Synthesis, Photophysical Behavior, and Electronic Structure of Push−Pull Purines

Direct Regioselective C-H Cyanation of Purines

A direct regioselective C-H cyanation of purines was developed through a sequential triflic anhydride activation, nucleophilic cyanation with TMSCN, followed by a process of base-mediated elimination of triflous acid (CF₃SO₂H). In most cases, the direct C-H cyanation occurred on the electron-rich imidazole motif of purines, affording 8-cyanated purine derivatives in moderate to excellent yields. Various functional groups, including allyl, alkynyl, ketone, ester, nitro et al. were tolerated and acted as a C8 directing group. The electron-donating 6-diethylamino, as C2-directing group substituent, can switch the regioselectivity of purine from 8- to 2-position, enabling the synthesis of 8- and 2-cyano 6-dialkylaminopurines from corresponding 6-chloropurine in different reaction order. Further functional manipulations of the cyano group allow the conversions of 8-cyanopurines to corresponding purine amides, imidates, imidothioates, imidamides, oxazolines, and isothiazoles.

Rational Design of Quinoxalinone-Based Red-Emitting Probes for High-Affinity and Long-Term Visualizing Amyloid-β In Vivo

Alzheimer's disease (AD) is a progressive neurodegenerative disease with insidious onset, and the deposition of amyloid-β (Aβ) is believed to be one of the main cause. Fluorescence imaging is a promising technique for this task, but the Aβ gold standard probe ThT developed based on this still has shortcomings. The development of a new fluorescent probe to detect Aβ plaques is thought to be essential. Herein, a series of red to near-infrared emitting fluorescent probes QNO-ADs with newly quinoxalinone skeleton are designed to detect Aβ plaques. They all demonstrate excellent optical properties and high binding affinity (∼K_d = 20 nM) to Aβ aggregates. As the most outstanding candidate, QNO-AD-3 shows significant signal-to-noise (S/N) ratio at the level of in vitro binding studies, and the brilliant fluorescence staining results in favor of grasping the approximate distribution of Aβ plaques in the brain slice. In vivo Aβ plaques imaging suggests that QNO-AD-3 can cross the BBB and have a long retention time in the brain with low biological toxicity. In addition, the results of docking theoretical calculation also provide some references for the design of Aβ probe. Overall, given the high affinity of QNO-AD-3 and the ability to monitor Aβ plaques for a long time that is not common now, we believe QNO-AD-3 will be an effective tool for an Aβ-related matrix and AD disease research in the future.

Mechanofluorochromism of (D-π-)2A-type azine-based fluorescent dyes

Bathochromic or hypsochromic shift-type mechanofluorochromism (b-MFC or h-MFC) was found for (D–π–)₂A-type azine-based fluorescent dyes OUY-2, OUK-2, and OUJ-2 possessing intramolecular charge-transfer (ICT) characteristics from two (diphenylamino)carbazole–thiophene units as D (electron-donating group)–π (π-conjugated bridge) moieties to a pyridine, pyrazine, or triazine ring as A (electron-withdrawing group): grinding of the recrystallized dyes induced red or blue shifts of the fluorescent colors, that is, bathochromic or hypsochromic shifts of the fluorescence maximum wavelengths (λ^fl-solid_max). The degrees of MFC evaluated by the absolute value of differences (Δλ^fl-solid_max) in λ^fl-solid_max before and after grinding of the recrystallized dyes increased in the order of OUY-2 (+7 nm) < OUK-2 (−17 nm) < OUJ-2 (+45 nm), so that OUJ-2 exhibits obvious b-MFC, but OUK-2 exhibits h-MFC. X-ray powder diffraction (XRD) and differential scanning calorimetry (DSC) demonstrated that the recrystallized dyes were in the crystalline state but the ground dyes were in the amorphous state. When the ground solids were heated above their crystallization temperatures (T_c), the colors and fluorescent colors recovered to the original ones before grinding or converted to other ones, that is, heating the ground solids in the amorphous state induced the recrystallization to recover the original microcrystals or to form other microcrystals due to polymorph transformation. However, (D–π–)₂Ph-type fluorescent dye OTK-2 having a phenyl group as a substitute for the azine rings exhibited non-obvious MFC. Molecular orbital (MO) calculations indicated that the values of the dipole moments (μ_g) in the ground state were 4.0 debye, 1.4 debye, 3.2 debye, and 2.9 debye for OTK-2, OUY-2, OUK-2, and OUJ-2, respectively. Consequently, on the basis of experimental results and MO calculations, we have demonstrated that the MFC of the (D–π–)₂A-type azine-based fluorescent dyes is attributed to reversible switching between the crystalline state of the recrystallized dyes and the amorphous state of the ground dyes with changes in the intermolecular dipole–dipole and π–π interactions before and after grinding. Moreover, this work reveals that (D–π–)₂A fluorescent dyes possessing dipole moments of ca. 3 debye as well as moderate or intense ICT characteristics make it possible to activate the MFC.

