Kondo Jiro

Copper ions bind to the N3 positions of both C and FdU (5-fluorouracil) in the C–FdU and FdU–C base pairs of duplex DNA.

Thymidine analogue with a 1,2‐diamino side chain at the 3N position is synthesized and converted into an amidite unit for oligonucleotide synthesis. It is used for preparing oligonucleotides containing a 1,2‐diamino side chain as X residue. Thermal denaturation studies are performed on a duplex containing an X–X pair in the presence and absence of metal ions. Among various metal ions used in this research, Cd(II), Co(II), Cu(II), Ni(II), and Zn(II) ions increased the duplex stability. The results prove the new strategy to design metallo‐base pairs containing various metal ions.

Abstract The technology for sequence-specific detection of RNA is in high demand in the medical field as well as in basic research in life sciences. Various methods for detecting RNA have been developed so far, but all of them are designed based solely on the rules of base complementarity, which leads to the false detection of unrelated RNAs with very similar sequences. In this study, we challenged the biomimetics approach at the molecular level to develop a sequence-specific RNA probe by mimicking a well-known RNA structural motif, the kink-turn motif, which exists in various functional RNAs. Our probe was designed in such a way that the formation of the kink-turn motif is induced only when it hybridizes with the target RNA, resulting in the exposure of the fluorescent base introduced into the probe. As we expected, both the RNA-based and DNA-based probes sensitively and selectively detected the target RNA as an increase in fluorescence intensity. We also confirmed the actuation mechanism of the probes by X-ray crystallography. This study showed that the RNA structural motifs remaining as a result of natural selection could be applied to biomimetics at the molecular level.

Fluorescence imaging is a key tool in biological and medical sciences. Despite the potential for increased imaging depth in the near‐infrared range, the limited availability of bright emitters hinders its widespread implementation. In this work, a DNA‐stabilized silver nanocluster (DNA–AgNC) with bright emission at 960 nm in solution is presented, which redshifts further to 1055 nm in the solid and crystalline states. The atomic structure, composition and charge of this DNA–AgNC are determined by combining single‐crystal X‐ray diffraction and electrospray ionization–mass spectrometry. This unique atomically precise silver nanocluster consists of 28 silver atoms, of which are neutral (Ag₂₈¹⁶⁺), arranged in a rodlike shape, and measures just over 2 nm in length. Interestingly, differences are observed in the number of chlorido ligands between the solution and crystalline states, highlighting the important but not yet fully understood role of chlorides in fine‐tuning the optical properties of this class of emitters. The structure of this silver nanorod, along with the fully characterized photophysical properties, represents a cornerstone for understanding the intricate interactions between silver and DNA bases, as well as paving the way for the rational design of the next‐generation imaging probes.

For the success of structure-based drug design, three-dimensional structures solved by X-ray crystallography at atomic resolution are mandatory. In order to obtain high-quality single crystals with strong diffraction power, crystallization under microgravity conditions has been attempted for proteins. Since nucleic acid duplexes have chemical, structural and crystallographic characteristics that differ from those of globular proteins, such as intermolecular repulsion due to negative charge and molecular and crystallographic anisotropies, it is interesting to investigate whether microgravity crystallization improves the crystal growth of nucleic acids. However, to our knowledge there has been only one report on nucleic acid crystallization in a microgravity environment, and there have been no reports of successful structural analysis. Here, we conducted the crystallization of a DNA/RNA heteroduplex in space. The heteroduplex was successfully crystallized in a microgravity environment, and the size and appearance of the crystals were improved compared with control experiments conducted on Earth. Although the effect of the counter-diffusion method is likely to be more significant than the effect of microgravity in this study, we were able to analyze the structure at a higher resolution (1.4 Å) than our previously reported crystal structure (1.9 Å).