Synthesis, spectral luminescent and scintillation properties of organic luminophores based on carbonyl-containing derivatives of 2-(fur-2-yl)-5-phenyloxazole

A series of derivatives of 2-(fur-2-yl)-5-phenyloxazole with various substituents in the 5-position of the furan ring and furan-containing analogs of 1,4-bis(5-phenyloxazol-2-yl)benzene are synthesized. Their spectral-luminescent properties are investigated.Institute of Single Crystals, National Academy of Sciences of Ukraine, Kharkov 310001Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 317–323, March, 1999.     

5-Alkynyl-2′-deoxyuridines, containing bulky aryl groups: evaluation of structure-anti-HSV-1 activity relationship

Four 5-alkynyl-2′-deoxyuridines containing different bulky substituents and flexible linkers between the triple bond and the aromatic residue have been prepared and tested against HSV-1 in Vero cells. Two nucleosides containing carbonyl groups, 5-(4-benzoylphenoxypropyn-1-yl)-2′-deoxyuridine (19a) and 5-(estron-3-yloxypropyn-1-yl)-2′-deoxyuridine (19c), showed low cytotoxicity and moderate antiviral activity. The flexible linker appears not to be favorable for antiviral properties of 5-alkynyl-2′deoxyuridines: 5-[(perylen-3-yl)methoxypropyn-1-yl]-2′-deoxyuridine (19d) showed considerable cytotoxicity and no antiviral activity in contrast to the active and nontoxic 5-(perylen-3-ylethynyl)-2′-deoxyuridine (9), a nucleoside with a rigid triple-bond-connection of the aromatic system to the nucleobase.     

Hemicyanine-linked pyrimidine mimics as solvatochromic fluorophores with visible excitation wavelengths

The design of solvatochromic fluorescent nucleosides with visible excitation wavelengths is a goal towards the generation of modified oligonucleotides for fluorimetry-based molecular imaging. Herein, two hemicyanine-linked C5-2′-deoxyuridine nucleosides (PyI-dU and APPy-dU) have been synthesized by first generating hemicyanine-alkyne precursors that were attached via the alkyne moiety to 5-iodo-2′-deoxyuridine (5-I-dU) by Sonogashira coupling. The photophysical properties of the hemicyanine-linked dU probes have been characterized and compared to the corresponding properties of the hemicyanine-alkyne precursors. The nucleoside probe PyI-dU exhibits optical features that mimic the properties of the free hemicyanine-alkyne precursor, while the APPy-dU probe displays more favorable optical properties (longer excitation wavelength, brighter emission in water) than its precursor that is ascribed to π-stacking interactions between the hemicyanine dye with the dU nucleobase. Overall, probe APPy-dU is a superior solvatochromic fluorophore than PyI-dU suggesting its greater utility for fluorescent imaging applications.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

Helical self-assembled chromophore clusters based on DNA-like architecture

DNA duplexes were functionalized covalently by clusters of five adjacent chromophores consisting of 5-(pyren-1-yl)-2′-deoxyuridine (Py-U) and 5-(10-methyl-phenothiazin-3-yl)-2′-deoxyuridine (Pz-U). The chromophores form a regular helical π-array along the major groove of duplex DNA when the 5-fold chromophore-modified oligonucleotides are hybridized with an unmodified counter strand. As a result, these chromophores interact significantly and their fluorescence and absorption properties can be modulated by the sequence within the π-array. The 5-fold Py-U stack shows a strongly enhanced emission. The presence of intervening Pz-U groups quenches the fluorescence of the Py-U chromophores. Such modulation of the optical properties within a chromophore stack is potentially useful for optical nanodevices and as nucleic acid sensors for molecular diagnostics. The duplex architecture of DNA is suitable to provide the supramolecular structural scaffold for a directed arrangement of chromophores.     

Ru(II) and Os(II) nucleosides and oligonucleotides: synthesis and properties

A general and versatile method for the site-specific incorporation of polypyridine Ru(II) and Os(II) complexes into DNA oligonucleotides using solid-phase phosphoramidite chemistry is reported. Novel nucleosides containing a [(bpy)(2)M(3-ethynyl-1,10-phenanthroline)](2+) (M = Ru, Os) metal center covalently attached to the 5-position in 2'-deoxyuridine are synthesized, and their electrochemical as well as photophysical properties are studied. The Ru(II) nucleoside exhibits a rather long-lived excited state in phosphate buffer pH 7.0 (tau = 1.08 micros) associated with a relatively high emission quantum efficiency (phi = 0.051). The solvent dependence of the absorption and emission spectra is consistent with an emissive MLCT state where charge localization takes place on the extended heterocycle-linked phenanthroline. In contrast, the Os(II)-containing nucleoside is quite nonemissive in aqueous environment (tau = 0.027 micros, phi = 1 x 10(-4)). The metal-containing nucleosides are converted into their phosphoramidites and are utilized for the high-yield preparation of modified oligonucleotides. The novel oligonucleotides, characterized by absorption and emission spectroscopy, enzymatic digestion, and electrophoresis, form stable duplexes. Circular dichroism spectra confirm that the global conformation of the double helix is not altered by the presence of these polypyridyl complexes in the major groove. Metal-containing phosphoramidites with predetermined absolute configuration at the octahedral coordination center are synthesized and utilized for the synthesis of diasteromerically pure metal-containing DNA oligonucleotides. Emission spectroscopy suggests a higher protection of the Delta metal center from the bulk solvent and better accommodation within the major groove.     