Bathochromic or hypsochromic shift-type mechanofluorochromism (b-MFC of h-MFC) was found for (D–π–)₂A-type azine-based fluorescent dyes: grinding of the recrystallized dyes induced bathochromic or hypsochromic shifts of the fluorescence bands.

Photophysical and Electrical Properties of Highly Luminescent 2/6-Triazolyl-Substituted Push-Pull Purines

New push-pull N(9)-alkylated 6-piperidino-2-triazolylpurine and 2-piperidino-6-triazolylpurine derivatives are synthesized, and their optical and optoelectronic properties are comprehensively characterized with experimental and computational methods. The compounds possess intense violet or blue fluorescence with fluorescence quantum yields of up to 91% in solution and 40% in host-free films. Depending on their structural composition, the compounds have ionization energy in the range of 5.25-6.04 eV, electron affinity of 2.18-3.15 eV, and triplet energy of 2.52-2.95 eV. Due to the presence of hole-transporting purine and electron-transporting triazole fragments, compounds exhibit bipolar charge-transportation ability. Despite the favorable emissive properties of the studied push-pull purines, their electroluminescence in thin films is quenched owing to large current densities that are present even at a moderate driving voltage. This marks application directions related to a predominantly charge-transportation functionality as the most suitable for this compound class.

Transition-metal free cyano 1,3 migration of unsaturated cyanohydrins

A novel approach of transition-metal-free cyano 1,3-migration of β,γ- and α,β-unsaturated cyanohydrins is reported.

Proof of principle of a purine D-A-D' ligand based ratiometric chemical sensor harnessing complexation induced intermolecular PET

A comprehensive photophysical study of a series of purines, doubly decorated at C2 and C6 positions with identical fragments ranging from electron acceptor to donor groups of different strengths, is presented. The asymmetry of substitutions creates a unique molecular D-A-D' structure possessing two independent electronic charge transfer (CT) systems attributed to each fragment and exhibiting dual-band fluorescence. Moreover, the inherent property of coordination of metal ions by purines was enriched due to a presence of nearby triazoles used as spacers for donor or acceptor fragments. New molecules present a bidentate coordination mode, which makes the assembly of several ligands with one metal cation possible. This property was exploited to create a new concept of a ratiometric chemical fluorescence sensor involving the photoinduced electron transfer between branches of different ligands as a mechanism of fluorescence modulation.

