The Distance Between Donor and Acceptor Affects the Proportion of C1′ and C2′ Oxidation Products of DNA in a <sup>Br</sup>U-Containing Excess Electron Transfer System

Tashiro, Ryu; Ohtsuki, Akimichi; Sugiyama, Hiroshi

doi:10.1021/ja106184w

Cited by 25 publications

(16 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To identify the oxidation products at low conversion rates (approximately 20%) [17,23], we first determined the rates of dsDNA oxidation. The oxidation rate of dsDNA is shown in Figure 4, and the conversion rates of the dsDNA at 30 min reached approximately 20%.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

et al. 2014

View full text Add to dashboard Cite

Guanine is the most easily oxidized among the four DNA bases, and some guanine-rich sequences can form quadruplex structures. In a previous study using 6-mer DNA d(TGGGGT), which is the shortest oligomer capable of forming quadruplex structures, we demonstrated that guanine oxidation products of quadruplex DNA differ from those of single-stranded DNA. Therefore, the hotooxidation products of double-stranded DNA (dsDNA) may also differ from that of quadruplex or single-stranded DNA, with the difference likely explaining the influence of DNA structures on guanine oxidation pathways. In this study, the guanine oxidation products of the dsDNA d(TGGGGT)/d(ACCCCA) were analyzed using HPLC and electrospray ionization-mass spectrometry (ESI-MS). As a result, the oxidation products in this dsDNA were identified as 2,5-diamino-4H-imidazol-4-one (Iz), 8-oxo-7,8-dihydroguanine (8oxoG), dehydroguanidinohydantoin (Ghox), and guanidinohydantoin (Gh). The major oxidation products in dsDNA were consistent with a combination of each major oxidation product observed in single-stranded and quadruplex DNA. We previously reported that the kinds of the oxidation products in single-stranded or quadruplex DNA depend on the ease of deprotonation of the guanine radical cation (G•+) at the N1 proton. Similarly, this mechanism was also involved in dsDNA. Deprotonation in dsDNA is easier than in quadruplex DNA and more difficult in single-stranded DNA, which can explain the formation of the four oxidation products in dsDNA.

show abstract

Section: Resultsmentioning

confidence: 99%

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

et al. 2014

View full text Add to dashboard Cite

show abstract

“…95,96 The reactivity of the C2′-radical is also affected by the nucleic acid structure and the distance between it and the electron-deficient nucleobase. 97,98 The C2′-oxidized abasic site ( 18 ) is observed in B-DNA, whereas the respective ribonucleotides are produced in Z-DNA. The product distribution obtained upon irradiating BrdU and/or IdU in DNA has been used by Sugiyama to probe nucleic acid structure.…”

Section: C2′-radical Generation and Reactivity In Dna Ribonucleosmentioning

confidence: 99%

Reactivity of Nucleic Acid Radicals

Greenberg

2016

Advances in Physical Organic Chemistry

View full text Add to dashboard Cite

Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers’ structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.

show abstract

“…In PPIs, the pyrene moiety is used as an electron donor (8,11), and pyrrole-imidazole polyamide, which recognizes each of the four Watson–Crick base pair sequences, is used for sequence-specific binding to DNA (18–21). To detect electron transfer in DNA, 5-bromouracil (5-BrU)-containing DNA was used as an electron acceptor.…”

Section: Introductionmentioning

confidence: 99%

“…To detect electron transfer in DNA, 5-bromouracil (5-BrU)-containing DNA was used as an electron acceptor. 5-BrU is readily reduced into its anion radical, which generates the uracil-5-yl radical in DNA and immediately abstracts hydrogen from the deoxyribose backbone or the appropriate hydrogen donor; this leads to the generation of uracil, which can be detected using various methods (10,11,22,23). We demonstrated that, under irradiation conditions, our PPI sequences specifically inject electrons into the 5-BrU residue in DNA.…”

Section: Introductionmentioning

confidence: 99%

Sequence-specific electron injection into DNA from an intermolecular electron donor

Morinaga

Takenaka

Hashiya

et al. 2013

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Electron transfer in DNA has been intensively studied to elucidate its biological roles and for applications in bottom-up DNA nanotechnology. Recently, mechanisms of electron transfer to DNA have been investigated; however, most of the systems designed are intramolecular. Here, we synthesized pyrene-conjugated pyrrole-imidazole polyamides (PPIs) to achieve sequence-specific electron injection into DNA in an intermolecular fashion. Electron injection from PPIs into DNA was detected using 5-bromouracil as an electron acceptor. Twelve different 5-bromouracil-containing oligomers were synthesized to examine the electron-injection ability of PPI. Product analysis demonstrated that the electron transfer from PPIs was localized in a range of 8 bp from the binding site of the PPIs. These results demonstrate that PPIs can be a useful tool for sequence-specific electron injection.

show abstract

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

Cited by 25 publications

References 30 publications

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

Reactivity of Nucleic Acid Radicals

Sequence-specific electron injection into DNA from an intermolecular electron donor

Contact Info

Product

Resources

About

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

Cited by 25 publications

References 30 publications

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

Analysis of Guanine Oxidation Products in Double-Stranded DNA and Proposed Guanine Oxidation Pathways in Single-Stranded, Double-Stranded or Quadruplex DNA

Reactivity of Nucleic Acid Radicals

Sequence-specific electron injection into DNA from an intermolecular electron donor

Contact Info

Product

Resources

About

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