Oligonucleotide that can reversibly alter the duplex-forming ability in response to an external factor has potential to be applied to various genome technologies, e.g. antisense and gene diagnosis technology. A novel bridged nucleoside which is capable of sensing an oxidant and reductant was designed and synthesized. The nucleoside formed a disulfide bridge between C2′ and C4...
Palladium on carbon-ethylenediamine complex [Pd/C(en)] catalyzed deuteration of N6-benzyladenine-d5, which is a plant growth regulator, to introduce 5 deuterium atoms, while use of Pd/C as a catalyst led to a complete removal of N6-benzyl group. The corresponding deuterated N6-benzyladenine was successfully used as a surrogate compound for the quantitative analysis of residual...
Synthesis of 5′-fluoro-2′-β-methylneplanocin analogues (5) was carried out. The cyclopentenone 16 was prepared from methyl mannopyranoside by using ring closing metathesis, stereoselective introduction of methyl group, and seleno cyclization as representative steps. Introduction of a fluorine atom was conducted by electrophilic fluorination. Antiviral activity of 5 will also be...
With an aim to synthesize 4′-substituted cordycepins, the 4′-phenylthio precursor 4 was prepared from adenosine through an electrophilic addition to the 3′,4′-unsaturated derivative 2 by using NIS/PhSH system. Nucleophilic substitution of 4 with a series of alcohols in the presence of NBS gave the respective 4′-α-alkoxy cordycepins 6 as the major stereoisomer. Use of DAST, in...
Synthesis of 4′-C-ethynyl-2′-deoxy-4′-thionucleosides was carried out based on electrophilic glycosidation using 4-C-ethynyl-4-thiofuranoid glycal. The glycal 15 was prepared as follows: oxidative cleavage of 6 with Pb(OAc)4 forming the aldehyde 7, aldol reaction of 7 and subsequent silylation to furnish 8, conversion of the formyl group of 8 into an ethynyl group, and finally β...
Several 9-(2-C-cyano-2-deoxy-l-β-D-arabino-pentofuranosyl)purine derivatives were tested against Kaposi's sarcoma-associated herpesvirus (KSHV)-infected primary effusion lymphoma (PEL) cells. The guanine derivative (2, CNDAG) as well as the 2-amino-6-substituted-purine derivatives 3, 4 and 5 inhibited KSHV-positive cell growth but showed no cytotoxicity against KSHV-negative...
Evanescent-field-coupled (EFC) waveguide-mode sensors recently been shown to be suitable for detecting various biomolecules. In the present studies, we demonstrated that both nucleic acids hybridization and nucleic acids-protein interactions can be analyzed using perforated evanescent-field-coupled waveguide-mode nanobio-sensors.
In bacteriophage λ, formation of a transcriptional antitermination complex consisting of the λ N protein, nut RNA transcript (boxA-boxB), host factors, and RNA polymerase is mediated by the interaction of the boxB RNA with the RNA-binding domain of N. In order to understand the spacial requirements of this boxB/N interaction within the complex, the effects of changes in the...
A 2′-deoxyuridylate dimer cyclized via cross-linkage by an ethylene (UetpU) or a propylene (UprpU) linker at the 5-position was incorporated into DNA oligomers. Fluorescence resonance energy transfer (FRET) experiments showed that they bent at approximately 90°. We investigated binding abilities of UetpU and UprpU DNA oligomers to HMGB1 A-box protein, which specifically binds to...
Human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) is known to play a role in intrinsic cellular immunity against human immunodeficiency virus type 1 (HIV-1). The antiretroviral activity of APOBEC3G is associated with hypermutation of viral DNA through cytidine deamination. APOBEC3G contains two cytidine deaminase domains that are characterized by...
All living organisms store the information necessary to maintain life in their DNA. Any process that damages DNA and causes loss or corruption of that information threatens the viability of the organism. One-electron oxidation is such a process. Loss of an electron from DNA generates a radical cation that is located primarily on its nucleobases. The radical cation migrates...