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D-π-)2A fluorescent dyes

The donor-acceptor-π-conjugated (D-π-)₂A fluorescent dyes OUY-2, OUK-2 and OUJ-2 with two (diphenylamino)carbazole thiophene units as D (electron-donating group)-π (π-conjugated bridge) moiety and a pyridine, pyrazine or triazine ring as electron-withdrawing group (electron-accepting group, A) have been designed and synthesized. The photophysical and electrochemical properties of the three dyes were investigated by photoabsorption and fluorescence spectroscopy, Lippert-Mataga plots, cyclic voltammetry and density functional theory calculations. The photoabsorption maximum (λ_max,abs) and the fluorescence maximum (λ_max,fl) for the intramolecular charge-transfer characteristic band of the (D-π-)₂A fluorescent dyes show bathochromic shifts in the order of OUY-2 < OUK-2 < OUJ-2. Moreover, the photoabsorption bands of the (D-π-)₂A fluorescent dyes are nearly independent of solvent polarity, while the fluorescence bands showed bathochromic shifts with increasing solvent polarity (i.e., positive fluorescence solvatochromism). The Lippert-Mataga plots for OUY-2, OUK-2 and OUJ-2 indicate that the Δμ (= μ_e - μ_g) value, which is the difference in the dipole moment of the dye between the excited (μ_e) and the ground (μ_g) states, increases in the order of OUY-2 < OUK-2 < OUJ-2. Therefore, the fact explains our findings that OUJ-2 shows large bathochromic shifts of the fluorescence maxima in polar solvents, as well as the Stokes shift values of OUJ-2 in polar solvents are much larger than those in nonpolar solvents. The cyclic voltammetry of OUY-2, OUK-2 and OUJ-2 demonstrated that there is little difference in the HOMO energy level among the three dyes, but the LUMO energy levels decrease in the order of OUY-2 > OUK-2 > OUJ-2. Consequently, this work reveals that for the (D-π-)₂A fluorescent dyes OUY-2, OUK-2 and OUJ-2 the bathochromic shifts of λ_max,abs and λ_max,fl and the lowering of the LUMO energy level are dependent on the electron-withdrawing ability of the azine ring, which increases in the order of OUY-2 < OUK-2 < OUJ-2.

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

The synthesis of novel fluorescent N(9)-alkylated 2-amino-6-triazolylpurine and 7-deazapurine derivatives is described. A new C(2)-regioselectivity in the nucleophilic aromatic substitution reactions of 9-alkylated-2,6-diazidopurines and 7-deazapurines with secondary amines has been disclosed. The obtained intermediates, 9-alkylated-2-amino-6-azido-(7-deaza)purines, were transformed into the title compounds by CuAAC reaction. The designed compounds belong to the push-pull systems and possess promising fluorescence properties with quantum yields in the range from 28% to 60% in acetonitrile solution. Due to electron-withdrawing properties of purine and 7-deazapurine heterocycles, which were additionally extended by triazole moieties, the compounds with electron-donating groups showed intramolecular charge transfer character (ICT/TICT) of the excited states which was proved by solvatochromic dynamics and supported by DFT calculations. In the 7-deazapurine series this led to increased fluorescence quantum yield (74%) in THF solution. The compounds exhibit low cytotoxicity and as such are useful for the cell labelling studies in the future.

Colorimetric and ratiometric fluorescence sensing of water based on 9-methyl pyrido[3,4-b]indole-boron trifluoride complex

In this work, 9-methyl pyrido[3,4-b]indole-boron trifluoride complex, 9-MP-BF3, was designed and developed as a colorimetric and ratiometric fluorescent sensor for the detection of water in the low- and high-water-content regions in solvents. In the low-water-content region, a new photoabsorption band at around 360 nm and a fluorescence band at around 370 nm gradually appeared due to the dissociation of 9-MP-BF3 into 9-methyl pyrido[3,4-b]indole (9-MP) by water molecules with a simultaneous decrease in the photoabsorption band at around 390 nm and the fluorescence band at around 460 nm originating from 9-MP-BF3. In the moderate-water-content region, the photoabsorption band at around 360 nm and the fluorescence band at around 370 nm gradually shifted to a longer wavelength region with an increase in the fluorescence intensity, which could be ascribed to the formation of a hydrogen-bonded complex (9-MP-H2O) with water molecules. Furthermore, in the high-water-content region, two photoabsorption bands at around 305 nm and 390 nm and one fluorescence band at around 460 nm gradually reappeared with simultaneous decrease in the photoabsorption band at around 290 nm and the fluorescence band at around 370 nm, which was attributed to the formation of a hydrogen-bonded proton transfer complex (9-MP-H+) with water molecules. Thus, this work revealed the mechanism of a colorimetric and ratiometric fluorescent sensor based on pyrido[3,4-b]indole-boron trifluoride complex for the detection of water over a wide range from low water content to high water content in solvents.

