Modulation of biological network constituted by diverse interactions among biologically active molecules has provided innovative biotechnologies. Here, we report RNA aptamers that bind to photoresponsive peptide (KRAzR; Lys-Arg-Azobenzene-Arg) containing azobenzene chromophore, which can change its geometrical structure by phohtoirradiation. Aptamers were identified by 10 cycles...
In this study, cationic dyes (methylstilbazole) were introduced into ODN. When two complementary ODNs, both of which tethered this dye, were hybridized, the melting temperature drastically increased. The duplex was further stabilized by introducing multiple dyes.
New hetero aggregates where different dyes stacked alternately were prepared by hybridizing two DNAs, each of which tethered a different dye in the centre of strand. Spectral changes due to exciton coupling between different kinds of dyes were observed. Especially, hetero aggregates of Methyl Red and 2- nitro-4′-dimethylaminoazobenzene showed substantial narrowing of the band...
A photoresponsive DNA nano-pincette was constructed by using azobenzene-modified DNA as materials. When the azobenzene-modified part hybridizes with its complementary sequence on the pincette, the duplex formation closes it. On the contrary, the pincette is opened after the formed duplex dissociates. Based on reversible photoswitching of this DNA hybridization, the pincette...
The present paper reveals that double crossover-DNAs (DX) serve as scaffolds for the multiple arrangement of a [Ru(bpy)3]2+-bound zinc finger (ZF) protein, Ru-ZF. This series of results would lead to the realization of the two-dimensional arrangement of functional molecules and nanomaterials on DX-tiles.
We report the direct modification of SPIOs with a biomolecule, and the sequence-specific assembly of the modified SPIOs was achieved with the aptamer-small molecule interaction. In addition, the transverse relaxation rate of the aqueous solutions containing the modified SPIOs was altered by the dispersion state.
In this work the trapping and conversion of visible light energy into chemical energy is examined using a supramolecular assembly. This consists of a light absorbing antenna and a porphyrin redox centre both covalently attached to a DNA strand, which in turn is bound to a lipid membrane. The excitation energy is finally trapped as a benzoquinone radical anion that could...
DNA structures made of guanine tetrads present remarkable properties and are thus first choice candidates for applications in nanofabrication. Starting from the work of Kotlyar et al., we report here that the klenow exo− fragment of DNA polymerase I can extend poly(dG)-poly(dC) from various 5′-modified (dG)10− (dC)10 templates. This allows the production of end-functionalized...
The inherent self-assembly properties of DNA make it ideal in nanotechnology. We present a fully addressable DNA nanostructure with the smallest possible unit cell, a hexagon with a side-length of only 3.4 nm.2,3 Using novel three-way oligonucleotides, where each side has a unique double-stranded DNA sequence that can be assigned a specific address, we will build a non-repetitive...
Tape-like DNA nanostructures of 26 nm width with regularly arranged nanometer-scale wells have been prepared by bundling nine DNA helices. Just one streptavidin tetramer (d = 5 nm) is size-selectively captured in each 6.8 × 10 × 2.0 nm well when two biotins are attached to two opposite edges of the well. Accordingly, precise streptavidin nanoarray of 28 nm periods is constructed...
Oligonucleotides can be covalently linked to peptides composed of any sequence of amino acids by SPFC. The peptides incorporated into the conjugates include nuclear localizing signals (NLS), nuclear export signals (NES), membrane fusion domain of some viral proteins and some designed peptides with amphipathic character. Evaluation of biological properties of DNA-peptide...
The poly(1-vinylimidazole) (PVIm) with sever al alkyl groups has been synthesized as a new pH-sensitive DNA car rier. The resulting alkylaed PVIm (PVIm-R) was water -soluble in spite of the hydrophobic alkyl groups and the deprotonation of the imidazole groups at physiological pH. Hemolysis assay showed the PVIm-R enhanced membr ane disruptive ability at endosomal pH, owing to...
