Nucleic acids symposium series最新文献

A pro-apoptotic protein Bax is a Bcl-2 family member and forms homodimers and also heterodimerizes with death antagonists, Bcl-2 and Bcl-XL. To elucidate the detail of function of Bax in cells, we constructed a hammerhead ribozyme targeted to the Bax mRNA. The level of Bax protein in Hela-K cells expressing Bax-ribozyme was decreased compared with that of wild type Hela-K cells. Therefore, the Bax-ribozyme should be useful for the future investigations of the details of apoptosis pathway.

In vitro selection has been used as a method to determine the optimal binding site for DNA-binding proteins. We report here in vitro selection of dsDNA sequences that bind to mutated-GCN4-bZIP peptides. The GCN4-bZIP peptide mutated from alanine to histidine on a position-14 that contacts with DNA bound to different sequence from a binding site of wild type peptide.

DNA catenanes have been prepared by the reaction of T4 DNA ligase with linear DNA in the presence of nicked DNA. Single molecular images of DNA catenanes and large circular DNAs have been clearly observed by AFM using a tapping mode at room temperature and in an ambient atmosphere.

Poly-L-lysine(pL) was chemically modified based on two essential features which we recently reported and subjected to the gene-transfer experiment in vitro. Introduction of 25 mol% serine residue to pL slightly enhanced the gene expression level, while trimethylation of epsilon-ammonium groups of lysine did not. Only when pL was modified in both way, giving N2-trimethyl poly(lysine-co-serine), markedly enhanced gene expression was observed. The cellular uptake and localization of DNA in the cells were similar for each cationic polypeptide. DNA forming complex with the polypeptides containing serine residue was found to be well transcribed in in vitro transcription/translation system, suggesting the hydrophilic nature may allow polypeptide/DNA complexes to be recognized by the transcriptional factors and lead the subsequent effective gene expression.

The entire genome of the pRi1724 (217.6-kb) in the mikimopine type Agrobacterium rhizogenes strain MAFF03-01724 has been completely sequenced. The vir region covering 30.2-kb has found to be composed of 21 genes resembling virH1, virA, virB1-11, virG, virC1-2, and virD1-5. The structural organization of the pRi1724 vir operons in this study is exactly the same as that of the previously reported vir operons of other Ri or Ti plasmids, although the size of some ORFs showed little variations among the plasmids. We also found virE3 gene in the pRi1724 (1), but different from Ti plasmids, virE1 and virE2 that are also important for the virulence do not exist in the vir region of pRi1724.

New electrochemically active DNA ligand 1 was synthesized by the connection of ferroceneacetic acid at the terminal amino moieties of two imide substituents of naphthalene diimide. Electrochemical experiments in aqueous solution containing DMSO showed that the selectivity for double stranded DNA of 1 has increased from that of ligand 2 previously reported. The peak current of 1 shifted toward the negative side from that of 2, thereby shortening the time required for gene detection.

We analyzed the thermodynamics of purine motif triplex formation by isothermal titration calorimetry. The signs of calorimetric enthalpy change, delta Hcal, and entropy change, delta S, of the triplex formation were negative in the temperature range between 15 and 35 degrees C. Since an observed negative delta S was unfavorable for the triplex formation, the triplex formation was driven by a large negative delta Hcal. delta Hcal decreased with increasing temperature, yielding a negative heat capacity change, delta Cp, of approximately -1.2 kcal mol-1 K-1. We found that the binding constant, Ka, increased with increasing temperature, leading to an apparent positive van't Hoff enthalpy change, delta Hvh, which was in sharp contrast with the large negative delta Hcal. The analyses of the observed temperature dependence of Ka and delta Hcal and the negative delta Cp suggest that the purine motif triplex formation near room temperature is not a simple two-state binding process but exhibits multiple states, which was previously observed for the pyrimidine motif triplex formation near room temperature.

To investigate mismatch of base-pairings in relation to mutagenesis by oxyamines, crystal structures of two DNA dodecamers with the sequence d(CGCZAA TTmo4CGCG) (Z = A or G), containing N4-methoxy-cytosine (mo4C), have been determined by X-ray analysis. These dodecamers essentially form right-handed B-form duplexes, respectively. In the dodecamer with Z = A, the two mo4C residues are adapted in imino form with the anti methoxyl group to form pairs with A on the opposite strand in a manner of Watson-Crick fashion. While in the dodecamer with Z = G, one mo4C in amino form with the anti methoxyl group forms a normal Watson-Crick pair with G, but the other one in imino form with syn methoxyl conformation wobbles with G. Based on these results, possible mutation mechanism has been proposed.

Polycation comb-type copolymer that is composed of polylysine backbone and dextran side chains (PLL-g-Dex) has previously been shown to stabilize duplex and triplex DNAs quite effectively. In this study, we have conjugated PLL-g-Dex with oligonucleotides (ODN) aiming to increase the triplex stabilizing efficiency of the copolymer. Here we have demonstrated that the copolymer-TFO conjugates selectively stabilize triplex DNA. Also its potential to form triplex DNA was found to be greater than PLL-g-Dex/ODN mixture.

To study RNA-peptide interactions, we performed an in vitro selection of RNA on a 27 MHz quartz-crystal microbalance (QCM) on which a simple R5 helix peptide was immobilized as a model of N peptide from bacteriophade lambda. The consensus sequences including a GNRA tetraloop were obtained from a random RNA pool after the 7th cycle selection.