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, Optoelectronic Properties, Self-Association, and Base Pairing of Nucleobase-Functionalized Oligothiophenes

Device-relevant π-conjugated oligothiophenes with the canonical nucleobases directly embedded into the π-framework have been designed, synthesized, and characterized. These oligomers offer the ability to tune optoelectronic properties via the intimate merging of the nucleobase molecular electronic structure with base-pairing fidelity. Analysis of their optical and electronic properties in a hydrogen-bond-disrupting solvent (DMF) indicates that the nucleobase identity influences the intrinsic electronic properties of the semiconductors. These differences are supported by DFT calculations which demonstrate that the HOMO/LUMO orbitals are distributed differently for each compound. The solubility and competition between self-association and base pairing in a hydrogen-bond-supporting solvent (chloroform) was studied to better understand the oligomer behavior under conditions relevant for downstream solution processing into thin-film devices. These solution studies reveal that in each case base-pairing is preferred to self-aggregation; the relatively weak heteroassociation of 1A-1U (35 ± 5 M^-1) should be amenable to facile solution processing and successive hydrogen bond formation in the solid state, while the strong heteroassociation between 1G and 1C (>10⁴ M^-1) should enable assemblies to be preformed in solution. These results are expected to enable the synthesis of more complex π-conjugated architectures and facilitate their extension to optoelectronic devices.

A colorimetric and fluorescent sensor for water in acetonitrile based on intramolecular charge transfer: D–(π–A)2-type pyridine–boron trifluoride complex

A D–(π–A)₂-type pyridine–boron trifluoride complex, YNI-2-BF3, was developed as a colorimetric and fluorescent sensor based on intramolecular charge transfer for the detection of water in solvents.

Synthesis of 8-Substituted 2'-Deoxyisoguanosines via Unprotected 8-Brominated 2-Amino-2'-deoxyadenosine

A variety of applications of 8-alkynylated nucleosides has prompted the synthesis of new purine analogues. Bromination of unprotected 2-amino-2'-deoxyadenosine with Br₂ /AcOH/AcONa gives 2-amino-8-bromo-2'-deoxyadenosine (87%). The brominated derivative is converted to 8-alkynylated 2-amino-2'-deoxyadenosines by palladium-catalyzed Sonogashira cross-coupling reaction via microwave assistance (81 - 95%). The resulting compounds are further transformed to 8-alkynylated 2'-deoxyisoguanosines (52 - 70%). The physical properties of new compounds are investigated.

Excitation-dependent fluorescence from atomic/molecular layer deposited sodium-uracil thin films

Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.

Synthesis and optical and electrochemical properties of julolidine-structured pyrido[3,4-b]indole dye

The julolidine-structured pyrido[3,4-b]indole dye ET-1 possesses the ability to act as a calorimetric and fluorescent sensor for Brønsted and Lewis acids.

