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. Using synthetic oligonucleotides, we found that similar photoreactivities were maintained at the 5'-(G/C)AABrUT-3' sequence, providing ribonolactone as a major product with concomitant release of adenine base. In this paper, the photoreactivities of various oligonucleotides possessing the 5'-BrUT-3' sequence were examined to elucidate the essential factors of this photoreaction. HPLC product analysis indicated that the yield of 2'-deoxyribonolactone largely depends on the ionization potential of the purine derivatives located 5'-upstream of 5'-BrUT-3', as well as the electron-donating ability of their pairing cytosine derivatives. Oligonucleotides that possess G in the complementary strand provided the ribonolactone with almost the same efficiency. These results clearly suggest that the photoinduced charge transfer from the G-5' upstream of 5'-BrUT-3' sequence, in the same strand and the complementary strand, initiates the reaction. To examine the role of intervening A/T base pair(s) between the G/C and the 5'-BrUT-3' sequence, the photoreactivities of a series of oligonucleotides with different numbers of intervening A/T base pairs were examined. The results revealed that the hotspot sequence consists of the electron-donating G/C base pair, the 5'-BrUT-3' sequence as an acceptor, and an appropriate number of A/T base pairs as a bridge for the charge-transfer process.

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. When the temperature is changed from low to high, the RNA device changes from the off to on signal; however, the DNA device changes from on to off. The response of these RNA and DNA based devices against thermal stimulus was completely reversible.

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. These observations will be useful in studying the molecular basis of the sequence-dependent DNA-damaging process in UV-irradiated 5-halouracil-containing DNA.