Bioinspired Conjugates for Chemical Biology

DNA, which is composed of four nucleobases, exhibits increasingly interesting and important functions in the fields of biochemistry, biotechnology, and nanomaterials due to its sequence specific recognition (hybridization) of the counterstrand and formation of a double-helical structure. The rule of hybridization is ingeniously simple: A only pairs with T, and G only with C. Recently, DNA and RNA are regarded as very promising nano-materials for constructing various nano-architectures and nano-machines, which are based on the spontaneous hybridization of DNA (or RNA) with its complementary counterstrand. Hence, if double-stranded DNA can be converted into two single-strands reversibly at will, we can control the mechanical motion of these machines.

In our laboratory, we have for the first time succeeded in the reversible photo-regulation of the formation and dissociation of DNA duplex by designing photoresponsive DNA carrying azobenzene (Angew. Chem. Int .Ed. 1999, 38, 2393-2395.). After modification of azobenzene and sequence design of photoresponsive DNA, we attained perfect photo-control of hybridization and developed new photoresponsive DNA that can be operated with only visible light (λ > 400 nm) which does not damage living cells. With our photoresponsive DNA and RNA, we could successfully photo-control almost all the reactions related to oligonucleotides and nanomaterials composed of DNA and RNA, such as photo-regulation of gene expression, photon-fuelled DNA machine, and so on. In addition, we could also developed photo-responsive T7 promoter and succeeded in the on-off photo-switching of transcription and following translation with this promoter.

As an external stimulus, light has the following advantages: 1) light does not contaminate the reaction system, 2) the excitation wavelength is controllable by designing the photoresponsive molecule, and 3) control of irradiation time and/or local excitation is easy. Hence, our photoresponsive DNA has attracted many researchers in the world, are applied to various systems by others. At present, our photoresponsive oligonucleotide can be purchased from the following Japanese company (only photoresponsive DNA carrying non-modified azobenzenes).

DNA is a supramolecule in which four nucleobases are strictly aligned within a double-helical structure. We have prepared dye clusters with pre-determined size, orientation and sequence by incorporating dyes into DNA. We have also succeeded in preparation of hetero dye cluster. We aim to elucidate novel physical phenomena between different dyes such as hetero excitonic interaction and hetero photocycloaddition reaction.

We have synthesized aTNA and SNA by modifying DNA with acyclic backbones. aTNA formed extremely stable duplex with complementary aTNA. In contrast, stable hetero duplex was formed between SNA and DNA or RNA. We are developing nucleic acid drugs and probes by using aTNA and SNA.

Fluorescent-labeled oligonucleotides are powerful tools for biochemical and biological research. However, most fluorophores are quenched through electron/hole transfer by natural nucleobases. We have prepared artificial bases of cyclohexane derivatives, which can suppress electron transfer. Quantum yields of fluorophores were drastically enhanced by incorporating the artificial bases. Highly-emissive labeling agents and probes would be prepared by using these molecules.

RNA interference is the endogenous gene silencing system which can be induced by short interfering RNAs (siRNAs) and has been considered to be a powerful tool which can knock-down the disease-related gene. Although siRNA has potential to be a therapeutic use, we have several issues to be overcome; Delivery system, low stability, off-target effect, and so on. We are developing a novel design of siRNA by introducing the original artificial nucleic acids.