Managing protein–protein interactions is essential for resolving unknown biological events at the molecular level and developing drugs. We have designed and synthesized a side-chain-crosslinked helical peptides based on the binding domain of a pro-apoptotic protein (Bad) that induces programed cell death. The peptide showed high helical content and bound to its target, Bcl-X_L, more strongly than its non-crosslinked counterparts. When HeLa cells were incubated with the crosslinked peptide, the peptide entered the cytosol across the plasma membrane. The peptide formed a stable complex with Bcl-X_L localized at the outer mitochondrial membrane, and this binding event caused the release of cytochrome c from the intermembrane space of mitochondria into the cytosol. This activated the caspase cascade: 70 % of HeLa cells died by the apoptosis pathway (without evidence of necrosis).

The Sonogashira coupling of γ-CD-encapsulated alkynylpyrenes with terphenyl-type stopper molecules gave a doubly alkynylpyrene-threaded [4]rotaxane. The rotaxane showed only excimer emission, with a high fluorescence quantum yield of Φ_f=0.37, arising from the spatially restricted excimer within the cavity of the γ-CD. The excimer emission suffered little from self-quenching up to a concentration of 1.5×10⁻⁵ M and was circularly polarized with a high g_lum value of −1.5×10⁻². The strong circularly polarized luminescence may result from the two stacked pyrenes existing in the rotaxane in an asymmetrically twisted manner.

The Sonogashira coupling of γ-CD-encapsulated alkynylpyrenes with terphenyl-type stopper molecules gave a doubly alkynylpyrene-threaded [4]rotaxane. The rotaxane showed only excimer emission, with a high fluorescence quantum yield of Φ_f=0.37, arising from the spatially restricted excimer within the cavity of the γ-CD. The excimer emission suffered little from self-quenching up to a concentration of 1.5×10⁻⁵ M and was circularly polarized with a high g_lum value of −1.5×10⁻². The strong circularly polarized luminescence may result from the two stacked pyrenes existing in the rotaxane in an asymmetrically twisted manner.

Tetrameric and octameric 2,6-pyridylene ethynylene oligomers linked to a β-D-glucopyranoside template through an o-phenylene linker were prepared and studied for their higher-order structure. These oligomers formed chiral helical structures through intramolecular hydrogen bonding between the ethynylpyridine moiety and the glucoside template. The rigidity of the o-phenylene linker stabilizes the helical structure to improve its CD activity and resistance against protic surroundings. Furthermore, the helical stabilization was enhanced by the addition of Cu(OTf)₂ and Zn(NO₃)₂ salts.

Diarylethene-bridged peptides were developed to photoregulate biomolecular interactions. The peptides are made up of diarylethene-bridged and DNA-binding regions at their N- and C termini, respectively. The two regions could be independently designed and combined as desired. The α-helicities of the peptides were photoregulated in on/off or off/on manners, and the manner depended on the positions of two ornithine (Orn) residues for cross-linking reaction at the diarylethene-bridged region. In the case of the on/off manner, when the diarylethene structure adopted the open form on the peptides, the peptides folded into stable α-helices. Upon UV irradiation, the diarylethene moiety isomerized to its closed form to destabilize the helical structures. Quartz crystal microbalance (QCM) analysis showed that the open isomer strongly associated with a target DNA, as compared with the closed one. When the closed-form peptide existing in the DNA complex was irradiated with a fluorescent lamp in the middle of the QCM monitoring, the frequency change (ΔF) was enhanced by the diarylethene photoisomerization.

We have developed an induced circular dichroism (ICD) probe with a chromophore-linked alkynyldeoxyribose skeleton for analyzing higher-order structures of DNA duplexes in the visible-light region. When CG-repeated oligonucleotides (ODNs) with the probe at their 5′ ends adopted Z-form duplexes at a high NaCl concentration, strong ICD signals were observed at the absorptive region of the chromophore. On the other hand, their B-form duplexes, formed at a low NaCl concentration, produced a faint ICD signal. The specific ICD for the Z-form duplexes was found to appear only when the chromophores were attached at the 5′ ends of each of the ODNs. Furthermore, the chromophoric alkynylnucleoside residues effectively promoted the B to Z transition of the ODN.