diversity and modular spectral characteristics while not compromising binding affinity or selectivity is a relevant task. An on-resin intramolecular Suzuki-Miyaura cross-coupling (SMC) between l- or d-7-bromotryptophan (7BrTrp) and a phenothiazine (Ptz) boronic acid affords fluorescent cyclic RGD pseudopeptides, c(RGD(W/w)Ptz). Ring closure by SMC establishes a phenothiazine-indole moiety with axial chirality. An array of eight novel compounds has been synthesized, among them one fluorescent compound with good affinity to integrin αV β3 . The fluorescence properties of the analogues can be efficiently tuned depending on the substituents in Ptz moiety even for fluorescence emission in the visible (red) spectral range.

Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA

Nucleosides and 2'-deoxyribonucleoside triphosphates (dNTPs) bearing phenothiazine (PT) attached to a nucleobase (cytosine or 7-deazaadenine) either directly or through an acetylene linker were prepared through Suzuki or Sonogashira cross-coupling and triphosphorylation, and were studied as building blocks for polymerase construction of modified DNA. The directly PT-substituted dNTPs were better substrates for polymerases than the alkyne-linked dNTPs but all of them were used in enzymatic synthesis of DNA using primer extension, nicking enzyme amplification, PCR or 3'-tail labelling by terminal deoxynucleotidyl transferase. The phenothiazine served as an oxidizable redox label (giving two analytically useful signals of oxidation on electrode) for nucleosides and DNA and was also used in orthogonal combination with previously developed benzofurazane or nitrophenyl labels for redox coding of DNA bases. Therefore, the title PT-linked dNTPs are useful additions to the portfolio of nucleotides for enzymatic synthesis of redox-labelled DNA for electrochemical analysis.

Palladium-catalyzed synthesis of fluoreones from bis(2-bromophenyl)methanols

Palladium plays a dual role in synthesizing fluorenones from bis(2-bromophenyl)methanols.

CBr4 promoted intramolecular aerobic oxidative dehydrogenative arylation of aldehydes: application in the synthesis of xanthones and fluorenones

A simple and practical carbon tetrabromide promoted intramolecular aerobic oxidative dehydrogenative coupling reaction has been developed to provide a straightforward ring closure protocol for 2-aryloxybenzaldehydes to furnish xanthones. The reaction was performed under metal-, additive- and solvent-free conditions with good tolerance of functional groups. The present method is also applicable to the synthesis of fluorenones by using 2-arylbenzaldehydes as substrates. Preliminary studies of the reaction mechanism indicated that the reaction may proceed through a radical pathway.

Pd/Cu-catalyzed dual C–H bond carbonylation towards the synthesis of fluorazones

Pd catalyzed oxidative dual C–H bond activation/carbonylation still remains a great challenge due to the generation of by-products via C–C bond formation. Herein, we developed a straightforward Pd/Cu-catalyzed oxidative dual C–H bond carbonylation process to access biologically and pharmaceutically important fluorazones from easily available N-aryl pyrroles and CO utilizing O₂ as the terminal oxidant.

Hole-Accepting-Ligand-Modified CdSe QDs for Dramatic Enhancement of Photocatalytic and Photoelectrochemical Hydrogen Evolution by Solar Energy

Solar H2 evolution of CdSe QDs can be significantly enhanced simply by introducing a suitable hole-accepting-ligand for achieving efficient hole extraction and transfer at the nanoscale interfaces, which opens an effective pathway for dissociation of excitons to generate long-lived charge separation, thus improving the solar-to-fuel conversion efficiency.

Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe

Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.

Synthesis of Fluoren-9-ones and Ladder-Type Oligo-p-phenylene Cores via Pd-Catalyzed Carbonylative Multiple C-C Bond Formation

A new route to various substituted fluoren-9-ones has been developed via an efficient Pd-catalyzed carbonylative multiple C-C bond formation. Under a CO atmosphere, using commercially available aryl halides and arylboronic acids as substrates, this three-component reaction proceeded smoothly in moderate to excellent yields with good functional-group compatibility. The mechanistic investigations suggested a sequential process for the reaction that forms o-bromobiaryls in the first stage followed by a cyclocarbonylation reaction. This chemistry has been successfully extended to construct ladder-type oligo-p-phenylene cores.

Synthesis of fluorenones by using Pd(ii)/Mg–La mixed oxide catalyst

Palladium(ii)/magnesium–lanthanum mixed oxide (Pd(ii)/Mg–La mixed oxide) catalyst was used in the dehydrogenative cyclization of benzophenones to afford fluorenones.

Hole transfer in LNA and 5-Me-2'-deoxyzebularine-modified DNA

We report the measurement of hole-transfer rate constants (k(ht)) in locked nucleic acid (LNA) and 5-Me-2'-deoxyzebularine (B)-modified DNA. LNA modification, which makes DNA more rigid, caused a decrease of more than 2 orders of magnitude in k(ht), whereas B modification, which increases DNA flexibility, increased k(ht) by more than 20-fold. The present results clearly showed that hole-transfer efficiency in DNA can be increased by increasing DNA flexibility.

HOMO energy gap dependence of hole-transfer kinetics in DNA

DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).

Hole transfer from single quantum dots

Photoinduced hole transfer dynamics from single CdSe/CdS(3ML)/CdZnS(2ML)/ZnS(2ML) core/multishell quantum dots (QDs) to phenothiazine (PTZ) molecules were studied by single QD fluorescence spectroscopy to investigate the static and dynamic heterogeneities of the hole transfer process as well as its effect on the blinking dynamics of QDs. Ensemble-averaged transient absorption and fluorescence decay measurements show that excitons in QDs dissociate by transferring the valence band hole to PTZ with a time constant of 50 ns for the 1:1 PTZ-QD complex, and the subsequent charge recombination process (i.e., electron transfer from the conduction band of the reduced QD to oxidized PTZ to regenerate the complex in the ground state) occurs mainly on the 100 to 1000 ns time scale. Single QD-PTZ complexes show pronounced correlated fluctuations of fluorescence intensity and lifetime with time. In addition to the dynamic fluctuation, there are considerable heterogeneities of average hole transfer rate among different QD-PTZ complexes. The hole transfer process has little effect on the statistics of the off-states, which is often believed to be positively charged QDs with a valence band hole. Instead, it increases the probability of weakly emissive or "gray" states.

Fluorenone synthesis by palladacycle-catalyzed sequential reactions of 2-bromobenzaldehydes with arylboronic acids

A new, anionic four-electron donor-based (type I) palladacycle-catalyzed sequential reaction of 2-bromobenzaldehydes with arylboronic acids based on the addition reaction, cyclization via C-H activation-oxidation sequence is described. Our study provided an efficient access to a variety of substituted fluorenones/indenofluorenediones from readily available arylboronic acids and 2-bromobenzaldehydes.