Synthesis of highly soluble fluorescent π-extended 2-(2-thienyl)benzothiazole derivatives via oxidative cyclization of 2-thienylthioanilide as the key step

In this Letter, we synthesize highly soluble push–pull type fluorescent 2-(2-thienyl)benzothiazole dyes and evaluate their photophysical properties. The key step is the synthesis of 2-(5′-bromothien-2′-yl)-6-alkoxybenzothiazole (2) via oxidative cyclization of 2-thienylthioanilide using PhI(OAc)₂ as the oxidant. The target dyes could be easily synthesized by the Suzuki–Miyaura cross-coupling reaction of 2 and an appropriate π-donor. The photophysical properties of the 2-thienylbenzothiazole chromophore were controlled by the π-donor moiety. It was found that 2 exhibited large Stokes shifts (5345 cm⁻¹) and a high quantum efficiency for fluorescence (Φ_F = 0.94 in CH₂Cl₂). Therefore, it can be expected to be a useful photofunctional material in liquid crystal laser dyes and nonlinear optical materials.     

Synthesis of unnatural 3′-phospha-2′-deoxyfuranose nucleoside analogues

This Letter describes the synthesis of racemic analogues of unnatural 2′-deoxy nucleoside with a phosphorus atom replacing the carbon atom in the 3′-position. A seven-step sequence was developed in racemic series to afford unnatural 3′-phospha-2′-deoxyfuranose nucleosides. The phospha nucleoside analogues were tested against HCV, but did not show any antiviral activity at a 10 μM maximum concentration used for the inhibition assays of analogues 2-T, 2-C and 4-Tα.     

3′-Amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides for the synthesis of fully amide-linked RNA mimics

A convenient protocol is developed for the synthesis of 3′-[N-(fluorenylmethoxycarbonyl)-amino]-5′-carboxymethyl derivatives of all four natural ribonucleosides from cheap chiral pool compound glucose. Synthesis of fully amide-linked RNA analogues of small oligonucleotides containing, for the first time, all four nucleoside amino acids using standard solid phase Fmoc-chemistry is described.     

Azetidines-Containing Fluorescent Purine Analogs: Synthesis and Photophysical Properties

Analogues of N,N-dimethyladenine exploiting both thieno-and isothiazolo-pyrimidine cores were modified with 3-subsituted azetidines to yield visibly emissive and responsive fluorophores. The emission quantum yields, among the highest seen for purine analogues (0.64 and 0.77 in water and dioxane respectively), correlated with the Hammett inductive constants of the substituents on the azetidine ring. Ribosylation of the difluoroazetidino-modified nucleobase yielded an emissive nucleoside that displayed a substantially lower emission quantum yield in water, compared to the precursor nucleobase. Importantly, high emission quantum yield was restored in deuterium oxide, which highlights the potential impact of the sugar moiety on the photophysical features of fluorescent nucleosides, a functionality usually considered non-chromophoric and photophysically benign.     

Solution-processed red iridium complexes based on carbazole-phenylquinoline main ligand: Synthesis, properties and their applications in phosphorescent organic light-emitting diodes

New carbazole-phenylquinoline (CVz-PhQ) based iridium complexes were designed and synthesized for their application in red phosphorescence organic light-emitting diodes (PhOLEDs) and their photophysical, electrochemical and electroluminescence (EL) properties were investigated. The PhOLEDs were fabricated using bis[9-(2-(2-methoxyethoxy)ethyl)-3-(4-phenylquinolin-2-yl)-9H-carbazolato-N,C2′]iridium 2-pyrazinecarboxylic acid (EO-CVz-PhQ)₂Ir(prz) and bis[9-(2-(2-methoxyethoxy)ethyl)-3-(4-phenylquinolin-2-yl)-9H-carbazolato-N,C2′]iridium 5-methyl-2-pyrazinecarboxylic acid (EO-CVz-PhQ)₂Ir(mprz) as the emitter and PVK, co-doped with OXD-7 as the electron transport material and TPD as the hole transport material, as the polymer host. The red emissive PhOLEDs, based on the ITO/poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS)/4,4′,4″-tris(carbazole-9-yl)triphenylamine (TCTA)/poly(N-vinylcarbazole) (PVK):N,N′-diphenyl-N,N′-(bis(3-methylphenyl)-[1,1-biphenyl]-4,4′-diamine (TPD):1,3-bis[5-(4-tert-butylphenyl)-1,3,4-oxadiazole-2-yl]benzene (OXD-7):Ir complex/cathode configuration, exhibited a maximum external quantum efficiency of 3.68% and a maximum luminance efficiency of 6.69 cd/A. Furthermore, by introducing a TCTA interlayer, the PhOLEDs showed only a slight efficiency roll off of 5.4% from a low current density (1.81 mA/cm²) to a high current density (44.59 mA/cm²).     

