Mitsunobu Nakamura

B- to Z-DNA transitions play a crucial role in biological systems and have attracted the interest of researchers for their applications in DNA nanotechnology. DNA and DNA analogues have also been used as templates to construct helical chromophore associations with π interactions. In this work, the B- to Z-DNA transition-induced switching of pyrene in an association manner was evaluated using DNA duplexes with non-nucleosidic pyrene residues in the middle of d(CG) repeat sequences. One of the pyrene-labeled DNAs was shown to exhibit inverted exciton coupled circular dichroism signals upon pyrene association through a B- to Z-DNA transition. This observation indicates that pyrene association switches the DNA conformation from right- to left-handed. Interestingly, the fluorescence of the pyrene-labeled DNA duplex also dynamically changed upon switching of the pyrene in an association-based manner. Taken together, these studies demonstrate that pyrene-labeled DNA shows promise as a chiroptical molecular switch.

The construction of zipper-like chromophore-arrays in the major groove of duplex DNA remains a challenge because only a few chromophores for this application have been discovered. To address the challenge, dual-chromophore labeled DNAs having a self-complementary sequence were prepared using a solid-phase, post-synthetic, copper-catalyzed, alkyne-azide cycloaddition. The resulting chromophore-arrays on the labeled DNA duplexes were characterized. The dual-tetraphenylethene (TPE) or dual-pyrene (Py) labeled DNA formed self-complementary B-form duplexes and resulted in the construction of chromophore-arrays in the major groove. The TPE-arrays, in which TPEs were arranged in a zipper-like fashion, slightly destabilized the duplex because of their bulkiness and exhibited aggregation-induced-emission. The Py-arrays, in which Pys were not arranged in a zipper-like fashion, had no effect on duplex stability and exhibited weak excimer emission because Py was sufficiently small for free rotation in the major groove.

Abstract In this report, we describe the circularly polarized luminescence (CPL) of the RNA duplexes having one to four 2′‐O‐pyrene modified uridines (Upy) and the DNA duplexes having two, four, and six pyrene modified non‐nucleosidic linkers (Py). Both the pyrene π‐stack arrays formed on the RNA and DNA double helical structures exhibited pyrene excimer fluorescence. In the pyrene‐modified RNA systems, the RNA duplex having four Upys gives CPL emission with glum value of <0.01 at 480?nm. The structure of pyrene stacks on the RNA duplex may be rigidly regulated with increase in the Upy domains, which resulted in the CPL emission. In the DNA systems, the pyrene‐modified duplexes containing two and four Pys exhibited CPL emission with glum values of <0.001 at 505?nm. The pyrene π‐stack arrays presented here show CPL emission. However, the glum values are relatively small when compared with our previous system consisting of the pyrene‐zipper arrays on RNA.

The construction of one-dimensional chromophore aggregates of naphthalenediimide (NDI) and bis(2-thienyl)diketopyrrolopyrrole (TDPP) using 40-mer oligodeoxythymidines (dT40) as a scaffold was previously reported. Furthermore, the chromophore-aggregate (NDI-dT40/TDPP-dT40) co-immobilized heterojunction gold electrode exhibited a more efficient photocurrent than the TDPP?dT40-immobilized electrode with selective photoexcitation of TDPP-dT40. In this work, a system comprising three components (in which the chromophore aggregates of diphenyl-diketopyrrolopyrrole (PDPP-dT40) are employed as a third component) was examined in order to enhance photocurrent efficiency. Selective photoexcitation of TDPP-dT40 on the NDI-dT40/TDPP-dT40/PDPP-dT40 electrode shows photocurrent responses with greater quantum yield than those of the TDPP-dT40, NDI-dT40/TDPP-dT40 and TDPP-dT40/PDPP-dT40 electrodes. The results suggest the addition of PDPP-dT40 can control charge separation and charge recombination between the electron and the hole (generated by an electron transfer from the photoexcited TDPP-dT40 to NDI-dT40).The construction of one-dimensional chromophore aggregates of naphthalenediimide (NDI) and bis(2-thienyl)diketopyrrolopyrrole (TDPP) using 40-mer oligodeoxythymidines (dT40) as a scaffold was previously reported. Furthermore, the chromophore-aggregate (NDI-dT40/TDPP-dT40) co-immobilized heterojunction gold electrode exhibited a more efficient photocurrent than the TDPP?dT40-immobilized electrode with selective photoexcitation of TDPP-dT40. In this work, a system comprising three components (in which the chromophore aggregates of diphenyl-diketopyrrolopyrrole (PDPP-dT40) are employed as a third component) was examined in order to enhance photocurrent efficiency. Selective photoexcitation of TDPP-dT40 on the NDI-dT40/TDPP-dT40/PDPP-dT40 electrode shows photocurrent responses with greater quantum yield than those of the TDPP-dT40, NDI-dT40/TDPP-dT40 and TDPP-dT40/PDPP-dT40 electrodes. The results suggest the addition of PDPP-dT40 can control charge separation and charge recombination between the electron and the hole (generated by an electron transfer from the photoexcited TDPP-dT40 to NDI-dT40).

