Taiga Fujii

A polycation-chaperoned in-stem molecular beacon system

In the presence of poly(L-lysine)-graft-dextran, an in-stem molecular beacon involving three perylene-anthraquinone pairs in the stem region had a signal/background ratio of as high as 570. Response speed was also remarkable; equilibrium was attained within 5 minutes after addition of substrate DNA at 20 °C.

Selective labeling of mature RISC using a siRNA carrying fluorophore–quencher pair

RNA interference (RNAi) is an endogenous gene silencing system that has been harnessed to inhibit expression of specific genes through the introduction of short double-stranded RNAs, called small interfering RNAs (siRNAs) into cells. After entry into a cell, an siRNA is assembled into the RNA-induced silencing complex (RISC) and suppresses the target gene translation through interaction between the antisense (guide) strand of the siRNA and the target mRNA. To evaluate the intracellular fate of siRNAs, we performed imaging analyses using siRNAs labeled with newly designed fluorophore–quencher clusters introduced through the base surrogate with D-threoninol as a scaffold. Fluorescence microscopy analyses indicated that mature RISC containing fluorescently labeled antisense strand was localized within P-bodies. Thus, the antisense strand uptake into the RISC machinery was successfully visualized.

Design of an artificial functional nanomaterial with high recognition ability

An artificial macromolecule was designed as a novel nanomaterial with the backbone of phosphodiester and the side chain of functional molecules and nucleobases. The functional molecules tethered on d-threoninol and the nucleosides on d-ribose can be lined up with any sequence and any ratio by using standard phosphoramidite chemistry. The nucleobases that form Watson–Crick base pairs provide the sequence recognition which is required for constructing complicate nanostructures. The multiple functional molecules give applicable and advanced functions such as photoresponsiveness when azobenzenes were used. Unexpectedly, a stable double helix was formed even in the case that the ratio of azobenzene molecules and base pairs was as high as 2:1. More interestingly, this artificial duplex showed high sequence specificity: the stability decreased greatly when a mismatched base pair was present. Furthermore, the formation and dissociation of the constructed artificial duplex were reversibly and completely modulated with light irradiation. By using this new nanomaterial, a variety of functional nanostructures and nanodevices are promising to be designed. The possibility of our system being used for DNA computing is also discussed.

Design of a functional nanomaterial with recognition ability for constructing light-driven nanodevices

An artificial macromolecule (foldamer) was designed as a novel nanomaterial with the backbone of phosphodiester and the side chain of functional molecules and nucleobases. The functional molecules tethered on D-threoninol and the nucleosides on D-ribose can be lined up with any sequence and ratio by using standard phosphoramidite chemistry. The nucleobases that form Watson-Crick base pairs provide the sequence recognition which is required for constructing complicate nanostructures. The multiple functional molecules give applicable and advanced functions such as photoresponsiveness when azobenzenes were used. Unexpectedly, a stable double helix was formed even in the case that the ratio of azobenzene molecules and base pairs was as high as 2:1. More interestingly, this artificial duplex showed high sequence specificity: the stability decreased greatly when a mismatched base pair was present. Furthermore, the formation and dissociation of the constructed artificial duplex were reversibly and completely modulated with light irradiation. By using this new nanomaterial, a variety of functional nanostructures and nanodevices are promising to be designed.

Femtosecond Photoisomerization Study on Azobenzene-Derivative Bound by DNA

First observation of femtosecond absorbance change in azobenzene-derivative (AzD) bound by double-strand DNA, that by single-strand DNA and Azd shows trans-to-cis photoisomerization rate per pulse in the former is much lower than in the latter.

Incorporation of cationic dyes into DNA for distinct stabilization of duplex

In this study, cationic dyes (methylstilbazole) were introduced into ODN. When two complementary ODNs, both of which tethered this dye, were hybridized, the melting temperature drastically increased. The duplex was further stabilized by introducing multiple dyes.