Synthesis of Main Chain Purine-Based Copolymers and Effects of Monomer Design on Thermal and Optical Properties

The ability to incorporate diverse monomeric building blocks enables the development of advanced polymeric materials possessing a wide range of properties that suits them for myriad applications. Herein, that synthetic toolbox is expanded through the first report of purine-based copolymers in which purines are incorporated directly into the polymer main chain. Stille cross-coupling of dibromopurine monomers with benzodithiophene (BDT) comonomers is used to generate these "poly(purine)s", and variations in the substitution pattern of the purine monomer and BDT side-chains provides insight into the role of monomer design on their resultant thermal and photophysical properties. Specifically, thermal analyses show that poly(purine)s exhibit high thermal stability and high glass transition temperatures depending on the BDT side-chain substituents and substitution pattern of the purine-derived comonomer. Furthermore, optical properties measured via UV-vis and fluorescence spectroscopies show dependence on monomer substitution pattern. These findings demonstrate the viability of synthesizing poly(purine)s via metal-catalyzed cross-coupling reactions and highlight the potential to tailor poly(purine) properties via simple alterations of comonomers.

Solution-state photophysics of N-carbazolyl benzoate esters: dual emission and order of states in twisted push–pull chromophores

The stepwise photoinduced charge transfer in a series ofN-carbazolyl benzoate ester push–pull chromophores has been studied in solution.

A fluorescent surrogate of thymidine in duplex DNA

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

Synthesis, optical properties, and electronic structures of nucleobase-containing π-conjugated oligomers

The molecular recognition properties of the nucleobases instruct the formation of complex three-dimensional architectures in natural and synthetic systems; relatively unexplored is their use as building blocks for π-conjugated materials where they might mutually tune electronic and supramolecular structures. Toward this goal, an introductory set (1a-d and 2a-d) of six purine-terminated and two pyrimidine-terminated π-conjugated oligomers has been synthesized and used to develop experimental electronic and photophysical structure-property trends. Unlike 2,2':5',2″-terthiophene (TTT) derivatives 2a-d, intramolecular charge transfer dominates oligomers 1a-d bearing a 4,7-bisthienylbenzothiadiazole (TBT) spacer due to the strong electron-accepting ability of its benzothiadiazole (BTD) ring. The resulting donor-acceptor-donor systems feature lower HOMO-LUMO gaps than the terthiophene-linked nucleobases (ΔE(g) ∼ 1.8 eV vs 2.4 eV based on electrochemical measurements), and the lowest so far for π-conjugated molecules that include nucleobases within the π-framework. Experiments reveal a dependence of photophysical and electronic structure on the nature of the nucleobase and are in good agreement with theoretical calculations performed at the B3LYP/6-31+G** level. Overall, the results show how nucleobase heterocycles can be installed within π-systems to tune optical and electronic properties. Future work will evaluate the consequences of these information-rich components on supramolecular π-conjugated structure.

Efficient synthesis and in vivo incorporation of acridon-2-ylalanine, a fluorescent amino acid for lifetime and Förster resonance energy transfer/luminescence resonance energy transfer studies

The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein conformational change because it is a long lifetime, visible wavelength fluorophore that is small enough to be incorporated during ribosomal biosynthesis. Incorporation of Acd into proteins expressed in Escherichia coli requires efficient chemical synthesis to produce large quantities of the amino acid and the generation of a mutant aminoacyl tRNA synthetase that can selectively charge the amino acid onto a tRNA. Here, we report the synthesis of Acd in 87% yield over five steps from Tyr and the identification of an Acd synthetase by screening candidate enzymes previously evolved from Methanococcus janaschii Tyr synthetase for unnatural amino acid incorporation. Furthermore, we characterize the photophysical properties of Acd, including quenching interactions with select natural amino acids and Förster resonance energy transfer (FRET) interactions with common fluorophores such as methoxycoumarin (Mcm). Finally, we demonstrate the value of incorporation of Acd into proteins, using changes in Acd fluorescence lifetimes, Mcm/Acd FRET, or energy transfer to Eu(3+) to monitor protein folding and binding interactions.

