Nucleic acids research. Supplement (2001)最新文献

Phosmidosine and a variety of its analogs were synthesized by reaction of N-diisopropyl-N'-(N tritylaminoacyl)phosphorodiamidite derivatives with appropriately protected 8-oxoadenosine derivatives. It was found that replacement of the methyl group of the N-acylphosphoramidate linkage with longer alkyl groups resulted in significant stabilization of the ester linkage. Among the phosmidosine analogs synthesized, the O-ethyl derivative was easily synthesized and was found to be sufficiently stable under acidic and neutral conditions. These stable phosmidosine analogs exhibited similar antitumor activities against several cancer cell lines. The structure-activity relationship is also discussed.

Stretched single DNA molecules were prepared on substrates by Langmuir-Blodgett (LB) method for the restriction site mapping. Stretched single Lambda DNA and EcoRI bound to the DNA were observed by scanning near-field optical microscope (SNOM). As a result, the specific binding sites of EcoRI on the Lambda DNA molecules were determined.

N-terminal specific radioisotope (RI) labelling of a protein posessing lysine as the N-terminal residue (Lys-XBD) was achieved under mild enzymatic reaction condition using L/F-tRNA-protein transferase. To expose a single lysine moiety only at the N-teminal site, we overexpressed pelB signal peptide-Lys-XBD fusion protein using the bacterial expression host BL21(DE3). The pelB signal peptide was sponteneously cleaved in E. coli to obtain the desired Lys-XBD.

Nicotinamide 8-Br-hypoxanthine dinucleotide (8-Br-NHD+) was cyclised at the N-1 position by ADP-ribosyl cyclase from Aplysia californica to give cyclic 8-Br-inosine diphosphoribose, a novel membrane-permeant analogue of cyclic-ADP ribose and agonist in human T cells. Adenine-substituted analogues of adenophostin A with potent Ca2+ releasing activity were synthesized; docking studies using the binding core of the Ins(1,4,5)P3 receptor identified specific residues that could be of importance in determining the hyperagonist nature of adenophostin activity.

We could obtain the DNA aptamers that can bind strongly and selectively to ATP (Ka = 6.7 x 10(7) M(-1)) from four way junction random DNAs by using in vitro selection on a quartz-crystal microbalance.

To array Cu2+ ions within a double-stranded DNA along the helix axis in a controllable manner, a series of artificial oligonucleotides, d(5'-GHnC-3') (n = 1-5), were synthesized, where H is a hydroxypyridone nucleobase. Right-handed double helices of the oligonucleotides, nCu2+ x d(5'-GHnC-3')2 (n = 1-5), were quantitatively formed through Cu2+-mediated metallo-base pairing (H-Cu2+-H). The Cu2+ ions incorporated into each duplex were aligned along the helix axes with the Cu2+-Cu2+ distance of 3.7 +/- 0.1 A. The unpaired d electrons of the Cu2+ ions were coupled ferromagnetically with one another to form magnetic chains.

The photochemical DNA computing of 5-vinyluracil ((V)U) containing oligodeoxynucleotides (ODNs) tethered multiple "DNA words" is demonstrated. A new MARK and UNMARK operation based on the (V)U mediated reversible DNA photoligation has been developed for multiple-word DNA computing. The utility of this operation for DNA computing is demonstrated by solving a small Satisfiability problem (SAT problem) in which information was encoded in three tandem words.

RNA molecules express the specific structure containing A-form helices and non-helical regions, such as loops and bulges. The adenosine moiety plays a key role in helical packing and/or loop and/or bulge interactions. It is well known as A-platform, tetraloop, and A-minor motif. For the formation of these motifs, there are specific interactions to the adjacent RNA segments and/or protein and/or metal ions beside the specific base sequences. The database focusing on adenine's structural roles, structural information about the assemblage and the space distribution of base moieties can be a useful tool. The user can obtain the selected list with the several descriptors including kink parameters for the structure definition and sequence properties. In addition to this nucleic acid system, RNA-drug related compound system would be included.

To select antisense oligonucleotides (AONs) that specifically target the genes of rat organic anion transporting polypeptide (oatp) subtypes, in vitro selection and an alignment program were used. When we incorporated a couple of our original 2'-O,4'-C-ethylene nucleoside (ENA) residues into the AONs at both the 3' and 5' ends, the inhibitory activity of these oatp subtype-specific AONs was enhanced. This strategy of combining in vitro selection with the use of an alignment program as well as incorporating ENA residues, was effective in synthesizing oatp subtype-specific AONs.