Control of the Fluorescence of DNA‐templated Silver Nanoclusters by Adenosine Triphosphate and Mercury(II)

Several DNA templates with the sequence 5′‐T _n TAACCCCTAACCCCT ‐3′ (n = 0, 15, 30, and 45) were used to prepare DNA template–silver nanoclusters (DNA –Ag NCs ). The T _n sequence acts as a recognition element for Hg²⁺, while the rest of the sequence acts as a template for DNA –Ag NCs . At pH 3.0, the fluorescence intensity of DNA –Ag NCs is enhanced by ATP , and the enhanced fluorescence is quenched by Hg²⁺. The length of polyT shows a slight effect on the sensitivity for the detection of Hg²⁺ but almost no effect on the optical properties of DNA –Ag NCs . The fluorescence response of DNA –Ag NCs (T₁₅‐DNA –Ag NCs ) vs. Hg²⁺ concentration shows two linear ranges over 10–100 and 100–1000 nM , mainly because of the fluorescence quenching due to DNA conformational changes through T–Hg²⁺–T coordination and the formation of an amalgam with Ag NCs , respectively. The sensitivity of the T₁₅‐DNA –Ag NC probe was validated through the analysis of Hg²⁺ in spiked pond water. Based on the switch‐on and switch‐off fluorescence properties of T₁₅‐DNA –Ag NCs , an IMPLICATION logic gate was fabricated using the concentrations of ATP and Hg²⁺ as inputs and the fluorescence intensity at 585 nm as output.     

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.     

Sequence Dependence of Fluorescent Quenching of Chromophores Covalently Bonded to Oligo-DNAs before and after Duplex Formation

The labeling of oligo- and polynucleotides with fluorescent probes is an important technique for the analysis of DNAs and RNAs. The effect of duplex formation with complementary oligo-DNA on the quenching behavior of two fluorescent chromophores (eosin, Eo and tetramethylrhodamine, TMR) attached to the 5′-terminal of various 10mer oligo-DNAs was investigated and the dependence of the quenching on DNA base sequence is discussed. We found that guanine residues played a major role in the quenching of the fluorescence of the chromophores. Guanine residues on the complementary DNA near the chromophores, in particular, had a significant influence on the quenching.     

A DNA–Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA‐Based Solar Cells

A fullerene was covalently attached to a (dA)₂₀ template that serves as structural scaffold to self‐assemble an ordered and mixed array of ethynyl‐pyrene‐ and ethynyl‐Nile‐red‐nucleoside conjugates. Fluorescence spectroscopy revealed evidence for energy transfer between the two different chromophores. Moreover, fluorescence quenching is significantly enhanced by the attached fullerene in mixed assemblies of different chromophore ratios. This indicates exciton dissociation by electron transfer from the photo‐generated exciton on the chromophore stack to the fullerene. The fullerene–DNA‐conjugate was integrated as a photo‐active layer in solar cells that showed charge‐carrier generation in the spectral regime of all three components of the conjugate. This work clearly demonstrates that DNA is suitable as structural element for chromophore assemblies in future organic optoelectronic devices, such as solar cells.     

Benzophenone and zinc(II) phthalocyanine dichromophores-labeled poly (aryl ether) dendrimer: synthesis,characterization and photoinduced energy transfer

A series of benzophenone chromospheres and zinc(II) phthalocyanine dichromophores labeled poly (aryl benzyl ether) dendrimer (G_n-DZnPc(BP)_8n, n = 1?2) were synthesized. Their structures were characterized by elemental analysis, ¹H NMR, IR, UV–vis and matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF MS). Their photophysical properties were examined by steady-state and time-resolved fluorescence methods. Both the poly (aryl benzyl ether) dendrimer and BP terminal chromophores had a significant effect on photophysical properties of the zinc(II) phthalocyanine core. Time-resolved spectroscopic measurements indicated that the lifetime of benzophenone (donor) chromophore was longer than that of the zinc(II) phthalocyanine (acceptor). The fluorescence of the peripheral benzophenone chromophores was quenched by the phthalocyanine group attached to the focal point. All of these observations suggest that an intramolecular singlet energy transfer occurs in G_n-DZnPc(BP)_8n molecules. The light-harvesting abilities of these molecules increased with generations due to an increase in the number of benzophenone chromophores. The energy transfer efficiencies were ca. 0.49 and 0.68 for generations 1 and 2, respectively, and the rate constants of the singlet-singlet energy transfer were ca. 10⁸ s^?1. The rate constants changed inconspicuously with increase of dendron generations. The intramolecular singlet-singlet energy transfer is proposed to proceed mainly via a Förster-type interaction mechanism involving the dendrimer backbone as a scaffold to hold the peripheral benzophenone chromophores and the phthalocyanine core together. This dendrimer was an effective new energy transmission complex with high efficiency and could be used as a potential light-harvesting system.     

