In Plasmodium falciparum, deoxyguanylate was found to be a substrate for several DNA metabolizing enzymes. Guanylate kinase utilizes dGMP with very low specificity, which is estimated to be the lowest among well-known prokaryotic and eukaryotic enzymes. Furthermore, thymidylate kinase, which is a pyrimidine specific enzyme, was found to phosphorylate dGMP with a surprisingly high...
L/F-transferase is known to catalyze transfer of hydrophobic amino acids from aminoacyl tRNA to the N-terminus of a protein possessing lysine or arginine as the N-terminus. Combining L/F-transferase with E. coli phenylalanyl-tRNA synthetase (ARS), we achieved non-ribosomal N-terminal-specific introduction of various kinds of nonnatural amino acids to a protein. A nonnatural amino...
Modified DNA containing silylated pyrene derivative at the 5′-terminus showed the obvious discrimination ability of the duplex formation, that the modified DNA showed the strong fluorescence emission in the presence of the complementary DNA, in spite of the very weak emission in the absence of the complementary DNA. The intensity of the fluorescence emission of the double strand...
Pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to increase the apparent Stokes’ shift of perylene. Multiple donors were introduced in the vicinity of acceptors via D-threoninol and natural base pairs were inserted between donors and acceptors in order to suppress undesired interactions between them. When two pyrene moieties were located in proximity to one...
We describe the synthesis and properties of oligonucleotides (ONs) containing biaryl units, which are composed of a bis(hydroxymethyl)benzene residue and a naphthalene or pyrene moiety. We found that by introducing the biaryl units into the ONs, the aromatic chromophores are suitably arrayed in the DNAs. Further, we succeeded in the detection of a single-base mismatch in RNA by...
Over the past few years, molecular oncology research has revealed that abnormalities in both protein coding genes (PCGs) and noncoding RNAs (ncRNAs) can be identified in tumors and that the interplay between PCGs and ncRNAs is causally involved in the initiation, progression and metastases of human cancers. MicroRNAs (miRNAs), which are among the most studied ncRNAs, are small 19...
For more effective DNA triplex formation under neutral conditions, we synthesized triplex-forming oligonucleotides (TFO) containing 8-thioxodeoxyadenine (s8A) residues in place of the protonated cytosines (Cs) required for the third base pairing with DNA duplexes. Consequently, it was found that s8A exhibited much stronger hybridization ability than C under neutral conditions...
When designing ligands for specific sequences in DNA duplexes, triple helix formation is a useful recognition motif, because base triplet formation is based on the simple rule of complementary Hoogsteen hydrogen bonding, CG.C+ and TA.T. However the triplexes containing CG.C+ triplets form only in a weak acidic solution, because cytosines in third strand need to be protonated to...
We report the synthesis and metal ion-binding properties of DNA duplexes containing 5-substituted uracil (XU) pairs, such as 5-bromouracil, 5-fluorouracil and 5-cyanouracil pairs. Thermal denaturation studies of these modified DNA duplexes revealed that the DNA duplexes were stabilized in the presence of HgII ions in acidic and neutral solutions. On the other hand, the duplexes...
Small silencing RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), regulate expression of their target genes via RNA-induced silencing complex (RISC). RISC assembly follows complex, ordered pathways, and RISC function is as diverse as cleavage, translational repression, and deadenylation of the target. We have recently shown how siRNAs and miRNAs are...
We have developed 2′-O-methyl-RNAs having phosphorylated cyclohexane at the 5′ and/or 3′-terminal adenine. These 2′-O-methyl-RNAs formed less stable duplex with the longer target RNA than that with the short target RNA. We tried to improve the short-RNA selective hybridization property by the synthesis of 2′-O-methyl-RNAs having terminal guanine modifications.
Three kinds of novel bridged nucleic acid (BNA) monomers bearing carbamate or urea bridged structures, were designed and synthesized. One of these monomers, a urea-type BNA monomer was successfully incorporated into oligodeoxynucleotides (ODNs), and properties of the ODNs were evaluated. The ODNs containing the urea-type BNA monomers showed RNA selective hybridizing profiles and...
P-Stereodefined oligodeoxyribonucleoside boranophosphates (PB-ODNs) were succecfully synthesized by the conversion of diastereopure H-phosphonate intermediates. Thermal denaturation studies clearly showed that the duplex stability of PB-ODNs with the complementary DNA and RNA depends on the stereochemistry of the boranophosphate linkages.
Next generation 4′-selenonucleosides as potential antiviral and antitumor agents were synthesized using a Pummerer type condensation as a key step.
Synthesis of benzoquinone ansa-adenosines, which are rationally designed as Hsp90 inhibitors by extracting and fusing a natural substrate, ATP, and a natural product, geldanamycin, was described. This simpler scaffold design provides practical synthesis of a set of analogs and demonstrates synthetic innovation.
Type your abstract here. (Font: Times or Times New Roman, 10 pt, bold) Access to DNA sequence information on a genomic scale has enabled the design of large sets of oligonucleotides for high-throughput assays. The ability to synthesize oligonucleotides directly from sequence information has facilitated many key advances in genomics, including the development of synthetic biology...
A solid phase oligonucleotide (ON) synthesis on porous silicon (PSi) chip is presented. The prepared Si- OH surface were analyzed by FT-IR and the OH functions were quantified by reaction with 3′- phosphoramidite nucleotide building block. Short ONs were synthesized on the chip surface and the coupling yields evaluated.
Synthesis of new non-nucleosidic building blocks that incorporate 2,2′-biquinoline is described. Starting from readily available bicinchoninic acid, the corresponding bifunctional monomeric reagents for solid-phase oligonucleotide synthesis, phosphoramidite and H-phosphonate, have been prepared. The compounds developed may be useful for the design of sequence-specific artificial...
Naphthalenediimide (1) carrying two β-cyclodextrins (βCDs) was successfully synthesized by click chemistry between pentynylnaphthalenediimide and azido βCD. Absorption spectra of 1 showed hypochromic and red shifts upon addition of sonicated calf thymus DNA as a double stranded DNA. Kinetic studies showed its slow association with and dissociation from calf thymus DNA. These...
We have reported that poly(l-lysine)-graft-dextran (PLL-g-Dex) accelerates DNA hybridization and increases stability of a double stranded DNA (dsDNA). Furthermore, PLL-g-Dex was found to stimulate the DNA strand exchange reaction between dsDNA and its complementary single stranded DNA (ssDNA). In order to better understand these phenomena, we evaluate PLL-g-Dex/DNA interaction by...
Water-soluble PEG derivatives having both amino- and carboxyl-pendants (PEG-ACs) were synthesized, and examined for their transcription- and transfection-enhancing activity on DNA/polycation complexes. PEG-AC could be deposited onto the surface of DNA/polyethylenimine(PEI) complexes, and enhanced their transcriptional activity. Fluorescence anisotropy study showed that the...
Loop-loop interactions mediate the recognition between RNA hairpins leading to the formation of so-called kissing complexes. Both the size and the sequence of the loop are critical for ensuring stable interaction. Using in vitro selection we have characterized a few loop sequences that lead to the formation of highly stable kissing complexes. These sequences constitute targets of...
We describe a new strategy for multi-pyrene-modification of RNA sequences to form a unique structure of pyrene arrays on duplex RNA that exhibits remarkably strong excimer fluorescence.
We studied the RNA oligomers having pyrenylmethyl substituents at the 2′-O-sugar residues. It has been shown that the pyrene-modified RNAs can form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism spectra revealed that the multiply incorporated pyrenes are projected toward the outside of RNA duplexes and...