Synthesis of 5-(2-Pyrenyl)-2′-deoxyuridine as a DNA Modification for Electron-Transfer Studies: The Critical Role of the Position of the Chromophore Attachment

BN-Phenanthrene- and BN-Pyrene-Based Fluorescent Uridine Analogues

Two unprecedented fluorescent nucleosides that feature BN-doped polycyclic aromatic hydrocarbons are presented. One of them, having a BN-modified phenanthrene moiety incorporated, shows blue fluorescence but suffers from poor stability under aqueous conditions. The other nucleoside comprises an internally BN-doped pyrene as the chromophore. It shows green fluorescence in various solvents and is stable under aqueous and alkaline conditions.

Bichromophoric Photosensitizers: How and Where to Attach Pyrene Moieties to Phenanthroline to Generate Copper(I) Complexes

Pyrene is a polycyclic aromatic hydrocarbon and organic dye that can form superior bichromophoric systems when combined with a transition metal-based chromophore. However, little is known about the effect of the type of attachment (i.e., 1- vs 2-pyrenyl) and the individual position of the pyrenyl substituents at the ligand. Therefore, a systematic series of three novel diimine ligands and their respective heteroleptic diimine-diphosphine copper(I) complexes has been designed and extensively studied. Special attention was given to two different substitution strategies: (i) attaching pyrene via its 1-position, which occurs most frequently in the literature, or via its 2-position and (ii) targeting two contrasting substitution patterns at the 1,10-phenanthroline ligand, i.e., the 5,6- and the 4,7-position. In the applied spectroscopic, electrochemical, and theoretical methods (UV/vis, emission, time-resolved luminescence and transient absorption, cyclic voltammetry, density functional theory), it has been shown that the precise choice of the derivatization sites is crucial. Substituting the pyridine rings of phenanthroline in the 4,7-position with the 1-pyrenyl moiety has the strongest impact on the bichromophore. This approach results in the most anodically shifted reduction potential and a drastic increase in the excited state lifetime by more than two orders of magnitude. In addition, it enables the highest singlet oxygen quantum yield of 96% and the most beneficial activity in the photocatalytic oxidation of 1,5-dihydroxy-naphthalene.

Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles

Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.

Para-N-Methylpyridinium Pyrenes: Impact of Positive Charge on ds-DNA/RNA and Protein Recognition, Photo-Induced Bioactivity, and Intracellular Localisation

The 2- and 2,7- substituted para-N-methylpyridinium pyrene cations show high-affinity intercalation into ds-DNAs, whereas their non-methylated analogues interacted with ds-DNA/RNA only in the protonated form (at pH 5), but not at physiological conditions (pH 7). The fluorescence from non-methylated analogues was strongly dependent on the protonation of the pyridines; consequently, they act as fluorescence ratiometric probes for simultaneous detection of both ds-DNA and BSA at pH 5, relying on the ratio between intensities at 420 nm (BSA specific) and 520 nm (DNA specific), whereby exclusively ds-DNA sensing could be switched-off by adjustment to pH 7. Only methylated, permanently charged pyrenes show photoinduced cleavage of circular DNA, attributed to pyrene-mediated irradiation-induced production of singlet oxygen. Consequently, the moderate toxicity of these cations against human cell lines is strongly increased upon irradiation. Detailed studies revealed increased total ROS production in cells treated by the compounds studied, accompanied by cell swelling and augmentation of cellular complexity. The most photo-active 2-para-N-methylpyridinium pyrene showed significant localization at mitochondria, its photo-bioactivity likely due to mitochondrial DNA damage. Other derivatives were mostly non-selectively distributed between various cytoplasmic organelles, thus being less photoactive.