Photochromic molecules, or photochromes, can be reversibly isomerized between two, more or less, thermally stable forms by exposure to light of different wavelengths. Spiropyrans is an important group of photochromes which in their colorless initial state consist of two ring systems connected at a spiro carbon in a closed orthogonal fashion (1c in Scheme 1). Upon irradiation by...
The steady-state fluorimetric titration curves for trimeric purine nucleoside phosphorylase (PNP) by two ligands, were analysed using the DynaFit program. Results of this analysis indicate that three binding sites of PNP molecule interact with each other and that the character of this interaction is different for both ligands. The DynaFit program is very useful in studies of...
A simple and in principle universal method is proposed for measuring enzyme/ligand dissociation constants. The method is based on measuring enzyme activity remaining after heat treatment in the absence and in the presence of ligands. The method is especially suitable for enzymes interacting with nucleosides, nucleosides and oligonucleotides since for such enzymes convenient...
We here describe the synthesis of a series of novel bicyclic ribonucleoside derivatives, with 18-crown-6 ether moieties attached via their ribose 2- and 3- positions, as first examples of crown ether ring-fused nucleosides, to be evaluated as antiviral and/or antitumoral agents.
A number of structurally diverse nucleoside phosphonic acids have been tested against human recombinant thymidine phosphorylase and human platelets supernatant using 2′-deoxy-5-nitrouridine as the substrate. We have selected several inhibitors working at micromolar level as lead structures for further evaluation.
The Gibbs binding energy and entropy/enthalpy contributions to the interaction of calf spleen purine nucleoside phosphorylase (PNP) with the novel multisubstrate analogue DFPP-DG, as well as with DFPP-G and (S)-PMP-DAP were determined by fluorescence and calorimetric studies. Results were compared with findings for guanine - a natural reaction product and inhibitor.
We synthesized a series of carbocyclic nucleoside inhibitors of cytidine deaminase (CDA) based on a seven-membered 1,3-diazepin-2-one moiety. In the key step, the seven-membered ring was formed by a ring-closing-metathesis reaction. Therefore, the bis-allylurea moiety had to be protected by benzoylation in order to obtain an orientation suitable for ring closure. To our surprise...
Various methods were used in the syntheses of a number of pyrimidine acyclic nucleoside phosphonates and their derivatives such as a nucleophilic fluorination, Suzuki–Miyaura coupling reactions and phosphorylation. These new compounds were further investigated for their potential biological activity. Based on results obtained the ability to inhibit human thymidine phosphorylase...
There is a need for novel, effective, and cell- and gene-specific therapeutics for cancer. Modified oligonucleotides can be used to modulate specifically and potently the expression of several genes that are upregulated in breast and prostate cancer and have been found to be causal to the tumor phenotype. Synergistic downregulation of these genes may be a potent therapeutic...
Dendritic cell (DC) development begins in the bone marrow and immature progenitors reach their sites of residence in lymphoid organs. The mechanism of DC development in the bone marrow and in peripheral lymphoid organs is poorly understood. Here, we examined the effects of synthetic oligodeoxynucleotides containing a CpG motif (CpG-ODNs) on the development of DC from the bone...
We have established structure-activity relationships of novel truncated D-4′-thioadenosine derivatives from D-mannose as potent and selective A3 adenosine receptor (AR) antagonists. At the human A3 AR, most of N6-substituted analogues showed high potency and selectivity and acted as pure antagonists in a cyclic AMP functional assay. Among compounds tested, 2-chloro-N6-3...
4-Seleno analogue of 1-β-arabinofuranosyl cytosine (ara-C) was synthesized via 4′-selenouridine as a key intermediate, which was easily prepared from D-ribose. The arabino configuration was achieved by chemoselective ring opening of the 2,2′-anhydro-4′-selenouridine. The synthesized 4′-seleno-ara-C showed potent antitumor activity (IC50 = 1.5 μM) against stomach cancer cells...
Novel 2-5A analogs composed of 3′-O, 4′-C-alkylene adenosine were synthesized as potent RNase L activators. When we examined their properties, including their RNase L activating ability and their stability to exonuclease, we found that these 2-5A analogs showed high RNase L activation and high resistance to enzymatic degradation without the modification of an essential adenosine...