Biomolecule-Based Switching Devices that Respond Inversely to Thermal Stimuli

Tashiro, Ryu; Sugiyama, Hiroshi

doi:10.1021/ja044138j

Cited by 63 publications

(66 citation statements)

References 33 publications

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“…The intense fluorescence of Ap in Z-DNA is in accord with the previous finding of almost no charge-transfer between the different four-base p stacks observed in the Br U photoreaction of Z-DNA. [14] The intense fluorescence of ODN 1-2 in the Z-conformation can be explained by the following reasons for disruption of charge-transfer. 1) Ap is located at the 5'-end of the four-base p stacks lacking a quenching base at the 5'-side.…”

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confidence: 99%

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A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

Tashiro

Sugiyama

2003

Angew Chem Int Ed

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confidence: 99%

“…Such a molecular thermometer can be applied in the investigation of localized temperature on a microscale. Because we previously reported that the pathway for electron transfer is different between B-and Z-DNA, [14] the B-Z transition could be useful …”

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confidence: 99%

A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

Tashiro

Sugiyama

2003

Angew Chem Int Ed

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“…Surprisingly, these phenomena were completely inverted in RNA. 79 At higher temperatures, RNA converted to the Z form to enhance emission. At low temperature, DNA emitted fluorescence and at high temperature, RNA emitted fluorescence.…”

Section: Monitoring Conformational Change Of B-z Formmentioning

confidence: 99%

Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature

Sugiyama¹

2007

Bulletin of the Chemical Society of Japan

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Fifty years after the discovery of the double-helical structure of DNA, the complete sequence of the human genome has been determined. All genetic information, which is necessary for life, is written in 30 billion base pairs of DNA. Many diseases, including cancer, and hereditary and viral diseases, can now be understood at the DNA sequence level. Local DNA conformations are also thought to play an important role in biological processes, such as gene expression. Therefore, DNA sequences and local DNA conformations are the targets of novel drugs that would precisely switch certain genes on or off. Modified bases that perform various functions can also be incorporated into defined DNA sequences. DNA can now be synthesized by the phosphoramidite method and amplified by PCR, and by using organisms such as Escherichia coli, DNA becomes a promising unit for nanotechnology applications. In this review, I focus on our efforts in understanding the DNA reactivity, structure, and function of DNA. The prospective uses of the chemical biology of DNA will also be discussed.Chemistry has greatly contributed to the understanding of cellular processes by allowing the identification of metabolic pathways, enzymatic processes, and signal transduction mechanisms. Understanding of the chemistry of nucleic acids has played a key role in the progressive development of molecular biology and life science through the development of many epoch-making techniques, such as the DNA sequencing, the synthesis of oligonucleotides, and PCR amplification. During my Ph.D. course, I started research on photochemistry between DNA and proteins as a model of photoinduced DNA-protein crosslinking for examining the ternary structure of the nucleosome and understanding the mechanisms of photodamage of DNA. We found that the "-amino group of the lysine residues of histone crosslinked with thymine residues in DNA.1 Interestingly, the crosslink site was cleaved upon heating to regenerate the thymine ring on the "-amino group of the lysine residues in the protein by Michael addition (Figure 1). At that time, not so many researchers were interested in chemical modification in a nucleosome.Because we applied this photoreaction for T specific cleavage of DNA, 1d I was attracted to the molecular mechanisms of DNA modification at an atomic level. I had the chance to study the mechanism of action of the antitumor antibiotic bleomycin at Sidney Hecht's group at the University of Virginia from 1984 to 1986. We investigated how these glycopeptides recognize specific DNA sequences and efficiently oxidize C4 0 deoxyribose to induce DNA strand cleavage using synthetic oligonucleotides with defined sequences. 2 We identified the formation of C4 0 hydroxy abasic sites in addition to the known oxidative direct-strand scission via a Criegee type rearrangement of the C4 0 hydroperoxy intermediate. 3 We found that the C4 0 hydroxy abasic site generated by Fe-bleomycin underwent aldol condensation and subsequent elimination and rearrangement to produce cyclic hydroxy pentenon...

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“…Much attention has been focused on chemically modified nucleic acids that can alter their properties by some external stimuli [1][2][3]. Photo-responsive nucleic acids have been realized by regulation of hydrogen bonding [4] and stacking effects [5] between nucleobases.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and Properties of 2'-Deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5 Position

et al. 2015

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Nucleic acids that change their properties upon photo-irradiation could be powerful materials for molecular sensing with high spatiotemporal resolution. Recently, we reported a photo-isomeric nucleoside bearing azobenzene at the C5 position of 2'-deoxyuridine (dU Az ), whose hybridization ability could be reversibly controlled by the appropriate wavelength of light. In this paper, we synthesized and evaluated dU Az analogues that have various para-substitutions on the azobenzene moiety. Spectroscopic measurements and HPLC analyses revealed that the para-substitutions of the azobenzene moiety strongly affect the photo-isomerization ability and thermal stability of the cis-form. The results suggest that proper substitution of the azobenzene moiety can improve the properties of dU Az as a light-responsive nucleic acid probe.

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Biomolecule-Based Switching Devices that Respond Inversely to Thermal Stimuli

Cited by 63 publications

References 33 publications

A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

A Nanothermometer Based on the Different π Stackings of B‐ and Z‐DNA

Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature

Synthesis and Properties of 2'-Deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5 Position

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