Syntheses and photophysical properties of 5'-6-locked fluorescent nucleosides

Nine fluorescent 5'-6-locked nucleosides were synthesized by condensation of various 1,2-diketones with 5-amino-2'-deoxycytidine. The nucleosides have different substituents on the pyrazine core structure, ranging from two methyl groups to polyaromatic rings. The photophysical properties of each nucleoside were determined, with the nucleosides displaying diverse absorption and emission maxima, extinction coefficients and quantum yields. The nucleoside with the highest fluorescence brightness was phosphitylated and incorporated into an oligonucleotide by means of automated oligonucleotide synthesis. The labelled oligonucleotide in aqueous buffer exhibited a substantially lowered extinction coefficient and quantum yield compared to the nucleoside in THF. The photophysical properties of the nucleoside were also compared in different DNA structural contexts, a single strand, a 14-mer duplex, a 14-mer duplex with an 11-mer overhang, and a 25-mer nicked duplex labelled at the nick site. Circular dichroism and melting temperature studies verified that the nucleoside did not perturb or destabilize the DNA helixes. In fact, when incorporated at the nick site, the nucleoside was found to stabilize the nicked duplex notably compared to its unmodified counterpart. The brightness of the fluorescent nucleoside in DNA increased as the polarity of its surroundings decreased, being highest in the 25-mer nicked duplex where exposure to the polar solvent is minimized by stacking to the adjacent bases on both the 3'- and 5'-side. The nucleosides brightness in the nicked duplex was also found to increase with lowered temperature, in accordance with expected temperature-dependent changes in the stacked-unstacked equilibrium at the nick site.

C8-heteroaryl-2'-deoxyguanosine adducts as conformational fluorescent probes in the NarI recognition sequence

The optical, redox, and electronic properties of C(8)-heteroaryl-2'-deoxyguanosine (dG) adducts with C(8)-substituents consisting of furyl ((Fur)dG), pyrrolyl ((Pyr)dG), thienyl ((Th)dG), benzofuryl ((Bfur)dG), indolyl ((Ind)dG), and benzothienyl ((Bth)dG) are described. These adducts behave as fluorescent nucleobase probes with emission maxima from 379 to 419 nm and fluorescence quantum yields (Φ(fl)) in the 0.1-0.8 range in water at neutral pH. The probes exhibit quenched fluorescence with increased solvent viscosity and decreased solvent polarity. The (Fur)dG, (Bfur)dG, (Ind)dG, and (Bth)dG derivatives were incorporated into the G(3) position of the 12-mer oligonucleotide 5'-CTCG(1)G(2)CG(3)CCATC-3' that contains the recognition sequence of the NarI Type II restriction endonuclease. This sequence is widely used to study the biological activity (mutagenicity) of C(8)-arylamine-dG adducts with adduct conformation (anti vs syn) playing a critical role in the biological outcome. The modified NarI(X = (Fur)G, (Ind)G, (Bfur)G, or (Bth)G) oligonucleotides were hybridized to the complementary strand containing either C (NarI'(C)) or G (NarI'(G)) opposite the probe. The duplex structures were characterized by UV melting temperature analysis, fluorescence spectroscopy, collisional fluorescence quenching studies, and circular dichroism (CD). The emission of the probes showed sensitivity to the opposing base in the duplex, and suggested the utility of fluorescence spectroscopy to monitor probe conformation.

A computational approach to tuning the photochemistry of platinum(IV) anticancer agents