Synthesis, photophysical characterization, and enzymatic incorporation of a microenvironment-sensitive fluorescent uridine analog

The synthesis of a microenvironment-sensitive base-modified fluorescent ribonucleoside analog based on a 5-(benzo[b]thiophen-2-yl)pyrimidine core, enzymatic incorporation of its corresponding triphosphate into RNA oligonucleotides, and photophysical characterization of fluorescently modified oligoribonucleotides are described.     

Novel oligonucleotide analogues containing a morpholinoamidine unit

Morpholinoamidines were devised as new cationic units in oligonucleotides, by combining morpholino-nucleosides (to simplify the nomenclature, we will use the term morpholino-nucleosides to refer to nucleoside analogues in which the ribose ring was transformed into a morpholine) with internucleoside guanidines. Here, methodology was developed to synthesize oligonucleotides containing morpholinoamidines formed by morpholino-uridine and 5′-amino-5′-deoxythymidine. Morpholinoamidine was produced by solid-phase reaction of Alloc-morpholinocarbothioamide with 5′-aminonucleoside resin and Mukaiyama's reagent activation. Two 14-mer oligonucleotides containing a single morpholinoamidine were synthesized and their affinity properties were investigated by forming DNA double and triple helices. Duplexes were slightly stabilized by a 3′ unit, but were less stable if internally positioned. Notably, triplexes were significantly stabilized at pH 7.0.     

Synthesis of unnatural 2- and 3-deoxyfuranose analogues

This Letter describes the synthesis of two racemic analogues of unnatural 3′-deoxy and 2′-deoxy sugars, where a phosphorus atom replaces the carbon atom in the 2′- or 3′-position. Two methods of four- and 5-steps were developed affording these new unnatural sugar analogues.     

Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing

The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tC^O) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tC^O compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.     

Synthesis of a technetium-99m-labeled thymidine analog: a potential HSV1-TK substrate for non-invasive reporter gene expression imaging

{2-[5-(2′-Fluoro-2′-deoxyuridin-5-yl)pent-4(E)-enyl] [2-(2-mercaptoethyl)aminoethyl]aminoethanethiolato(3)-N,N′,S,S′}oxo-[^99mTc]technetium(V), a potential viral thymidine kinase substrate, was synthesized by coupling 2′-fluoro-2′-deoxyuridine analog with a N2S2 radiometal chelator, followed by [Tc-99m]technetium conjugation. The chemical structure of the radioactive probe was characterized by ¹H NMR and high resolution MS using Re-188 conjugated mimics. The radiochemical purity and yield were identified as 98% and 42%, respectively.     

Synthesis and hybridization properties of 2′-O-(tetrazol-5-yl)ethyl-modified oligonucleotides

2′-O-(1H-Tetrazol-5-yl)ethyladenosine was synthesized using 2′-O-cyanoethyladenosine derivative as a key intermediate. The 2′-O-(1H-tetrazol-5-yl)ethyl modifications exhibited intriguing properties such as the change in the structure of the tetrazole residue between a protonated and a deprotonated form. The T_m experiments of various oligodeoxynucleotides having a 2′-O-(1H-tetrazol-5-yl)ethyl-modified adenosine showed reduced hybridization affinity in comparison to the unmodified oligonucleotides toward their complementary oligodeoxynucleotides. The mechanism of the reduced hybridization affinity was discussed on the basis of the structure and the physicochemical properties of the tetrazole moiety.     

Synthesis of 5,5′-diarylated 2,2′-bithiophenes via palladium-catalyzed arylation reactions

2,2′-Bithiophene and 3,3′-dicyano-2,2′-bithiophenes are diarylated directly with aryl bromides at the 5- and 5′-positions accompanied by C-H bond cleavage in the presence of Pd(OAc)₂ and a bulky phosphine ligand using Cs₂CO₃ as base. In the reaction using (2,2′-bithiophen-5-yl)diphenylmethanol as the substrate, monoarylation at the 5-position via C-C bond cleavage occurs selectively to give 5-aryl-2,2′-bithiophenes and the subsequent arylation with a different aryl bromide affords the corresponding unsymmetrically 5,5′-diarylated products.     

Synthesis of 1-(2′-O-methyl-β-d-ribofuranosyl)-5-nitroindole and its phosphoramidite derivative

The synthesis of 1-(2′-O-methyl-β-d-ribofuranosyl)-5-nitroindole, a new nucleoside containing the universal base 5-nitroindole, and its phosphoramidite derivative for incorporation into oligonucleotides is described.