Changes in Rat Retinal Ganglion Neuronotrophic Factor and Its mRNA During Postnatal Development

The monoclonal antibody specific to the retinal ganglion neuronotrophic factor (RGNTF) was used to localize and quantify the presence and amount of RGNTF during the postnatal development of the visual system in the rat.The results showed that in the 0-1-day age group, neurons at the superficial layers and deep part of superior colliculus, and as well as retinal ganglion cells were strongly stained with their RGNTF contents quantified to be 88%, 100% and 100%, respectively. In the 5-6-day age group, RGNTF contents were significantly reduced to merely 50%, 30% and 80%, respectively.The RGNTF contents reduced further to 0% as age increased to 2 years old. A ~(32)P-DNA probe specific to the first 7 amino acid sequence of RGNTF at its N-terminal end was synthesized and used for in situ hybridization studies. The results revealed that strong hybridized signals (i.e. mRNA of RGNTF) were localized in the same neurons in the superficial layers and deep part of the superior colliculus only in the 0-1-day age grou     

Gold Nanoparticle‐Catalyzed Silver Electrodeposition on an Indium Tin Oxide Electrode and Its Application in DNA Hybridization Transduction

In this work, we report a simple, rapid and sensitive approach for the electrochemical gold nanoparticle‐based DNA detection with an electrocatalytic silver deposition process. The catalytic and preferential silver electrodeposition on gold nanoparticle surfaces using an indium tin oxide (ITO) electrode at certain potentials, without any chemical pretreatments of the electrode, is demonstrated. More importantly, the application of this methodology for hybridization transduction is explored. The ITO electrode surface is first coated with an electroconductive polymer, poly(2‐aminobenzoic acid), to enable the chemical attachment of avidin molecules for the subsequent probe immobilization. The hybridization of the target with the probe in turn permits the binding of the gold nanoparticle labels to the transducer surface via biotin‐streptavidin interaction. The amount of bound gold labels, which is proportional to the amount of the target, is determined by the electrocatalytic silver deposition process. A significant improvement of the signal‐to‐background ratio is achieved with this scheme compared to the conventional chemical hydroquinone‐based silver deposition process.     

A Single‐Surface Electrochemical Biosensor for the Detection of DNA Triplet Repeat Expansion

Molecular diagnostics of inherited neurodegenerative disorders such as fragile X syndrome, myotonic dystrophy or Friedreich ataxia (FRDA) is based on analysis of the length of trinucleotide repetitive sequences in certain loci of genomic DNA. The current methods employ PCR and electrophoretic determination of the amplified DNA fragment size. We have recently shown that length of a triplet repetitive DNA sequence can be determined using a double‐surface electrochemical technique involving multiple hybridization of the expanded triplet repeat with short labeled reporter probe (spanning several trinucleotides). Here we propose a single‐surface sensor employing an analogous principle. Target DNA (tDNA) is adsorbed onto surface of a carbon (pyrolytic graphite or screen‐printed) electrode. Biotin‐labeled reporter probe (RP) is hybridized with the immobilized tDNA followed by binding of streptavidin‐alkaline phosphatase (ALP) conjugate. The ALP catalyzes production of an electroactive indicator (1‐naphthol) which is detected voltammetrically on the same electrode. Signal resulting from this electrochemical enzyme‐linked DNA hybridization assay is normalized to the amount of tDNA immobilized at the transducer surface either by measuring intrinsic tDNA voltammetric response, or using electrochemical labeling of the tDNA with osmium tetroxide 2,2′‐bipyridine complex. Detection of (GAA)_n?(TTC)_n triplet repeat expansion in nanogram quantities of PCR‐amplified tDNAs, including amplicons of patients' genomic DNA, is demonstrated. We show that our technique allow differentiation between normal and pathological alleles of X25 gene related to the FRDA.     

DNA and RNA sensor

The development of DNA sensors attracts recentresearch attention directed at gene analysis, such asdetection of genetic disorders, tissue matching andforensic applications[1,2]. In general, sensors based on the principle differ-ent from that of the tr…     

Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a library has an equal melting temperature. Each nucleotide adds its increment to the oligonucleotide temperature and it is assumed that A and T add 2 degrees C and C and G add 4 degrees C. The hybridization experiment using isothermic libraries should provide data with a lower number of errors due to an expected similarity of melting temperatures. From the computational point of view the problem of isothermic DNA sequencing with errors is hard, similarly like its classical counterpart. Hence, there is a need for developing heuristic algorithms that construct good suboptimal solutions. The aim of the paper is to propose a heuristic algorithm based on tabu search approach. The algorithm solves the problem with both positive and negative errors. Results of an extensive computational experiment are presented, which prove the high quality of the proposed method.     