Diazido Pt(IV) complexes are inert stable prodrugs that can be photoactivated to produce Pt(II) species with promising anticancer activity. Our studies of the photochemistry of Pt(IV) complexes, [Pt(X)(2) (Y)(2) (Z)(2) ](0/-1) (X=N-ligands (NH(3) , pyridine, etc.)/S(CH(3) )(2) /H(-) , Y=(pseudo)halogen (N(3) (-) , I(-) ), Z=OR(-) , R=H, Ac) by time-dependent density functional theory (TDDFT) show close agreement with spectroscopic data. Broad exploration of cis/trans geometries, trans influences, the nature of the OR(-) and (pseudo)halogen ligands, electron-withdrawing/donating/delocalising substituents on the N-ligands, and intramolecular H bonds shows that: 1) the design of platinum(IV) complexes with intense bands shifted towards longer wavelengths (from 289 to ∼330 nm) can be achieved by introducing intramolecular H bonds involving the OH ligands and 2-hydroxyquinoline or by iodido ligands; 2) mesomeric electron-withdrawing substituents on pyridine result in low-energy absorption with significant intensity in the visible region; and 3) the distinct makeup of the molecular orbitals involved in the electronic transitions for cis/trans-{Pt(N(3) )(2) } isomers results in different photoproducts. In general, the comparison of the optimised geometries shows that Pt(IV) complexes with longer PtL bonds are more likely to undergo photoreduction with longer-wavelength light. The novel complex trans,trans,trans-[Pt(N(3) )(2) (OH)(2) (NH(3) )(4-nitropyridine)] with predicted absorption in the visible region has been synthesised. The experimental UV/Vis spectrum in aqueous solution correlates well with the intense band in the computed spectrum, whereas the overlay in the low-energy region can be improved by a solvent model. This combined computational and experimental study shows that TDDFT can be used to tune the coordination environment for optimising photoactive Pt(IV) compounds as anticancer agents.

Fluorescent C-linked C8-aryl-guanine probe for distinguishing syn from anti structures in duplex DNA

The synthesis and optical properties of the carbon (C)-linked C(8)-(2"-benzo[b]thienyl)-2'-deoxyguanosine ((Bth)dG), which acts as a fluorescent reporter of syn versus anti glycosidic conformations in duplex DNA, are described. In the syn-conformation, the probe stabilizes a G:G mismatch, emits at ∼385 nm (excitation ∼285 nm), and shows an induced circular dichroism (ICD) signal at ∼320 nm. Molecular dynamics (MD) simulations predict a wedge (W)-conformation for the mismatched duplex with the C(8)-benzo[b]thienyl moiety residing in the minor groove. In contrast, the probe destabilizes the duplex when base paired with its normal pyrimidine partner C. With flanking purine bases, a major groove B-type duplex is favored with (Bth)dG present in the anti-conformation emitting at ∼413 nm (excitation ∼326 nm) and no ICD signal. However, with flanking pyrimidine bases, (Bth)dG adopts the syn-conformation when base paired with C, and MD simulations predict a base-displaced stacked (S)-conformation, with the opposing C flipped out of the helix. The different duplex (B-, S-, and W-) conformers formed upon incorporation of (Bth)dG are known to play a critical role in the biological activity of N-linked C8-dG adducts formed by arylamine carcinogens. Bulky environment-sensitive fluorescent C(8)-dG adducts that mimic the duplex structures formed by carcinogens may be useful in luminescence-based DNA polymerase assays.

Site-specific control of N7-metal coordination in DNA by a fluorescent purine derivative

A synthetic strategy that utilizes O6-protected 8-bromoguanosine gives broad access to C8-guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8-substituted 2'-deoxyguanosines are push-pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001-0.72) due to excited-state proton-transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal-binding affinity and specificity of 8-substituted 2'-deoxyguanosines. One derivative, 8-(2-pyridyl)-2'-deoxyguanosine (2PyG), exhibits selective binding of Cu(II), Ni(II), Cd(II), and Zn(II) through a bidentate effect provided by the N7 position of guanine and the 2-pyridyl nitrogen atom. Upon incorporation into DNA, 2-pyridine-modified guanine residues selectively bind to Cu(II) and Ni(II) with equilibrium dissociation constants (K(d)) that range from 25 to 850 nM; the affinities depend on the folded state of the oligonucleotide (duplex>G-quadruplex) as well as the identity of the metal ion (Cu>Ni≫Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site-specific control of metal localization in alternatively folded nucleic acids. Temperature-dependent circular-dichroism studies reveal metal-dependent stabilization of duplexes, but destabilization of G-quadruplex structures upon adding Cu(II) to 2PyG-modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.

