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Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media.
TLDR
The results of the favorable formation of the noncanonical nucleotide structures, and minimized conformational and thermal perturbations of the ordereducleotide structures in the cosolute-containing solutions implicate the significance of the intracellular environment on DNA and RNA structures in a cell. Expand
Dynamics and energetics of the base flipping conformation studied with base pair-mimic nucleosides.
TLDR
To investigate the dynamics and energetics of this unusual conformation in a double helix, base flipping induced by the base pair analogues of deoxyadenosine and deoxycytidine derivatives tethering a phenyl or naphthyl group was investigated. Expand
Stacking interaction in the middle and at the end of a DNA helix studied with non-natural nucleotides.
TLDR
The thermal stability of DNA duplexes containing a non-natural nucleotide tethered to a simple aromatic hydrocarbon group devoid of dipole moments and hydrogen bonding sites was measured to understand nucleic acid interactions and to design new non- natural nucleotides. Expand
Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules
TLDR
It is suggested that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. Expand
Base-pairing selectivity of a ureido-linked phenyl-2'-deoxycytidine derivative.
TLDR
Insight into the pairing selectivity of carbamoylated cytosine lesions produced in cells is provided, and applications of the 2'-deoxycytidine derivatives in medical technologies, molecular biology experiments, and synthesis of a supramolecular network of DNA strands are suggested. Expand
Use of a Ureido-Substituted Deoxycytidine Module for DNA Assemblies
TLDR
An N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution and the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. Expand
Functionalization of DNA by the base pair-mimic nucleosides.
TLDR
Interestingly, the duplex consisting of the DNA containing the base pair-mimic nucleosides and the complementary RNA strand caused the site-selective RNA hydrolysis except the Cphe-G pair, which suggests that theCphe has an ability of forming the base Pair with guanosine. Expand
Recognition of the base pair-mimic nucleosides by DNA polymerases.
TLDR
This study revealed that the phenyl group of the deoxycytidine derivative, C(phe) located outside the helix and allowed the base pair formation with guanine in a DNA duplex, although its Phenyl group could stack with the adjacent DNA bases as efficient as A(phe). Expand