Molecular Recognition and Visual Detection of G‐Quadruplexes by a Dicarbocyanine Dye

The interactions of a dicarbocyanine dye 3,3′‐diethylthiadicarbocyanine, DiSC₂(5) , with DNA G‐quadruplexes were studied by means of a combination of various spectroscopic techniques. Aggregation of excess dye as a result of its positive charge is promoted by the presence of the polyanionic quadruplex structure. Specific high‐affinity binding to the parallel quadruplex of the MYC promoter sequence involves stacking of DiSC₂(5) on the external G‐tetrads; the 5′‐terminal tetrad is the favored binding site. Significant energy transfer between DNA and the dye in the UV spectral region is observed upon DiSC₂(5) binding. The transfer efficiency strongly depends on the DNA secondary structure as well as on the G‐quadruplex topology. These photophysical features enable the selective detection of DNA quadruplexes through sensitized DiSC₂(5) fluorescence in the visible region.     

Water Soluble Nickel – metformin ternary complexes: Thermal,DNA binding and molecular docking studies

The Nickel (II) complexes [Ni(Cl)₂(metf)(o-phen)] (1), [Ni(Cl)₂(metf)(opda)] (2) , [Ni(Cl)₂(metf)(en)] (3) , [Ni(Cl)₂(metf)(2,2'-bipy)] (4) , (metf = metformin, o-phen = ortho-phenanthroline, opda = ortho-phenylenediamine, en = ethylenediamine, 2–2′ bipy = 2–2′ bipyridyl) were synthesized and characterized using LC–MS, elemental analysis, molar conductance measurements, TGA-DTA, IR spectroscopy, magnetic moment measurements and electronic spectroscopy. The central Ni²⁺ was found to be in octahedral geometry. The DNA interaction of these complexes have been studied by UV–visible absorption studies, fluorescence emission technique and viscosity measurement. The complexes showed absorption hyperchromism in UV–visible spectra with calf thymus DNA. The binding constants from UV–visible absorption studies were 7.42 × 10⁴, 0.74 × 10⁴, 3.19 × 10⁴, 5.9 × 10⁴ M⁻¹ for 1 , 2 , 3 and 4 , respectively and Stern-Volmer quenching constants from fluorescence studies were 0.16, 0.41, 0.23, 0.18, respectively. Viscosity measurements revealed that the binding of the complexes with DNA could be surface binding, mainly due to groove binding. The highest DNA cleavage activity of the complexes is recorded for complex 1 . The complexes were docked in to B-DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP* GP*TP*CP*GP*GP*T)-3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software. C Docker Intectraction energy of 1 , 2 , 3 and 4 complexes is 32.027, 31.427, 35.393 and 30.521 respectively. The highest docking score is seen for complex 3 .     

Spectroscopic Properties of Fluorescein and Rhodamine Dyes Attached to DNA

We report the spectroscopic properties of fluorescein, x-rhodamine, tetramethyl-rhodamine, attached to single strand, duplex DNA, and to the digestion products by DNAse I. The properties reported include: molar absorptivity, quantum yield, absorbance and fluorescence spectra, fluorescence lifetime, intrinsic lifetime (τ⁰), static quenching (S) and the Förster critical distances (R₀) between fluorescein and x-rhodamine or tetramethyl-rhodamine (acceptors). These spectroscopic properties depend strongly on the local dye environment. Fluorescein was studied: (1) attached to biotin (BF), (2) BF bound to avidin; and attached to two positions in DNA. X-rhodamine and tetramethyl-rhodamine were studied as free dyes and attached at the 5′-end of DNA. We propose a general method to determine the molar absorptivity and τ⁰ of a dye attached to DNA based on the reaction of a biotinylated and dye-labeled oligomer with standardized avidin. The molar absorptivity of a second dye attached to a DNA duplex can be obtained by comparing spectra of doubly and singly labeled sequences. S, arising from dye–DNA interactions can then be determined. R₀ for free and attached dyes showed differences from 1.1 to 4.2 Å. We present evidence for the direct interaction of dyes attached to the termini of various single-stranded DNA sequences.     

