Bipyridyl- and biphenyl-DNA: a recognition motif based on interstrand aromatic stacking

The synthesis and incorporation into oligonucleotides of C-nucleosides containing the two aromatic, non-hydrogen-bonding nucleobase substitutes biphenyl (I) and bipyridyl (Y) are described. Their homo- and hetero-recognition properties in different sequential arrangements were then investigated via UV-melting curve analysis, gel mobility assays, CD- and NMR spectroscopy. An NMR analysis of a dodecamer duplex containing one biphenyl pair in the center, as well as CD data on duplexes with multiple insertions provide further evidence for the zipper-like interstrand stacking motif that we proposed earlier based on molecular modeling. UV-thermal melting experiments with duplexes containing one to up to seven I- or Y base pairs revealed a constant increase in T(m) in the case of I and a constant decrease for Y. Mixed I/Y base pairs lead to stabilities in between the homoseries. Insertion of alternating I/abasic site- or Y/abasic site pairs strongly decreases the thermal stability of duplexes. Asymmetric distribution of I- or Y residues on either strand of the duplex were also investigated in this context. Duplexes with three natural base pairs at both ends and 50 % of I pairs in the center are still readily formed, while duplexes with blunt ended I pairs tend to aggregate unspecifically. Duplexes with one natural overhang at the end of a I-I base pair tract can both aggregate or form ordered duplexes, depending on the nature of the natural bases in the overhang.     

Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA

Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.     

Sulfonated Pyrene as a Photoregulator for Single-Stranded DNA Looping

Controlling the conformation and function of biomolecules through photoregulators holds great promise as a spatiotemporally controllable tool for disease control. In addition, introducing photoregulators into biomolecules has also found applications in constructing smart nanomaterials. In spite of the astonishing advances that have been made in the past few years, realizing highly controllable and efficient regulation over the conformation and function of biomolecules under physiological conditions is still challenging. Herein, sulfonated pyrene SPy was synthesized and used as a photoregulator to control the looping of single-stranded DNAs (ssDNAs) in aqueous solution. Due to its water solubility, SPy merits use in the study of biomolecules in aqueous solution. The looping of the doubly SPy -modified ssDNAs is stimulated by irradiation and regulated by SPy . Photoionization generates the radical cation of SPy ( SPy ^.+). The association of SPy ^{. +} with its neutral counterpart, SPy , gives rise to the dimer radical cation of SPy ( SPy₂ ^{. +} ). During the association process, the stabilization energy released to form SPy₂ ^{. +} provides a driving force for the looping of ssDNAs. Conversely, the formed loop conformations were trapped by the formation of SPy₂ ^{. +} , and this allowed the looping dynamics to be investigated. The results reported herein suggest potential of SPy as a photoregulator for controlling the conformation and function of biomolecules under physiological conditions.     

Artificial neural networks based on principal component analysis input selection for clinical pattern recognition analysis

Two clinical data sets were applied for pattern recognition in order to discover the correlation between urinary nucleoside profiles and tumours. One data set contains 168 clinical urinary samples, of which 84 specimens are from female thyroid cancer patients (malignant tumour group), and the other samples were collected from healthy women (normal group). However, 168 clinical urinary samples comprised the second data set, too. In all the specimens, each number of the samples for both uterine cervical cancer patients (malignant tumour group) and healthy females (normal group) is 60, and the other 48 samples were collected from uterine myoma patients (benign tumour group). For the two data sets, the separation and quantitative determination of the clinical urinary nucleosides were performed by capillary electrophoresis (CE). The pattern recognition was achieved applying multiple layer perceptron artificial neural networks (MLP ANN) based on conjugate gradient descent training algorithm. Moreover, applying the proposed principal component analysis (PCA) input selection scheme to MLP ANN, the accuracy rate of the pattern recognition was improved to some extent (or without any deterioration) even by much simpler structure of MLP ANN. The study showed that MLP ANN based on PCA input selection was a promising tool for pattern recognition.     

Synthesis and two-photon properties of a multi-polar chromophore based on tetra-quinoxalinylethylene scaffold

A new multi-branched fluorophore derived from tetra-quinoxalinylethylene as the core with diphenylaminofluorene units incorporated at the peripheral positions has been synthesized via Pd-catalyzed Suzuki coupling and experimentally shown to possess strong solvent effect on its fluorescence emission and lifetime behaviors. The initial characterization also found that this dye molecule exhibits two-photon activities and effective optical power limiting properties in the near-IR region under the irradiation of nanosecond laser pulses.     

Artificial Iono‐ and Photosensitive Membranes Based on an Amphiphilic Aza‐Crown‐Substituted Hemicyanine

Artificial iono‐ and photosensitive membranes based on an amphiphilic aza‐crown‐substituted hemicyanine are assembled on liquid and solid supports and their aggregation behaviour, which is influenced by the binding of metal cations and surface density, is studied. The photoinduced charge‐transfer properties of an analogous non‐amphiphilic hemicyanine in solution are also demonstrated. An asymmetric sandwich dimer model is proposed and existence of such dimers in solution is evidenced by transient absorption and fluorescence anisotropy experiments. Changes in absorption and emission spectra, as well as compression isotherms of the amphiphile observed in the presence of cations, are discussed in terms of 2D molecular reorganisation. Surface‐pressure‐controlled reversible excimer formation at the air–water interphase and excimer‐type emission of Langmuir–Blodgett films in the presence of cations are demonstrated and are discussed on the basis of fibre‐optic fluorimetry and fluorescence microscopy results.     