Synthesis and Properties of Perylene-Bridge-Anchor Chromophoric Compounds

The quest to control chromophore/semiconductor properties to enable new technologies in energy and information science requires detailed understanding of charge carrier dynamics at the atomistic level, which can often be attained through the use of model systems. Perylene-bridge-anchor compounds are successful models for studying fundamental charge transfer processes on TiO₂, which remains among the most commonly investigated and technologically important interfaces, mostly because of perylene's advantageous electronic and optical properties. Nonetheless, the ability to fully exploit synthetically the substitution pattern of perylene with linker (= bridge-anchor) units remains little explored. Here we developed 2,5-di-tert-butylperylene (DtBuPe)-bridge-anchor compounds with t-Bu group substituents to prevent π-stacking and one or two linker units in both the peri and ortho positions, by employing a combination of Friedel-Crafts alkylations, bromination, iridium-catalyzed borylation, and palladium-catalyzed cross-coupling reactions. Photophysical characterization and computational analysis by density functional theory (DFT) and time-dependent DFT (TD-DFT) were carried out on four DtBuPe acrylic acid derivatives with a single or a double linker in peri (12b), ortho (15b), peri,peri (18b), and ortho,ortho (21b). The energies of the unoccupied orbitals {LUMO, LUMO + 1, LUMO + 2} are strongly affected by the presence of a π-conjugated linker, resulting in a stabilization of these states and a red shift of their absorption and emission spectra, as well as the loss of vibronic structure in the spectrum of the peri,peri compound, consistent with the strong bonding character of this substitution pattern.

Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins

Two analogues to the fluorescent amyloid probe 2,5-bis(4'-hydroxy-3'-carboxy-styryl)benzene (X-34) were synthesized based on the trans-stilbene pyrene scaffold (Py1SA and Py2SA). The compounds show strikingly different emission spectra when bound to preformed Aβ1-42 fibrils. This remarkable emission difference is retained when bound to amyloid fibrils of four distinct proteins, suggesting a common binding configuration for each molecule. Density functional theory calculations show that Py1SA is twisted, while Py2SA is more planar. Still, an analysis of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) of the two compounds indicates that the degree of electronic coupling between the pyrene and salicylic acid (SA) moieties is larger in Py1SA than in Py2SA. Excited state intramolecular proton transfer (ESIPT) coupled-charge transfer (ICT) was observed for the anionic form in polar solvents. We conclude that ICT properties of trans-stilbene derivatives can be utilized for amyloid probe design with large changes in emission spectra and decay times from analogous chemical structures depending on the detailed physical nature of the binding site.

Preparation and characterization of pyrene modified uridine derivatives as potential electron donors in RNA

Charge transfer across double stranded DNA was observed for the first time about 20 years ago, and ever since it has been the subject of a large number of studies. RNA has been hardly investigated in this regard, which not least is due to the lack of suitably functionalized ribonucleotide building blocks to serve as electron sources upon incorporation into oligoribonucleotides. We have synthesized two uridine derivatives carrying pyrene or dimethylaminopyrene linked to C5 of the nucleobase. The key to successful synthesis was the adaptation of Suzuki-Miyaura conditions to the coupling of the pyrene moiety with the ribonucleoside. Final decoration of the pyrenylated nucleosides with standard 5'-O- and 2'-O-protecting groups and subsequent 3'-O-phosphitylation delivered the building blocks for incorporation into RNA. Spectroscopic analysis of the two pyrenylated uridines and of the accordingly modified oligonucleotides showed that in particular the dimethyaminopyrene functionalized nucleoside is a promising candidate as an electron source for RNA charge transport studies.

Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue

Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M⁻¹cm⁻¹ in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.