DNA-templated control of chirality and efficient energy transport in supramolecular DNA architectures with aggregation-induced emission

Two conjugates of tetraphenylethylene with d-2′-deoxyuridine (1d) and l-2′-deoxyuridine (1l) were synthesized to construct new supramolecular DNA-architectures by self-assembly. The non-templated assemblies of 1d and 1l show strong aggregation-induced emission and their chirality is exclusively controlled by the configuration of their sugar part. In contrast, the chirality of the DNA-templated assemblies is governed by the configuration of the DNA, and there is no configuration-selective binding of 1d to d-A₂₀ and 1l to l-A₂₀. The quantum yield of the assembly of 1d along the single-stranded DNA A₂₀ is 0.40; approximately every second available binding site on the DNA template is occupied by 1d. The strong aggregation-induced emission of these DNA architectures can be efficiently quenched and the excitation energy can be transported to Atto dyes at the 5′-terminus. A multistep energy transport “hopping” precedes the final energy transfer to the terminal acceptor. The building block 1d promotes this energy transport as stepping stones. This was elucidated by reference DNA double strands in which 1d was covalently incorporated at two distinct sites in the sequences, one near the Atto dye, and one farther away. This new type of completely self-assembled supramolecular DNA architecture is hierarchically ordered and the DNA template controls not only the binding but also the energy transport properties. The high intensity of the aggregation-induced emission and the excellent energy transport properties make these DNA-based materials promising candidates for optoelectronic applications.

DNA architectures with tetraphenylethylene are assembled in a non-covalent way. The strong aggregation-induced emission of the chromophores is quenched and the energy is transported to Atto dyes by a multistep energy “hopping”.     

Bifunctional DNA Architectonics: Three‐Way Junctions with Sticky Perylene Bisimide Caps and a Central Metal Lock

A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris‐bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe³⁺, Ni²⁺ and Zn²⁺ by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5′‐terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady‐state fluorescence. The PDI‐mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal‐ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher‐ordered structures as the result of DNA assemblies mediated by the PDI interactions.     

Synthesis and structural characterization of three supramolecular coordination polymers constructed from different metal ions and 2,2′-bipyridyl-3,3′-dicarboxylic acid

Three new supramolecular coordination polymers based on 2,2′-bipyridyl-3,3′-dicarboxylic acid (H₂BPDC) and Mn(II), Fe(II), and Zn(II) were synthesized under hydrothermal conditions and characterized with single-crystallographic X-ray analysis and IR spectrum. Complex 1 exhibits a 1-D, chain-like structure, which is further connected to 2-D supramolecular layer structure through hydrogen bonds. Complex 2 exhibits a 3-D supramolecular structure constructed from 1-D chains through hydrogen bonds and π–π interactions. Like 1, 3 also shows 2-D supramolecular layer structure based on 1-D chains. Furthermore, the fluorescence of 3 was studied.     

Inducement and stabilization of G-quadruplex DNA by a thiophene-containing dinuclear ruthenium(II) complex

G-quadruplex structures are attractive targets for the development of anticancer drugs, as their formation in human telomere could impair telomerase activity, thus inducing apoptosis in cancer cells. In this work, a thiophene-containing dinuclear ruthenium(II) complex, [Ru₂(bpy)₄(H₂bipt)]⁴⁺ {bpy = 2,2′-bipyridine, H₂bipt = 2,5-bis[1,10]phenanthrolin[4,5-f]-(imidazol-2-yl)thiophene}, was prepared and the interaction between the complex and human telomeric DNA oligomers 5′-G₃(T₂AG₃)₃-3′ (HTG21) has been investigated by UV-Vis, fluorescence and circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assay, polymerase chain reaction (PCR) stop assay, fluorescent intercalator displacement (FID) titrations, Job plot and color reaction studies. The results indicate that the complex can well induce and stabilize the formation of antiparallel G-quadruplex of telomeric DNA in the presence or absence of metal cations, and the ΔT_m value of the G-quadruplex DNA treated with the complex was obtained to be 12.8 °C even at levels of 50-fold molar of duplex DNA (calf-thymus DNA), suggesting that the complex exhibits higher G-quadruplex DNA selectivity over duplex DNA. The complex shows high interaction ability with G-quadruplex DNA at (1.17 ± 0.12) × 10⁷ M^?1 binding affinity using a 2:1 [complex]/[quadruplex] binding mode ratio. A novel visual method has been developed here for making a distinction between G-quadruplex DNA and duplex DNA by our ruthenium complex binding hemin to form the hemin-G-quadruplex DNAzyme.     

