The structure of dihydropyrroloindoles: A quantum-chemical estimation of conjugation in cyclohexadiene systems

A non-empirical quantum chemical calculation of isomeric 3,6-divinyl-3,4,5,6-tetrahydropyrrolo[3,2-e] indole 1 and 1,5-divinyl-1,4,5,8-tetrahydro[3,2-f]indole 2 structures carried out by DFT (B3LYP) method with 6-311++G(d, p) and 6-311++G(3df, p) basis sets showed the energy preference of 2 over 1 (1.33 kcal/mol and 1.47 kcal/mol, respectively). The structure of the molecule of 2 is planar while the molecule of 1 is non-planar due to the presence of sp ³-hybridized carbon atoms.     

CANADA: Designing nucleic acid sequences for nanobiotechnology applications

The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA‐based nanotechnology applications. The CANADA package contains software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11‐www.cs.uni‐dortmund.de/molcomp/downloads . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Contrast of Bonding and Characters for C6, B3N3, C6H6 and B3N3H6 Molecules

Through integrative consideration of NICS, MO, MOC and NBO, we precisely investigated delocalization and bonding characters of C₆, C₆H₆, B₃N₃ and B₃N₃H₆ molecules. Firstly, we originally discovered and testified that C₆ cluster was sp² hybridization. Negative NICS values in 0 and 1 Å indicated that C₆ had δ and Π aromaticity. Secondly, B₃N₃ with sp² hybridization had obvious δ aromaticity. Finally, WBI values approved that there were delocalization in C₆, C₆H₆ and B₃N₃ molecules, but B₃N₃H₆ structure did not have delocalization with the WBI 1.0. Moreover, total WBI values of carbon, boron and nitrogen atoms were four, three and three, respectively. Namely, the electrons of B₃N₃H₆ and B₃N₃ were localized in nitrogen atoms and they did not form delocalized bonding. In a word, bonding characters of carbon, boron and nitrogen atoms were dissimilar although the molecules composed of carbon, boron and nitrogen were regarded as isoelectronic structures.     

Electrocatalytic Oxidation of Nucleic Acids at Electrodes Modified with Nylon and Nitrocellulose Membranes

Electrocatalytic oxidation of guanine in DNA was detected at tin-doped indium oxide electrodes modified with nylon and nitrocellulose polymers. The catalytic oxidation occurs via oxidation at the electrode of the complex Ru(bpy) ₃ ²⁺ to the 3+ state, which is then reduced back to the 2+ state by guanine in DNA (bpy = 2,2-bipyridine). Catalysis is observed as a current enhancement in the cyclic voltammogram of Ru(bpy) ₃ ²⁺ when DNA is immobilized in the film. As seen in solution, the catalytic enhancement in the nitrocellulose film is lower at 800 mM NaCl than without added salt because electrostatic binding of the Ru(bpy) ₃ ²⁺ to the DNA at low salt increases the catalytic rate constant. The cyclic voltammogram of Os(bpy) ₃ ²⁺ , which does not oxidize guanine, exhibits less current in the presence of DNA because binding to the immobilized DNA precludes communication of the metal complex with the electrode. Electrodes modified with poly[C] gave no enhancement; however, catalytic current was observed upon hybridization to poly[G]. Exposure of the poly[C] electrode to random single-stranded DNA gave no catalytic current. Glassy carbon electrodes modified with the membranes behaved in a manner similar to that of the metal oxide electrodes.     

