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Peptide-lipid hybrid vesicles were prepared with complementary DNA strands in their lipid domains. Hybridization of the complementary DNA strands induced the controlled fusion of the vesicles during repeated heating and cooling cycles. Vesicle fusion was indicated by a decrease in the efficiency of Förster resonance energy transfer between lipid-localized probes (from 72 to 42%) and transmission electron microscopy analysis. We suggest that this approach is a general strategy for the creation of polymersomes with membrane-fusion functionality.

The representative DNA-labeling agent 5-ethynyl-2'-deoxyuridine (EdU) was chemically modified to improve its function. Chemical monophosphorylation was expected to enhance the efficiency of the substrate in DNA polymerization by circumventing the enzymatic monophosphorylation step that consumes energy. In addition, to enhance cell permeability, the phosphates were protected with bis-pivaloyloxymethyl that is stable in buffer and plasma, and degradable inside various cell types. The phosphorylated EdU (PEdU) was less toxic than EdU, and had the same or a slightly higher DNA-labeling ability in vitro. PEdU was also successfully applied to DNA labeling in vivo. In conclusion, PEdU can be used as a less toxic DNA-labeling agent for studies that require long-term cell survival or very sensitive cell lines.

Here we report a novel method to form a pseudorotaxane architecture using only a pair of reactive oligodeoxyribonucleotides (ODNs), which we designed and synthesized, and then performed the pseudorotaxane formation reaction with both DNA and RNA oligonucleotides. The reaction proceeded smoothly without any extra reagents at 37 °C and pH 7.2, leading to the formation of a stable complex on a denaturing polyacrylamide gel. Interestingly, the pseudorotaxane was formed with the cyclized ODN reversibly by the slipping process. This new pseudorotaxane formation represents a promising method for developing new DNA nanotechnologies and antisense oligonucleotides.

We have developed a fluorescence detection system for DNA, assisted by a comb-type cationic polymer (PLL-g-DX), for accelerating the reaction turnover. The combination of fluorogenic DNA probes with a comb-type cationic polymer has been demonstrated to be an effective means of signal amplification during the detection process. The method described herein represents a simple and enzyme-free detection., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Oligonucleotide-templated reactions are powerful tools for the detection of nucleic acid sequences. One of the major scientific challenges associated with this technique is the rational design of non-enzyme-mediated catalytic templated reactions capable of multiple turnovers that provide high levels of signal amplification. Herein, we report the development of a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe underwent a rapid templated reaction without any of the undesired background reactions. The fluorogenic reaction conducted in the presence of a template provided a 223-fold increase in fluorescence after 30 s compared with the nontemplated reaction. The probe provided an efficient level of signal amplification that ultimately enabled particularly sensitive levels of detection. Assuming a simple model for the templated reactions, it was possible to estimate the rate constants of the chemical reaction in the presence and in the absence of the template. From these kinetic analyses, it was possible to confirm that an efficient turnover cycle had been achieved, on the basis of the dramatic enhancement in the rate of the chemical reaction considered to be the rate-determining step. With maximized turnover efficiency, it was demonstrated that the probe could offer a high turnover number of 1500 times to enable sensitive levels of detection with a detection limit of 0.5 pM in the catalytic templated reactions.

Equal-opportunity dissolver: By attaching polyethylene glycol at its 5' end, DNA (PEG-DNA) can be solubilized in various organic solvents and was shown to form G-quadruplexes by CD spectroscopy. A complex containing iron(III) protoporphyrin IX (hemin) and G-quadruplex-forming PEG-DNA catalyzed an oxidative reaction in methanol (see scheme)., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We have developed an S(N)Ar reaction-triggered fluorescence probe using a new fluorogenic compound derivatized from 7-aminocoumarin for oligonucleotides detection.

Enzymatic ligation methods are useful in the diagnostic detection of DNA sequences. Here, we describe the investigation of nonenzymatic phosphorothioate--iodoacetyl DNA chemical ligation as a method for the detection and identification of RNA and DNA. The specificity of ligation on the DNA target is shown to allow the discrimination of a single point mutation with a drop in the ligation yield of up to 16.1-fold. Although enzymatic ligation has very low activity for RNA targets, this reaction is very efficient for RNA targets. The speed of the chemical ligation with an RNA target achieves a 70% yield in 5 s, which is equal to or better than that of ligase-enzyme-mediated ligation with a DNA target. The reaction also exhibits a significant level of signal amplification under thermal cycling in periods as short as 100-120 min, with the RNA or DNA target acting in a catalytic way to ligate multiple pairs of probes.

Oligonucleotide has been used as functional molecule such as recording device, or catalyst for chemical reaction. However, that utility has been limited, because it is only soluble in water. Recently, we succeeded in making chemically modified DNA which is clearly soluble in organic solvent. Using this technique, G-quadruplex was constructed in non-polar organic solvent such as 1,2-dichloroethane. The structure was analyzed by CD spectra.

Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points. [ABSTRACT FROM AUTHOR]

Abstract: The cp27 gene is a highly conserved and unique gene with important roles related to craniofacial organogenesis. The present study is a first analysis of the CP27 promoter and its regulation. Here, we have cloned the promoter of the mouse cp27 gene, examined its transcriptional activity, and identified transcription factor binding sites in the proximal promoter region. Two major transcription start sites were mapped adjacent to exon 1. Promoter function analysis of the 5′ flanking region by progressive 5′ deletion mutations localized transcription repression elements between −1993bp and −969bp and several positive elements between −968bp and the preferred transcription start site. EMSA and functional studies indicated two function-cooperative CCAAT boxes and identified the NF-Y transcription factor as the CCAAT activator controlling transactivation of the CP27 promoter. In addition, this study demonstrated that for its effective binding and function, NF-Y required not only the minimal DNA segment length identified by deletion studies, but also a defined nucleotide sequence in the distal 3′ flanking region of the CP27 proximal promoter CCAAT box. These results provide a basis for our understanding of the specific regulation of the cp27 gene in the NF-Y-mediated gene transcription network. [Copyright &y& Elsevier]

DNA is recognized as a nanomaterial, not as a biological material, in the research field of nanotechnology. This article reviews recent research on nanowires, nanoarchitectures, computing, aptamers, biocatalysts, devices, and machines using DNA. In these works, the characteristics of DNA including facile synthesis by the solid-phase method, self-assembly, electro-conductivity, information elements, amplification, switching, molecular recognition, and catalytic functions, were appropriately applied. Multiple functions of DNA could be used simultaneously, and activated independently, by molecular switching. Therefore, the combinations of functional sequences of DNA can produce unique materials. It is obvious that the DNA molecule is one of the most promising functional nanomaterials. However, the application of DNA molecules is still under study because of the big gap that exists between theory and practice. We eagerly anticipate a ‘coming out’ of DNA due to breakthroughs in nanobiotechnology. [Copyright &y& Elsevier]

Describes the development of a binding assay using vitro oligodeoxyribonucleotides (DNA). How the DNA were obtained; Binding of the DNA to the target molecule, thyroxine; Detection of thyroxine in liothyronine; Chemical structure of liothyronine.

Abstract: We have synthesized a 2′-aminomethyl branched-chain sugar nucleoside phosphorodithioate from 2,2′-anhydro uridine and subjected the material to a subsequent cyclization reaction under aqueous conditions using bi-functional linkers. The rate of the cyclization reaction was dependent on the leaving group on the bi-functional linkers. The generation of a chiral phosphorous peak from the achiral precursor, as indicated by 31P NMR, was identified as a good indicator for potentially probing the local and global features of the DNA structure. [Copyright &y& Elsevier]