Dual fluorescence of tetraphenylethylene-substituted pyrenes with aggregation-induced emission characteristics for white-light emission

This article presents a new strategy to achieve white-light emission from single tetraphenylethylene-substituted pyrenes (TPE-Pys) with aggregation-induced emission (AIE) characteristics. TPE-Pys were synthesized by a Pd-catalyzed coupling reaction of a boronic acid or pinacol ester of pyrene and tetraphenylethylene (TPE) derivatives and showed multicolor emission by introducing different substituents on the phenyl rings of TPE. TPE-Pys with a TPE unit at the 1-position and asymmetric TPE units at 2,7-positions show dual fluorescence in THF/water mixtures to realize white-light emission with CIE coordinates of (x = 0.30 and y = 0.41) and (x = 0.21 and y = 0.16), respectively. The structure-property relationship of TPE-Pys were investigated to elucidate the origin of the white emission. The results showed that due to the weak electronic interaction of pyrene and its chromophoric units at the 2,7-positions and the constraint of the rotation of the TPE unit at the 1-position of pyrene, each component can exhibit its own emission color. The combination of appropriate colors gives rise to white-light emission. Such a principle of molecular design may open a new avenue for preparing advanced multicolor and multifunctional optical materials for organic electronics.

Fluorogenic PNA probes

Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.

trans-Stilbenoids with Extended Fluorescence Lifetimes for the Characterization of Amyloid Fibrils

It was previously reported that two naphthyl-based trans-stilbene probes, (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol (1) and (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol (3), can bind to both native transthyretin (TTR) and misfolded protofibrillar TTR at physiological concentrations, displaying distinct emission maxima bound to the different conformational states (>100 nm difference). To further explore this amyloid probe scaffold to obtain extended fluorescence lifetimes, two new analogues with expanded aromatic ring systems (anthracene and pyrene), (E)-4-(2-(anthracen-2-yl)vinyl)benzene-1,2-diol (4) and (E)-4-(2-(pyren-2-yl)vinyl)benzene-1,2-diol (5), were synthesized employing the palladium-catalyzed Mizoroki-Heck reaction. (E)-4-Styrylbenzene-1,2-diol (2), 3, 4, and 5 were investigated with respect to their photophysical properties in methanol and when bound to insulin, lysozyme, and Aβ1-42 fibrils, including time-resolved fluorescence measurements. In conclusion, 4 and 5 can bind to both native and fibrillar TTR, becoming highly fluorescent. Compounds 2-5 bind specifically to insulin, lysozyme, and Aβ1-42 fibrils with an apparent fluorescence intensity increase and moderate binding affinities. The average fluorescence lifetimes of the probes bound to Aβ1-42 fibrils are 1.3 ns (2), 1.5 ns (3), 5.7 ns (4), and 29.8 ns (5). In summary, the variable aromatic moieties of the para-positioned trans-stilbenoid vinyl-benzene-1,2-diol with benzene, naphthalene, anthracene, and pyrene showed that the extended conjugated systems retained the amyloid targeting properties of the probes. Furthermore, both the anthracene and pyrene moieties extensively enhanced the fluorescence intensity and prolonged lifetimes. These attractive probe properties should improve amyloid detection and characterization by fluorescence-based techniques.

Pyrene Molecular Orbital Shuffle-Controlling Excited State and Redox Properties by Changing the Nature of the Frontier Orbitals

We show that by judicious choice of substituents at the 2- and 7-positions of pyrene, the frontier orbital order of pyrene can be modified, giving enhanced control over the nature and properties of the photoexcited states and the redox potentials. Specifically, we introduced a julolidine-like moiety and Bmes₂ (mes=2,4,6-Me₃ C₆ H₂ ) as very strong donor (D) and acceptor (A), respectively, giving 2,7-D-π-D- and unsymmetric 2,7-D-π-A-pyrene derivatives, in which the donor destabilizes the HOMO-1 and the acceptor stabilizes the LUMO+1 of the pyrene core. Consequently, for 2,7-substituted pyrene derivatives, unusual properties are obtained. For example, very large bathochromic shifts were observed for all of our compounds, and unprecedented green light emission occurs for the D/D system. In addition, very high radiative rate constants in solution and in the solid state were recorded for the D-π-D- and D-π-A-substituted compounds. All compounds show reversible one-electron oxidations, and Jul₂ Pyr exhibits a second oxidation, with the largest potential splitting (ΔE=440 mV) thus far reported for 2,7-substituted pyrenes. Spectroelectrochemical measurements confirm an unexpectedly strong coupling between the 2,7-substituents in our pyrene derivatives.

