Structural optimization of pseudorotaxane-forming oligonucleotides for efficient and stable complex formation.

Interlocked structures, such as rotaxane and catenane, combine both static and dynamic properties. To expand their unique properties into the chemical biology field, a spontaneous formation method of the interlocked structures with the target would be ideal. We have previously developed a pseudorotaxane-forming oligo DNA (prfODN) to spontaneously form topological DNA/RNA architectures.

Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA.

The G-quadruplex structure has been found in biologically significant regions of the genomic DNA, including the telomere and promoter regions, and is known to play an important role in a number of biological processes. In this paper, we report the development of alkylating probes for the G-quadruplex structure and evaluation of the properties of the modified G-quadruplex structure.

Selective alkylation of T-T mismatched DNA using vinyldiaminotriazine-acridine conjugate.

The alkylation of the specific higher-order nucleic acid structures is of great significance in order to control its function and gene expression. In this report, we have described the T-T mismatch selective alkylation with a vinyldiaminotriazine (VDAT)-acridine conjugate. The alkylation selectively proceeded at the N3 position of thymidine on the T-T mismatch.

Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides.

Circular nucleic acids have been utilized for versatile applications by taking advantage of the unique characteristic of their circular structure. In our previous study, we found that the chemically-cyclized ODN (cyODN) with double-tailed parts formed a pseudorotaxane structure with the target via the slippage process. We now report the investigation of the slippage properties and the mechanism of the slippage process using six different cyODNs.

Synthesis of peptide-conjugated light-driven molecular motors and evaluation of their DNA-binding properties.

Synthetic light-driven molecular motors are molecular machines capable of rotation under photo-irradiation. In this paper, we report the synthesis of peptide-conjugated molecular motors and evaluate their DNA-binding properties.

Fast DNA interstrand cross-linking reaction by 6-vinylpurine.

Oligonucleotides that incorporate a reactive moiety to form an interstrand cross-link have been widely studied for their potential toward inhibiting gene expression or as basic tools for chemical biology studies. The 6-vinylpurine (2) newly designed in the current study serves well as a new purine-base moiety for increasing cross-link reactivity to target cytosine. Thus, oligonucleotides containing 6-vinylpurine exhibit a more selective and much smoother DNA cross-linking ability to cytosine than the oligonucleotide analogs derived from 2-amino-6-vinylpurine (1) previously explored.

Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin.

Most photosynthetic dinoflagellates possess plastids containing chlorophyllsa+c,but species belonging to the genus Lepidodiniumare unique in bearing non-canonical plastids containing chlorophyllsa+b. According to the pioneering works on pigment composition data, it has been proposed that Lepidodiniumplastids were derived from a prasinophyte species, though this hypothesis was not supported by a recent phylogenetic analysis based on an alignment comprised of eight plastid proteins (Takishita et al. 2008, Gene 410: 26-26).