8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes

Natural nucleotides are not useful as fluorescent probes because of their low quantum yields. Therefore, a common methodology for the detection of RNA and DNA is the application of extrinsic fluorescent dyes coupled to bases in oligonucleotides. To overcome the many limitations from which fluorescent nucleotide-dye conjugates suffer, we have developed novel purine nucleosides with intrinsic fluorescence to be incorporated into oligonucleotide probes. For this purpose we synthesized adenosine and guanosine fluorescent analogues 7-25, conjugated at the C8 position with aryl/heteroaryl moieties either directly, or via alkenyl/alkynyl linkers. Directly conjugated analogues 7-14, exhibited high quantum yields, φ >0.1, and short λ(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, φ <0.075, and λ(em)<385 nm. The alkenyl conjugated analogues 15-21, exhibited λ(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited φ <0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, φ ≈ 0.8, suggesting better intramolecular charge transfer. We determined the conformation of selected adenosine analogues. Directly conjugated analogue 8 and alkynyl conjugated analogue 22, adapted the syn conformation, whereas alkenyl conjugated analogue 15 adapted the anti conformation. Based on the long emission wavelengths, high quantum yields, anti conformation and base-paring compatibility, we suggest analogues 17 and 21 for further development as fluorescent probes for the sensitive detection of genetic material.

Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA

Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.

Highly fluorescent guanosine mimics for folding and energy transfer studies

Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2′-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2′-deoxyguanosine (2PyG), 8-(2-phenylethenyl)-2′-deoxyguanosine (StG) and 8-[2-(pyrid-4-yl)-ethenyl]-2′-deoxyguanosine (4PVG). On DNA folding and stability, 8-substituted guanosines can exhibit context-dependent effects but were better tolerated by G-quadruplex and duplex structures than pyrimidine mismatches. In contrast to previously reported fluorescent guanine analogs, 8-substituted guanosines exhibit similar or even higher quantum yields upon their incorporation into nucleic acids (Φ = 0.02–0.45). We have used these highly emissive probes to quantify energy transfer efficiencies from unmodified DNA nucleobases to 8-substituted guanosines. The resulting DNA-to-probe energy transfer efficiencies (η_t) are highly structure selective, with η_t(duplex) < η_t(single-strand) < η_t(G-quadruplex). These trends were independent of the exact structural features and thermal stabilities of the G-quadruplexes or duplexes containing them. The combination of efficient energy transfer, high probe quantum yield, and high molar extinction coefficient of the DNA provides a highly sensitive and reliable readout of G-quadruplex formation even in highly diluted sample solutions of 0.25 nM.

Electronic structural dependence of the photophysical properties of fluorescent heteroditopic ligands - implications in designing molecular fluorescent indicators

Two fluorescent heteroditopic ligands (2a and 2b) for zinc ion were synthesized and studied. The efficiencies of two photophysical processes, intramolecular charge transfer (ICT) and photoinduced electron transfer (PET), determine the magnitudes of emission bathochromic shift and enhancement, respectively, when a heteroditopic ligand forms mono- or dizinc complexes. The electron-rich 2b is characterized by a high degree of ICT in the excited state with little propensity for PET, which is manifested in a large bathochromic shift of emission upon Zn(2+) coordination without enhancement in fluorescence quantum yield. The electron-poor 2a displays the opposite photophysical consequence where Zn(2+) binding results in greatly enhanced emission without significant spectral shift. The electronic structural effects on the relative efficiencies of ICT and PET in 2a and 2b as well as the impact of Zn(2+)-coordination are probed using experimental and computational approaches. This study reveals that the delicate balance between various photophysical pathways (e.g. ICT and PET) engineered in a heteroditopic ligand is sensitively dependent on the electronic structure of the ligand, i.e. whether the fluorophore is electron-rich or poor, whether it possesses a donor-acceptor type of structure, and where the metal binding occurs.

Characterization of nucleobase analogue FRET acceptor tCnitro

The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.