A Regioselective Synthesis of 6-Alkyl- and 6-Aryluracils by Cs2CO3- or K3PO4-Promoted Dimerization of 3-Alkyl- and 3-Aryl-2-Propynamides

A regioselective synthesis of 6-alkyl- and 6-aryluracils was developed by the dimerization of 3-alkyl- and 3-aryl-2-propynamides promoted by either Cs₂CO₃ or K₃PO₄. A range of 3-aryl-2-propynamides, with both electron-deficient and electron-rich 3-aryl substituents, were successfully reacted in high yields. Cs⁺ acts as a soft Lewis acid to polarize the carbon-carbon triple bond, and solid K₃PO₄ interacts with carbonyl oxygen, promoting intermolecular nucleophilic attack by the only weakly nucleophilic amide nitrogen. Experiments were conducted to support the proposed mechanism.

Three-State Fluorescence of a 2-Functionalized Pyrene-Based RNA Label

The pyrene-based RNA-fluorescence label 2-(2-pyrenylethynyl) adenosine (2PyA) shows triexponential fluorescence, which depends strongly on the excitation wavelength. Most strikingly, a structured, long-lived fluorescence is observed in solution at room temperature after excitation into the S₂ state, which is shifted hypsochromically by 30 nm compared to excitation into the S₁ state. This very unusual behavior is investigated in detail with steady-state and time-resolved emission spectroscopy, ultrafast transient absorption spectroscopy, and quantum chemical calculations with both wave functions (CC2-level) and density-functional theory (DFT). 2PyA is found to emit simultaneously from two different intramolecular charge transfer states (mesomeric and twisted, MICT and TICT) which are populated most efficiently via the S₁ state and a pyrene-like locally excited (LE) state. Rotational momentum derived from excess excitation energy is required to populate twisted LE configurations. Therefore, the LE state is most efficiently accessible via excitation to the S₂. The stabilization of the different substates is related to two distinct reaction coordinates: the adenine-pyrene distance and the adenine-pyrene tilt angle, respectively.

The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers

This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential. These features in the ultrafast dynamics are indicative of the rotational energy barriers in the first excited state.

Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides

Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs

The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture.

A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies

The design and the synthesis of a PNA oligomer containing a pyrenyl residue in the backbone were performed. PNA sequence was chosen complementary to a "G rich" target sequence involved in G-quadruplex formation. The pyrenyl unit replaced a nucleobase in the middle of the PNA through covalent linkage to the backbone by a carboxymethyl unit. A systematic study on the binding properties of this probe towards DNA and RNA complementary strands was carried out by UV and fluorescence spectroscopy. UV melting curves indicated that the PNA probe binds more tightly to RNA rather than to DNA. Thermodynamic data obtained by Van't Hoff fitting of the melting curves indicated that, in the case of RNA, a more favorable interaction occurs between the pyrenyl unit and the RNA nucleobases, leading to a very favorable enthalpic contribution.The fluorescence analysis showed specific quenching of the pyrene emission associated to the formation of the full-match PNA-DNA or PNA-RNA duplexes. Again, this behavior was more evident in the case of RNA, consistently with the stronger interaction of the pyrenyl unit with the complementary strand. In order to study the sequence specificity of the pyrenyl-PNA probe (pyr-PNA), recognition experiments on mismatched DNA and RNA sequences were also performed.

Photo-physical properties of 2-(1-ethynylpyrene)-adenosine: influence of hydrogen bonding on excited state properties

The photo-physical properties of 2-(1-ethynylpyrene)-adenosine (PyA), a fluorescent probe for RNA dynamics, were examined by solvation studies. The excited-state dynamics display the influence of the vicinity on the spectral features. Combining improved transient absorption and streak camera measurements along with a new analysis method provide a detailed molecular picture of the photophysics. After intramolecular vibrational energy redistribution (IVR), two distinct states are observed. Solvent class (protic/aprotic) and permittivity strongly affect the properties of these states and their population ratio. As a result their emission spectrum is altered, while the fluorescence quantum yield and the overall lifetime remain nearly unchanged. Consequently, the hitherto existing model of the photophysics is herein refined and extended. The findings can serve as basis for improving the information content of measurements with PyA as a label in RNA.