Fluorescent nucleic acids were prepared utilizing the polymerase extension (PEX) reaction to incorporate fluorescent molecules. 2'-Deoxyuridine triphosphate (dUTP) derivatives possessing pyrene molecules as fluorophores were synthesized using the aqueous-phase Sonogashira coupling between 5-Iodo-dUTP and acetylene-linked pyrene molecules. The incorporation of the pyrene (Py)-labeled deoxyuridine triphosphates (PyU) into DNA by polymerase was evaluated by polyacrylamide gel electrophoresis, demonstrating that the PyU can work as a good substrate for the PEX reaction. The fluorescent properties of the functionalized DNA prepared by the PEX reaction were characterized by steady-state fluorescence measurements. The Py-conjugated DNA showed typical emission spectra of the pyrene, and the DNA with two pyrene molecules connected to each other by a diethylene glycol linker exhibited a broadened emission attributed to the electronic interaction between the Py molecules.

Bis(2-thienyl)-diketopyrrolopyrrole having two $Zn^{II}$-cylcens (DPPCy) was synthesized. DPP-aggregates were constructed by self-organization of DPPCy and $dT_n$-DNAs. In the presence of L-ascorbic acid as an electron sacrifice reagent, the DPP aggregates immobilized on a gold electrode exhibit good anodic photocurrent responses as well as cathodic photocurrent responses in the presence of methyl viologen. The anodic photocurrent responses depend on the DNA lengths because of the formation of uniform DPP-aggregates corresponding to the DNA lengths. The present results show that photocurrent responses of the DPP-aggregates can be controlled by DNA lengths and electron sacrifice reagents.

We prepared various chromophores containing hydrogen bonding unit and investigated their change in photoluminescent properties induced by mechanical stimuli. We reported photoluminescent color and lifetime tuning of complex compound of dyes and acids.

Deoxyuridine triphosphate derivatives modified with pyrene was synthesized to functionalize DNA with fluorescent molecules based on the template DNA sequence. Incorporation of pyrene-labeled deoxyuridine triphosphates into DNA by DNA polymerase was investigated by using reverse-phase HPLC and polyacrylamide gel electrophoresis. The fluorescent properties of functionalized DNA were characterized by the steady-state fluorescence measurements.

Template-directed ligation of oligonucleotides by photochemical reaction has attracted much interest because of its biomedical and synthetic applications. In this study, we developed photoligaton of DNA by using a photoremovable protecting group and thiol-disulfide exchange reaction. A phosphoroamidite of o-nitrobenzyl derivatives were synthesized, and DNA modified with a nitrobenzyl-protected thiol group and disulfide group was synthesized by conventional phosphoroamidite chemistry using a DNA synthesizer. It was shown that photochemical reaction of a nitrobenzyl group with UV irradiation produced a free thiol group, leading to the DNA ligation through the thiol-disulfide exchange reaction.

We describe a new ferrocene-based redox-reporter that electronically couples to the DNA Π-electron system.

We synthesized multiple pyrene-modified RNA sequences having two kinds of consecutive sequences, UPyUPy and APyAPy, and investigated their duplex formations and the pyrene associations.