Electrochemical enzyme-linked immunoassay in a DNA hybridization sensor

In most of the currently developed electrochemical DNA hybridization sensors short single-stranded probe DNA is immobilized on an electrode and both the hybridization and detection steps are carried out on the electrode surface. Here we use a new technology in which DNA hybridization is performed on commercially available magnetic beads and detection on solid electrodes. Paramagnetic Dynabeads Oligo(dT)₂₅ (DBT) with covalently bound (dT)₂₅ probe are used for the hybridization with target DNA containing adenine stretches. Target DNA is modified with osmium tetroxide,2,2′-bipyridine (Os,bipy) and the immunogenic DNA-Os,bipy adduct is determined by the enzyme-linked immunoassay with electrochemical detection. Electroinactive 1-naphthyl phosphate is used as a substrate and the electroactive product (1-naphthol) is measured on the carbon electrodes. Alternatively Os,bipy-modified target DNA can be determined directly by measuring the osmium signal on the pyrolytic graphite electrode (PGE). A comparison between determinations of the 67-mer oligodeoxynucleotide on carbon electrodes using (a) the guanine oxidation signal, (b) direct determination of the DNA-Os,bipy adduct and (c) its electrochemical immunoassay showed immunoassay to be the most sensitive method. In combination with DBT, the DNA hybridization of long target deoxyoligonucleotides (such as 67- and 97-mers) and a DNA PCR product (226-base pairs) have been detected by immunoassay at high sensitivity and specificity.     

A microfluidic biosensor based on nucleic acid sequence recognition

The development of a generic semi-disposable microfluidic biosensor for the highly sensitive detection of pathogens via their nucleic acid sequences is presented in this paper. Disposable microchannels with defined areas for capture and detection of target pathogen RNA sequence were created in polydimethylsiloxane (PDMS) and mounted onto a reusable polymethylmethacrylate (PMMA) stand. Two different DNA probes complementary to unique sequences on the target pathogen RNA serve as the biorecognition elements. For signal generation and amplification, one probe is coupled to dye encapsulated liposomes while the second probe is coupled to superparamagnetic beads for target immobilization. The probes hybridize to target RNA and the liposome–target-bead complex is subsequently captured on a magnet. The amount of liposomes captured correlates directly to the concentration of target sequence and is quantified using a fluorescence microscope. Dengue fever virus serotype 3 sequences and probes were used as a model analyte system to test the sensor. Probe binding and target capture conditions were optimized for sensitivity resulting in a detection limit of as little as 10 amol L^–1 (10 pmol L^–1) . Future biosensors will be designed to incorporate a mixer and substitute the fluorescence detection with an electrochemical detection technique to provide a truly portable microbiosensor system.     

Molecular shape,shape of the geometrically active atomic states,and hybridization

In a recent publication [C. A. Nicolaides and Y. Komninos, Int. J. Quant. Chem. 67 , 321 (1998)], we proposed that in certain classes of molecules the fundamental reason for the formation of covalent polyatomic molecules in their normal shape is to be found in the existence of a geometrically active atomic state (GAAS) of the central atom, whose shape, together with its maximum spin‐and‐space coupling to the ligands, predetermines the normal molecular shape (NMS). The shape of any atomic state was defined as that which is deduced from the maxima of the probability distribution ϱ(cos θ₁₂) of the angle formed by the position vectors of two electrons of an N‐electron atom. Because the shape of the GAAS determines the NMS and because the NMS allows the construction of corresponding hybrid orbitals, we examined and discovered the connection between the GAAS shape and Pauling's function for the strength of two equivalent orthogonal orbitals at angle θ₁₂ with one another. It is shown that the computed ϱ(cos θ₁₂) of the GAAS can be cast in a form which allows the deduction of the composition of the hybrid orbitals of maximum spin states with configurations sp³, sp³d⁵, sp³d⁵f⁷, slⁿ, s²lⁿ and the demonstration of the central atom's tendency to form bonds in directions which coincide with the nodal cones of the hybrid bond orbitals. These results not only reinforce the validity of the theory as to the fundamental “mechanism” for the formation in the normal shape of coordination compounds and covalently bonded polyatomic molecules, but also provide the justification for the relevance and importance of the hybridization model. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 25–34, 1999     

Covalent DNA–Streptavidin Conjugates as Building Blocks for Novel Biometallic Nanostructures

Supramolecular aggregates of DNA, RNA, streptavidin, immunoglobulin, and nanocrystalline metal clusters can be generated by self-assembly on the basis of oligonucleotide hybridization (shown schematically). Following selective immunosorption on surface-immobilized antigen, the biometallic hybrid is detectable by electron microscopy.