The novel multi-arm DNA structures were designed using 2D-DNA Origami method, and these structures were folded into 3D hollow prism structures by introduction of connection strands into the arms. The opening of the prism structures were examined by a high-speed AFM, which showed the dissociation events of the connecting arms in the 3D-structures.
Triplex-forming oligonucleotides bind in the major groove of duplex DNA, generating three stranded structures containing T.AT and C+.GC triplets. Their sequence specific binding has potential uses in gene targeting but is limited by their low affinity, the requirement for low pH and the need for oligopurine targets. We have prepared nucleotide analogues to overcome these...
Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel...
Efficient methods for the modification of RNA molecules have been expected as innovative biological tools and therapeutic methods. In this study, the development of a general method for site-specific RNA modification by the functionality-transfer ODN probes has been investigated. Site-specific and cytosine-selective RNA modifications were achieved by the functionality-transfer...
We designed and synthesized dumbbell-shaped nanocircular RNAs for RNA interference applications, which consist of a stem and two loops1. RNA dumbbells are specifically recognized and cleaved by the human Dicer enzyme, and are thus transformed into double-stranded RNA in cells, although this RNA is resistant to degradation in serum. The structure was optimized to maximize its RNAi...
Telomeric repeat-containing RNA is a non-coding RNA molecule newly found in mammalian cells. However, structure and function of the telomeric RNA in chromosome ends have not yet been elucidated. Using a combination of NMR, CD and MALDI-TOFMS experiments, we have demonstrated that human telomere RNA can form a parallel G-quadruplex structure. Furthermore, we successfully found for...
The intermolecular DNA quadruplex is attractive materials for design of nanomolecular constructs and machines. This folding kinetics is, however, slow, hampering its application to these materials. We have reported that the cationic comb-type copolymer accelerated duplex and triplex formation. In this study, the effect of the copolymer on the intermolecular quadruplex folding was...
We examined the effects of molecular crowding conditions on the structures and thermodynamics of three-way junctions (TWJs) of DNA. To explore the crowding effects on the junction point, we further evaluated the number of water molecules associated with the whole TWJ as well as the individual arms. It was found that the number of water molecules taken up by the whole TWJ was...
Introduction of therapeutic genes into the cells of an organism in a safe and efficient way has become a challenging task in non-viral mediated gene therapy. Here, branched polyethylenimine (bPEI, 25 kDa) was converted into nanoparticles through electrostatic interactions with anionic polysaccharides (e.g. alginic acid, Al and hyaluronic acid, HA). A small library of PEI-Al and...
Recently, various microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) have been identified and play important roles in gene regulatory networks. However it is a little known about their biological functions. These small RNAs exhibit their function to form a ribonucleoprotein complex, the RISC (RNA-induced silencing complex), which modulates gene expression by...
DNA damage was monitored by fluorescent microscopy observations of DNA fluorescent images after hydrodynamic stretching on a microscope glass. DNA double-strand breaks lead to a decrease of the average length of observed fluorescent DNA molecules. Compared to conventional methods such as electrophoresis, the proposed method allows for the analysis of the DNA damage at very low...
We chemically synthesized a series of aminooxy derivatives to develop novel probes for sensitive detection of abasic (AP) sites in DNA. The results of the conjugation reactions showed that the probes could efficiently react to AP sites by introducing an aromatic or a guanidino group in their structures. In particular, the probe having both functional groups showed the most...
Accumulation of genetic changes due to the presence of unrepaired DNA lesions can lead to cancer development and other diseases. Nucleic acid modifications also play key roles in many essential life processes. We have developed a series of chemically modified nucleic acid analogues that can be applied to stabilize protein-nucleic acid interactions for structural and proteomic...
Several human pathogens possess nucleoside or nucleotide kinases with large substrate specificity compared to their human counterparts. This phenomenon has been successfully exploited for the specific targeting of prodrugs such as Acyclovir against herpes virus. Combined structural and biochemical studies of these enzymes can thus provide essential information for the rational...