Formation and reactivity of an (alkene)peroxoiridium(III) intermediate supported by an amidinato ligand

An Ir(I) complex of an acetamidinato ligand was synthesized by reaction of N,N'-diphenylacetamidine, PhN[double bond, length as m-dash]C(Me)NHPh, with either MeLi and [{Ir(cod)}2(μ-Cl)2] or [{Ir(cod)}2(μ-OMe)2] and was characterized by X-ray crystallography as a mononuclear complex, [Ir{PhNC(Me)NPh}(cod)] (1; where cod = 1,5-cyclooctadiene). Reaction of 1 with CO afforded a dinuclear carbonyl complex, [{Ir(CO)2}2{μ-PhNC(Me)NPh-κN:κN'}2] (2), as indicated by EI mass spectrometry and solution- and solid-state IR spectroscopy [νCO (n-pentane) = 2067, 2034 and 1992 cm(-1)]. Activation of O2 by 1 in solution at 20 °C was irreversible and produced an (alkene)peroxoiridium(iii) intermediate, [Ir{PhNC(Me)NPh}(cod)(O2)] (3), which was characterized by one- and two-dimensional NMR techniques and IR spectroscopy (for 3, νOO = 860 cm(-1); for 3-(18)O2, νOO = 807 cm(-1)). Complex 3 oxidized PPh3 to OPPh3, and its decay in the absence of added substrates followed by reaction with cod yielded 4-cycloocten-1-one and a minor amount of 1. In comparison with the results for the previously reported guanidinato complex [Ir{PhNC(NMe2)NPh}(cod)(O2)] (4), the formation of 3 and its reaction with PPh3 are significantly faster, indicating considerable ligand effects in these reactions.

Palladium-catalyzed Suzuki reaction in aqueous solvents applied to unprotected nucleosides and nucleotides

Nucleoside analogues have attracted much attention due to their potential biological activities.

Fluorescence quenching over short range in a donor-DNA-acceptor system

A new donor-DNA-acceptor system has been synthesized containing Nile red-modified 2'-deoxyuridine as charge donor and 6-N,N-dimethylaminopyrene-modified 2'-deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time-resolved femtosecond pump-probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73% for CG and the same for AT) is higher than that for one base pair (68% for CG and 37% for AT), while at a separation of three base pairs less than 10% quenching is observed. A comparison with the results of time-resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (∼10(12) s(-1)) that depends strongly and in a non-linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (∼10(11) s(-1)) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time-dependent density functional theory (TDDFT) calculations a combination of single-step superexchange and multistep hopping mechanisms can be proposed for this short-range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short-range systems.

Efficient synthesis of unprotected C-5-aryl/heteroaryl-2'-deoxyuridine via a Suzuki-Miyaura reaction in aqueous media

Following our previous results on an environmentally benign one-pot Sonogashira-cyclization protocol to obtain substituted furopyrimidine nucleosides under aqueous conditions, we investigate herein the Suzuki-Miyaura cross-coupling reactions of aryl and heteroaryl derivatives at the C5 position of unprotected 2'-deoxyuridine in the same media with a common catalyst system avoiding exotic ligands, since palladium acetate and triphenylphosphine afforded the expected products in moderate to good yields.

Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties

Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.

Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology

Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).

5-(Pyren-1-yl)uracil as a base-discriminating fluorescent nucleobase in pyrrolidinyl peptide nucleic acids

A pyrene-labeled uridine (U(Py)) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U(Py) base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T(m)) experiments. The fluorescence of the U(Py)-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7-41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U(Py) and dA, making the U(Py)-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.