Novel,Monomeric Cyanine Dyes as Reporters for DNA Helicase Activity

The dimeric cyanine dyes, YOYO-1 and TOTO-1, are widely used as DNA probes because of their excellent fluorescent properties. They have a higher fluorescence quantum yield than ethidium homodimer, DAPI and Hoechst dyes and bind to double-stranded DNA with high affinity. However, these dyes are limited by heterogeneous staining at high dye loading, photocleavage of DNA under extended illumination, nicking of DNA, and inhibition of the activity of DNA binding enzymes. To overcome these limitations, seven novel cyanine dyes (Cyan-2, DC-21, DM, DM-1, DMB-2OH, SH-0367, SH1015-OH) were synthesized and tested for fluorescence emission, resistance to displacement by Mg²⁺, and the ability to function as reporters for DNA unwinding. Results show that Cyan-2, DM-1, SH-0367 and SH1015-OH formed highly fluorescent complexes with dsDNA. Of these, only Cyan-2 and DM-1 exhibited a large fluorescence enhancement in buffers, and were resistant to displacement by Mg²⁺. The potential of these two dyes to function as reporter molecules was evaluated using continuous fluorescence, DNA helicase assays. The rate of DNA unwinding was not significantly affected by either of these two dyes. Therefore, Cyan-2 and DM-1 form the basis for the synthesis of novel cyanine dyes with the potential to overcome the limitations of YOYO-1 and TOTO-1.     

Using critical sets to solve the maximum independent set problem

A method that utilizes the polynomially solvable critical independent set problem for solving the maximum independent set problem on graphs with a nonempty critical independent set is developed. The effectiveness of the proposed approach on large graphs with large independence number is demonstrated through extensive numerical experiments.     

Stable (long-bonded) dimers via the quantitative self-association of different cationic, anionic, and uncharged pi-radicals: structures, energetics, and optical transitions

Unusual dimers with wide interplanar separations, that is, very long bonds with d(D) approximately 3.05 A, are common to the spontaneous self-association of various organic pi-radicals in solution and in the crystalline solid state, independent of whether they are derived from negatively charged anion radicals of planar electron acceptors (TCNE-*, TCNQ-*, DDQ-*, CA-*), positively charged biphenylene cation-radical (OMB+*), or neutral phenalene radical (PHEN*). All dimeric species are characterized by intense absorption bands in the near-IR region that are diagnostic of the charge-transfer transitions previously identified with intermolecular associations of various electron-donor/acceptor dyads. The extensive delocalizations of a pair of pi-electrons accord with the sizable values of (i) the enthalpies (-Delta H(D)) and entropies (-Delta S(D)) of pi-dimerization measured by quantitative UV-vis/EPR spectroscopies and (ii) the electronic coupling element H(ab) evaluated from the strongly allowed optical transitions, irrespective of whether the diamagnetic dimeric species bear a double-negative charge as in (TCNE)(2)(2-), (TCNQ)(2)(2-), (DDQ)(2)(2-), (CA)(2)(2-) or a double-positive charge as in (OMB)(2)(2+) or are uncharged as in (PHEN)(2). These long-bonded dimers persist in solution as well as in the solid state and suffer only minor perturbations with Delta d(D) < 10% from extra-dimer forces that may be imposed by counterion electrostatics, crystal packing, and so forth. The characteristic optical transitions in such diamagnetic two-electron dimers are shown to be related to those in the corresponding paramagnetic one-electron pimers of the same pi-radicals with their parent acceptor, both in general accord with Mulliken theory.     

Initiation and inhibition of dealloying of single crystalline Cu3Au (111) surfaces

Dealloying is widely utilized but is a dangerous corrosion process as well. Here we report an atomistic picture of the initial stages of electrochemical dealloying of the model system Cu(3)Au (111). We illuminate the structural and chemical changes during the early stages of dissolution up to the critical potential, using a unique combination of advanced surface-analytical tools. Scanning tunneling microscopy images indicate an interlayer exchange of topmost surface atoms during initial dealloying, while scanning Auger-electron microscopy data clearly reveal that the surface is fully covered by a continuous Au-rich layer at an early stage. Initiating below this first layer a transformation from stacking-reversed toward substrate-oriented Au surface structures is observed close to the critical potential. We further use the observed structural transitions as a reference process to evaluate the mechanistic changes induced by a thiol-based model-inhibition layer applied to suppress surface diffusion. The initial ultrathin Au layer is stabilized with the intermediate island morphology completely suppressed, along an anodic shift of the breakdown potential. Thiol-modification induces a peculiar surface microstructure in the form of microcracks exhibiting a nanoporous core. On the basis of the presented atomic-scale observations, an interlayer exchange mechanism next to pure surface diffusion becomes obvious which may be controlling the layer thickness and its later change in orientation.     

Accurate calculations of dynamic first hyperpolarizability: Construction of physically justified slater‐type basis sets

An efficient procedure for construction of physically rationalized Slater‐type basis sets for calculations of dynamic hyperpolarizability is proposed. Their performance is evaluated for the DFT level calculations for model molecules, carried out with a series of functionals. Advantages of new basis sets over standard d‐aug‐cc‐pVTZ and recently developed LPOL‐(FL,FS) Gaussian‐type basis sets are discussed. © 2014 Wiley Periodicals, Inc.     

Plasmonic Nanobiosensor with Chain Reaction Amplification Mechanism

Herein we demonstrate a plasmonic nanobiosensor that explores chain reaction amplification mechanisms to transduce chemical signals released in biocatalytic reactions, turning optical signals into a visual spectral range. The sensor has a very simple design: gold nanoparticles resting in the surface of a grafted P2VP film. Changes in the gold nanoparticles’ position causes changes in the plasmon coupling mode. This is detected by means of a maximum absorbance shift.     

Preparation of polymer composites on the base of polyurethanes and natural polysaccharides

A series of composites based on segmented polyurethanes (PU) as polymer matrices and natural polysaccharides – cellulose and starch – as fillers have been synthesized. Using IR method and Differential Scanning Calorimetry the peculiarities of the structure of composites and their behavior in the buffer solutions in conditions imitating natural soil environment have been investigated.     

Influence of the Aggregation of Homo-N-Mer Cyanine Dyes on the Nucleic Acids Detection Sensitivity

Novel benzothiazolopyridinium homo-n-mer cyanine dyes are proposed for nucleic acid fluorescent detection. Dependence of the sensitivity of detection in solution from the dye molecules/DNA base pairs ratio was studied. It was shown that the presence of the dye excess could significantly decrease the detection limit. We believe this could be explained by the formation of the dye aggregates on DNA surface.