PICOSECOND FLUORESCENCE FROM PHYCOCYANIN 612

The biliprotein, phycocyanin 612, was purified from a cryptomonad, Hemiselmis virescens. The protein, which is an α₂β₂ dimer having four spectrally different tetrapyrrole chromophores, was studied using picosecond fluorescence by exciting the various chromophores at three wavelengths, 565, 585 and 615 nm. These wavelengths were chosen to excite selectively the three highest energy chromophores. Decay times were measured as the excitation energy migrated from each of the three excited chromophores to the lowest-energy chromophore. The ps decay times were found to be 9, 13, and 12 ps for excitations at 565, 585, and 615 nm, respectively. A comparison is made between phycocyanin 612 and phycocyanin 645 with regard to the causes of their differing absorption maxima.     

Chromium‐metformin ternary complexes: Thermal,DNA interaction and Docking studies

Three chromium ternary complexes with metformin (met) as a primary ligand and bipyridine (bipy) or ortho‐phenylenediamine (opda) or ortho‐phenanthroline (phen) as secondary ligand were synthesized. These complexes [Cr (Cl)₂(Hmet)(bipy)]‐( 1 ), [Cr (Cl)₂(Hmet)(opda)]‐( 2 ) and [Cr (Cl)₂(Hmet)(phen)]‐( 3 ) were characterized by LC–MS, elemental analysis, molar conductance, thermal analysis, infrared spectroscopy, electronic spectroscopy. The geometrical structures have been found to be octahedral. Degradation pattern of the compounds is shown by thermal studies. The Kinetic parameters‐ energy of activation (E_a), enthalpy (ΔH), entropy (ΔS) and free energy changes (ΔG) have been determined by thermogravimetric data. Coats‐Redfern integration method with thirteen kinetic models was used to calculate the kinetic and thermodynamic parameters for the degradation of all the complexes. The stabilities of the complexes were obtained from their molecular orbital structures from which the quantum chemical parameters were calculated using the HOMO‐LUMO energies. UV–Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV–Vis spectrum with DNA. The binding constants K_b from UV–Vis absorption studies were 3.1x10⁴, 4.4x10⁴, 5x10⁴ M^?1 for 1, 2, 3 respectively and Stern–Volmer quenching constants (K_sq) from fluorescence studies were 0.137, 0.532, 0.631 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT‐DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decrease in the order of 3 > 2 > 1.The light switching properties of the complexes were also evaluated. The complexes were docked in to B‐DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)‐3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.     

2‐Phenanthrenyl–DNA: Synthesis,Pairing, and Fluorescence Properties

Three 2′‐phenanthrenyl‐C‐deoxyribonucleosides with donor (phenNH₂), acceptor (phenNO₂), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single‐modified duplexes can vary between ?2.7 to +11.3 °C in T_m and that of triple‐modified duplexes from +7.8 to +11.1 °C. Van′t Hoff analysis suggested that the observed higher thermodynamic stability in phenH‐ and phenNO₂‐containing duplexes is of enthalpic origin. A single phenH or phenNO₂ residue in a bulge position also stabilizes a corresponding duplex. If a phenNO₂ residue is placed in a bulge position next to a base mismatch this can lead, in a sequence‐dependent manner, to duplex destabilization. The phenNO₂ residue was found to be a highly efficient (10–100‐fold) quencher of phenH and phenNH₂ fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH₂ residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH₂ fluorescence was found, which is an indicator for electron‐ or energy‐transfer processes between the aromatic units.     

