Photo-Cross-Linking between U and Pyrene Residues in an RNA/DNA Hybrid.

In this study, we investigated the photoreaction of U in a pyrene-labeled DNA duplex, RNA duplex, and DNA/RNA hybrids. We found that the photoreactivity of U changed dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when U was incorporated into the RNA strand and the pyrene was conjugated to the 5' end of the DNA.

Photoreaction of DNA Containing 5-Halouracil and its Products.

5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent.

Effects of Physical Damage in the Intermediate Phase on the Progression of Amyloid β Fibrillization.

Understanding the mechanism responsible for the progression of amyloid deposition is important for developing methods to suppress this process in the treatment of Alzheimer's disease. The effects of physical damage during the transition phase of amyloid β fibril formation are unclear. In this study, we used high-speed atomic force microscopy to investigate the effects of damage to the intermediates of amyloid β in real time.

A Photoregulated DNA-Based Rotary System and Direct Observation of Its Rotational Movement.

Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light.

Linking two DNA duplexes with a rigid linker for DNA nanotechnology.

DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups.

Controlling electron rebound within four-base π-stacks in Z-DNA by changing the sugar moiety from deoxy- to ribonucleotide.

Charge transfer through DNA is of great interest because of the potential of DNA to be a building block for nanoelectronic sensors and devices. The photochemical reaction of 5-halouracil has been used for probing charge-transfer processes along DNA. We previously reported on unique charge transfer following photochemical reaction of 5-bromouracil within four-base π-stacks in Z-DNA.

Photoreactivities of 5-bromouracil-containing RNAs.

5-Bromouracil ((Br)U) was incorporated into three types of synthetic RNA and the products of the photoirradiated (Br)U-containing RNAs were investigated using HPLC and MS analysis. The photoirradiation of r(GCA(Br)UGC)(2) and r(CGAA(Br)UUGC)/r(GCAAUUCG) in A-form RNA produced the corresponding 2'-keto adenosine ((keto)A) product at the 5'-neighboring nucleotide, such as r(GC(keto)AUGC) and r(CGA(keto)AUUGC), respectively. The photoirradiation of r(CGCG(Br)UGCG)/r(C(m)GCAC(m)GCG) in Z-form RNA produced the 2'-keto guanosine ((keto)G) product r(CGC(keto)GUGCG), whereas almost no products were observed from the photoirradiation of r(CGCG(Br)UGCG)/r(C(m)GCAC(m)GCG) in A-form RNA.

The distance between donor and acceptor affects the proportion of C1' and C2' oxidation products of DNA in a BrU-containing excess electron transfer system.

We have investigated the products of (Br)U in excess electron transfer and have demonstrated that in DNA the proportion of products changes with the distance between the donor and acceptor. On the basis of a labeling experiment using H(2)(18)O, we have shown that hole migration from Py(•+) formed after charge separation is involved in the reaction.

Photoreaction at 5'-(G/C)AA(Br)UT-3' sequence in duplex DNA: efficient generation of uracil-5-yl radical by charge transfer.

The photoreactivities of 5-halouracil-containing DNA have widely been used for analysis of protein-DNA interactions and have recently been used for probing charge-transfer processes along DNA. Despite such practical usefulness, the detailed mechanisms of the photochemistry of 5-halouracil-containing DNA are not well understood. We recently discovered that photoirradiation of BrU-substituted DNA efficiently produced 2'-deoxyribonolactone at 5'-(G/C)AABrUBrU-3' and 5'-(G/C)ABrUBrU-3' sequences in duplex DNA.

Photochemical determination of different DNA structures.

The various conformations of DNA are thought to have important biological roles. Investigation of the local DNA conformational changes associated with biological events is therefore essential to an understanding of the functions of DNA. We have reported the photoreactivities of 5-halouracil in the five characteristic local DNA structures: the A, B and Z forms, protein-induced DNA kinks and the G-quadruplex form.

Detection of photoinduced electron transfer from Sso7d to DNA.

Sso7d is a chromosomal protein of hyperthermophilic Archaea. The crystal structure of Sso7d-d(GTAAT(Br)UAC)(2) has been clarified at high resolution, showing that the protein binds in the minor groove of DNA, causing a sharp kink of about 60 degrees . We demonstrated that electron transfer occurs efficiently from Sso7d to DNA by using inosine (I)-containing 5'-d(ITAAT(Br)UAC)-3'.

The molecular-thermometer based on B-Z transition of DNA.

A molecular thermometer utilizing the different pi-stacking of B- and Z-DNA was designed. Aminopurine, which is a fluorescent probe for charge-transfer processes, was introduced into B- and Z-DNA and the emission monitored. Z-DNA showed a marked increase in fluorescence compared with B-DNA, with the fluorescence intensity correlating linearly and reproducibly with temperature.

Photoreactivation of DNA by an archaeal nucleoprotein Sso7d.

Sso7d is a chromosomal protein of hyperthermophilic Archaea. The crystal structure of Sso7d-d(GTAAT(I)UAC)(2) has been clarified at high resolution, showing that the protein binds in the minor groove of DNA, causing a sharp kink of approximately 60 degrees. Recently, we found that photoirradiation of Sso7d and 5-iodouracil-((I)U)-containing 5'-d(GTAAT(I)UAC)-3' efficiently induced the abstraction of hydrogen from the methyl group of T(5) at the kink.

Biomolecule-based switching devices that respond inversely to thermal stimuli.

We demonstrate a molecular switch, on the basis of the characteristic properties of DNA and RNA, which indicates a completely inverted response to thermal stimuli using the transition between right- and left-handed helices. We designed a system using aminopurine (Ap), which can convert the pi-stack information of the transition from right-handed to left-handed DNA (B-Z transition) and RNA (A-Z transition) into an output giving a fluorescent signal. These two biomolecular devices together serve as "right-left" or "off-on" switches.

Efficient generation of 2'-deoxyuridin-5-yl at 5'-(G/C)AA(X)U(X)U-3' (X = Br, I) sequences in duplex DNA under UV irradiation.

The photoreactivity of 5-halouracil-containing DNA was investigated using 450 base pair DNA fragments under 302 nm irradiation. Heat-dependent cleavage selectively occurs at 5'-(G/C)AAXUXU-3' and 5'-(G/C)AXUXU-3' (X = Br, I) sequences in double-stranded DNA. HPLC product analysis indicated that 2'-deoxyribonolactone residues are effectively generated at these sequences.

Unique charge transfer properties of the four-base pi-stacks in Z-DNA.

To investigate the photoreactions of BrU in Z-DNA, the photoirradiation of 5'-d(C1G2C3G4BrU5G6C7G8)-3'/5'-d(C9mG10C11A12C13mG14C15G16)-3'(ODN 1-2) was investigated. In accord with previous observations, B-form ODN 1-2 with the 5'-GBrU sequence showed very weak photoreactivity. However, Z-form ODN 1-2 in 2 M NaCl underwent photoreaction to afford 5'-d(CGC)rGd(UGCG)-3' together with the formation of imidazolone (Iz) contained 5'-d(CIzCACmGCG)-3'.

Photochemistry of bromouracil containing Z-DNA.

To investigate the mechanism underlying the photoreaction of bromouracil in DNA, a detailed analysis of photoirradiated 5'-d(CGCG(Br)UGCG)-3'/5'-d(C(8MeO)GCAC(m)GCG)-3' was undertaken. We found that rG- and 2-aminoimidazolone-containing octanucleotides are formed efficiently in Z-form DNA. These results suggest that interstrand electron transfer initiates the photoreaction of bromouracil in Z-DNA.