Oligothiophenes Nano‐organized on a Cyclotetrasiloxane Scaffold as a Model of a Silica‐Bound Monolayer: Evidence for Intramolecular Excimer Formation

Excimer formation in a new class of terthiophene‐based fluorophores covalently bonded to a cyclotetrasiloxane scaffold has been demonstrated and the photophysical process ruling it has been investigated in detail and modeled theoretically. In contrast to the conventional systems in which long‐living fluorophores such as pyrene are linked in the same molecule, an excimer is formed only when two terthiophene‐based branches nano‐organized on the same cyclotetrasiloxane scaffold are close enough together when excitation takes place. In such a case, excimer formation is extremely efficient, and the new bound excited states are quite stable.     

Environment‐Sensitive Fluorophores with Benzothiadiazole and Benzoselenadiazole Structures as Candidate Components of a Fluorescent Polymeric Thermometer

An environment‐sensitive fluorophore can change its maximum emission wavelength (λ_em), fluorescence quantum yield (Φ_f), and fluorescence lifetime in response to the surrounding environment. We have developed two new intramolecular charge‐transfer‐type environment‐sensitive fluorophores, DBThD‐IA and DBSeD‐IA, in which the oxygen atom of a well‐established 2,1,3‐benzoxadiazole environment‐sensitive fluorophore, DBD‐IA, has been replaced by a sulfur and selenium atom, respectively. DBThD‐IA is highly fluorescent in n‐hexane (Φ_f=0.81, λ_em=537 nm) with excitation at 449 nm, but is almost nonfluorescent in water (Φ_f=0.037, λ_em=616 nm), similarly to DBD‐IA (Φ_f=0.91, λ_em=520 nm in n‐hexane; Φ_f=0.027, λ_em=616 nm in water). A similar variation in fluorescence properties was also observed for DBSeD‐IA (Φ_f=0.24, λ_em=591 nm in n‐hexane; Φ_f=0.0046, λ_em=672 nm in water). An intensive study of the solvent effects on the fluorescence properties of these fluorophores revealed that both the polarity of the environment and hydrogen bonding with solvent molecules accelerate the nonradiative relaxation of the excited fluorophores. Time‐resolved optoacoustic and phosphorescence measurements clarified that both intersystem crossing and internal conversion are involved in the nonradiative relaxation processes of DBThD‐IA and DBSeD‐IA. In addition, DBThD‐IA exhibits a 10‐fold higher photostability in aqueous solution than the original fluorophore DBD‐IA, which allowed us to create a new robust molecular nanogel thermometer for intracellular thermometry.     

A Rotational BODIPY Nucleotide: An Environment‐Sensitive Fluorescence‐Lifetime Probe for DNA Interactions and Applications in Live‐Cell Microscopy

Fluorescent probes for detecting the physical properties of cellular structures have become valuable tools in life sciences. The fluorescence lifetime of molecular rotors can be used to report on variations in local molecular packing or viscosity. We used a nucleoside linked to a meso‐substituted BODIPY fluorescent molecular rotor ( dC^bdp ) to sense changes in DNA microenvironment both in vitro and in living cells. DNA incorporating dC^bdp can respond to interactions with DNA‐binding proteins and lipids by changes in the fluorescence lifetimes in the range 0.5–2.2 ns. We can directly visualize changes in the local environment of exogenous DNA during transfection of living cells. Relatively long fluorescence lifetimes and extensive contrast for detecting changes in the microenvironment together with good photostability and versatility for DNA synthesis make this probe suitable for analysis of DNA‐associated processes, cellular structures, and also DNA‐based nanomaterials.     

DNA as a template for synthesis of fluorescent gold nanoclusters

Water-soluble blue-emitting gold nanoclusters have been synthesized using dsDNA as a template without any additional reducing agent. The features of the formed nanoclusters have been revealed by fluorescence and electronic absorption spectroscopy as well as transmission electron microscopy. The prepared gold nanoclusters have been highly stable at physiological pH without any further modification.     

A Rigid Dinuclear Ruthenium(II) Complex as an Efficient Photoactive Agent for Bridging Two Guanine Bases of a Duplex or Quadruplex Oligonucleotide

The rigid dinuclear [(tap)₂Ru(tpac)Ru(tap)₂]⁴⁺ complex ( 1 ) (TAP=1,4,5,8‐tetraazaphenanthrene, TPAC=tetrapyridoacridine) is shown to be much more efficient than the mononuclear bis‐TAP complexes at photodamaging oligodeoxyribonucleotides (ODNs) containing guanine (G). This is particularly striking with the G‐rich telomeric sequence d(T₂AG₃)₄. Complex 1 , which interacts strongly with the ODNs as determined by surface plasmon resonance (SPR) and emission anisotropy experiments, gives rise under illumination to the formation of covalent adducts with the G units of the ODNs. The yield of photocrosslinking of the two strands of duplexes by 1 is the highest when the G bases of each strand are separated by three to four base pairs. This corresponds with each Ru(tap)₂ moiety of complex 1 forming an adduct with the G base. This separation distance of the G units of a duplex could be determined thanks to the rigidity of complex 1 . On the basis of results of gel electrophoresis, mass spectrometry, and molecular modelling, it is suggested that such photocrosslinking can also occur intramolecularly in the human telomeric quadruplex d(T₂AG₃)₄.