A novel fluorescence enhancing F<Superscript>−</Superscript> probe based on intermolecular energy transfer

A supramolecular fluorescent sensor of F⁻ based on intermolecular energy transfer is described. The maximum absorption wavelength of a pyrrolic compound 1 is 472 nm, which is coincident with the emission wavelength of a dipyridylamine-anthracene compound 2. In the CH₂Cl₂ solution of 1 and 2, the fluorescence of 2 was quenched because of the presence of intermolecular energy transfer from 2 to 1. When F⁻ was added to this solution, the absorption maximum wavelength of 1 shifted from 472 to 594 nm due to a deprotonation process. Simultaneously, the fluorescence of 2 was recovered because of the interruption of the intermolecular energy transfer. Based on these observations, the combination of 1 and 2 can be regarded as a novel supramolecular fluorescence enhancing F⁻ probe.     

Photoactive Modified Hydroxyethylcellulose

A water‐soluble polymeric photosensitizer that contains naphthalene chromophores and absorbs light in the near UV region was obtained by modification of hydroxyethylcellulose. The excitation energy migrates along the naphthalene chromophores covalently attached to the polymer chain and can be used to induce photochemical reactions such as photoinduced electron transfer.

UV‐vis absorption (○), fluorescence emission (□), and fluorescence excitation (×) spectra of HENC in water at c_HENC = 0.232 g/L, and (+) emission spectrum of the lamps used for irradiations.     

Discrimination Between 8‐Oxo‐2′‐Deoxyguanosine and 2′‐Deoxyguanosine in DNA by the Single Nucleotide Primer Extension Reaction with Adap Triphosphate

The adenosine derivative of 2‐oxo‐1,3‐diazaphenoxazine (Adap) exhibits a superb ability to recognize and form base pairs with 8‐oxo‐2′‐deoxyguanosine (8‐oxo‐dG) in duplex DNA. In this study, the triphosphate of Adap (dAdapTP) was synthesized and tested for single nucleotide incorporation into primer strands using the Klenow Fragment. The efficiency of dAdapTP incorporation into 8‐oxo‐dG‐containing templates was more than 36‐fold higher than with dG‐containing templates, and provides better discrimination than does the incorporation of natural 2′‐deoxyadenosine triphosphate (dATP). The selective incorporation of dAdapTP into 8‐oxo‐dG templates was therefore applied to the detection of 8‐oxo‐dG in human telomeric DNA sequences extracted from H₂O₂‐treated HeLa cells. The enzymatic incorporation of dAdapTP into 8‐oxo‐dG‐containing templates may provide a novel basis for sequencing oxidative DNA damage in the genome.     

Carotenohematoporphyrins as Tumor-Imaging Dyes. Synthesis and In Vitro Photophysical Characterization*

Multichromophoric dyes for use in tumor imaging have been synthesized and photophysically characterized. Structurally, these dyes are dyads and triads that consist of one or two carotenoid polyenes covalently attached to hematoporphyrin (HP) or hematoporphyrin dimethyl ester (HPDME) moieties via ester linkages. The ground-state absorption of each compound shows that the electronic interaction between the chromophores is small. The fluorescence quantum yield for the dyad monocar-oteno- HPDME is 0.033 and the dicaroteno-HPDME triads have yields between 0.016 and 0.007, all of which are reduced with respect to the parent compound HPDME (0.09). Global analysis of the transient fluorescence decays of the dyads and triads requires two exponential components (?5–6ns and ?1–2ns) to fit the data, while a single exponential component with a lifetime of 9.3 ns describes the decay data of the parent HPDME. Possible mechanisms for the observed porphyrin fluorescence quenching by the nearby carotenoid are discussed. Nanosecond transient absorption reveals a carotene triplet with maximum absorption at 560 nm and a 5.0 μs lifetime. No transient was detected at 450 nm, indicating rapid (10 ns) triplet energy transfer from the hematoporphyrin to the carotenoid moieties in fluid as well as in rigid media. The yield of triplet energy transfer from the porphyrin to the carotenoid moiety is unity. Singlet oxygen, O₂(¹δ_g), studies support the transient absorption data, as none of these compounds is capable of sensitizing O₂(¹δ_g). Liposome vesicles were used to study the photophysical characteristics of the dyes in phospholipid membranes. Singlet oxygen was not sensitized by the dyads and triads in liposomes. Transient absorption measurements suggest that the triads are substantially aggregated within the phospholipid bilayer, whereas aggregation in the dyads is less severe.