Tuning the Hybridization of Local Exciton and Charge‐Transfer States in Highly Efficient Organic Photovoltaic Cells

Decreasing the energy loss is one of the most feasible ways to improve the efficiencies of organic photovoltaic (OPV) cells. Recent studies have suggested that non‐radiative energy loss ( ) is the dominant factor that hinders further improvements in state‐of‐the‐art OPV cells. However, there is no rational molecular design strategy for OPV materials with suppressed . Herein, taking molecular surface electrostatic potential (ESP) as a quantitative parameter, we establish a general relationship between chemical structure and intermolecular interactions. The results reveal that increasing the ESP difference between donor and acceptor will enhance the intermolecular interaction. In the OPV cells, the enhanced intermolecular interaction will increase the charge‐transfer (CT) state ratio in its hybridization with the local exciton state to facilitate charge generation, but simultaneously result in a larger . These results suggest that finely tuning the ESP of OPV materials is a feasible method to further improve the efficiencies of OPV cells.     

Specific liquid DNA hybridization kinetics measured by fluorescence polarization

The kinetics of specific DNA hybrid formation were monitored directly in solution. Detection was based on fluorescence polarization measurements of labelled oligonucleotides at different stages during the hybridization. The effect of mismatched base pairs on the kinetics was measured. Significant differences could be observed in the kinetics when as few as three mismatches were introduced by the polymerase chain reaction technique in the target DNA sequences.     

Rapid Synthesis of Propargyl-γ-Modified Peptide Nucleic Acid Monomers for Late-Stage Functionalization of Oligomers

The exceptional hybridization properties of peptide nucleic acids (PNAs) coupled with the ease of their synthesis has made this artificial nucleic acid mimetic a desirable platform for diagnostics, therapeutics and supramolecular engineering. PNA backbone modifications have been extensively explored to finetune physicochemical properties and for conjugation of functional molecules. Here, we detail the synthesis of a universal γ-propargyl-PNA backbone from serine, and its acylation with the four DNA canonical nucleobases. The availability of serine as d or l enantiomer provide simple accesses to PNA oligomers for hybridization with natural oligonucleotides or for orthogonal hybridization circuitry. We show that late-stage conjugation enables optimization of the physicochemical properties. This approach is appealing due to its orthogonality to Fmoc-SPPS, its flexibility and ease for introducing diversity by on-resin copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). We exemplified the utility of these novel monomers with PNA based hybridization chain reactions (HCRs).     

Integrating Photoluminescence and Ferromagnetism in Carbon Quantum Dot/ZnO by Interfacial Orbital Hybridization for Multifunctional Bioprobes

Integrating ferromagnetism (FM) and photoluminescence (PL) into one particular nanostructure as biological probe plays an irreplaceable role in accurate clinical diagnosis combining magnetic resonance and photoluminescence imaging technology. However, magnetic emergence generally needs a spin polarization at Fermi level to display a half-metallic electronic feature, which is not beneficial for preserving radiation recombination ability of photo-excited electron-hole carriers. To overcome this intrinsic difficulty, we propose a feasible atomic-hybridization strategy to anchor carbon quantum dots (CQDs) onto ZnO microsphere surface via breakage of C=O bonds at CQDs and subsequent Zn-3d and C-2p orbital hybridization, which not only ensures the carrier recombination but also leads to a room-temperature magnetism. Herein, the photoluminescence and magnetism coexist in this multifunctional heterojunction with outstanding biocompatibility. This work suggests that integration of magnetism and photoluminescence could be accomplished by particular interfacial orbital hybridization.     

An easily-automated assay for the physiological state quantification of Pseudomonas sp. M18

In order to foreknow poorly performing cultures before wasting energy to scale them to large cultures, industrial microbial fermentation can greatly benefit from knowledge of the physiological state of cells. The method currently proposed is an easily automated physiological state determination method. We have designed one universal rRNA-specific probe for bacteria and developed novel signal probe hybridization (SPH) assay featuring no RNA extraction and no PCR amplification steps necessary to quantify the physiological state of microbial cells. The microbial cell was lysed with sonication and SDS. Signal probes were applied to hybridize and protect the rRNA target. S1 nuclease was then applied to remove the excessive signal probes, the single-stranded RNA and the mismatch RNA/DNA hybrids. The remaining signal probe was captured with a corresponding capture probe immobilized on a microplate and quantified with a horseradish peroxidase-conjugated color reaction. We then systemically optimized our assay. Results showed that the cell limit of detection (LOD) and the cell limit of quantification (LOQ) were 2.64 × 10⁴ cells and 9.86 × 10⁴ cells per well of microplate, respectively. The limit of detection (LOD) and the limit of quantification (LOQ) of signal probe were 49.0 fM and 344.0 fM respectively. Using this technique, we quantified the 16S rRNA levels during the fermentation process of Pseudomonas sp. M18. Our results indicate that the 16S rRNA levels can directly inform us about the physiological state of microbial cells. This technique has great potential for application to the microbial fermentation industry.