Photoreactivities of 5-Bromouracil-containing RNAs

Morinaga, Hironobu; Kizaki, Seiichiro; Takenaka, Tomohiro; Kanesato, Shuhei; Sannohe, Yuta; Tashiro, Ryu; Sugiyama, Hiroshi

doi:10.1016/j.bmc.2012.11.010

Cited by 6 publications

(8 citation statements)

References 32 publications

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“…41 We were unable to trap 1 using O 2 in aerated solutions or thiol in degassed solutions. 25 Previously, we modulated the rate constant for deglycosylation from monomeric 1 by reducing the solvent polarity.…”

Section: Discussionmentioning

confidence: 99%

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Rutgeerts

Greenberg

2016

J. Org. Chem.

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The C2′-carbon hydrogen bond in ribonucleotides is significantly weaker than other carbohydrate carbon-hydrogen bonds in RNA or DNA. Independent generation of the C2′-uridine radical (1) in RNA oligonucleotides via Norrish Type I photocleavage of a ketone substituted nucleotide yields direct strand breaks via cleavage of the β-phosphate. The reactivity of 1 in different sequences and under a variety of conditions suggests that the rate constant for strand scission is significantly greater than 106 s−1 at pH 7.2. The initially formed C2′-radical (1) is not trapped under a variety of conditions, consistent with computational studies (Chem. Eur. J. 2009, 15, 2394.) that suggest that the barrier to strand scission is very low and that synchronous proton transfer from the 2′-hydroxyl to the departing phosphate group facilitates cleavage. The C2′-radical could be a significant contributor to RNA strand scission by hydroxyl radical, particularly under anaerobic conditions where 1 can be produced from nucleobase radicals.

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Section: Discussionmentioning

confidence: 99%

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Rutgeerts

Greenberg

2016

J. Org. Chem.

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“…100 In contrast to studies involving BrdU, no evidence for C1′-hydrogen atom abstraction by the uracil-5-yl radical ( 32 ) was obtained. Conformational differences between duplex RNA and DNA could contribute to this difference, but certainly the more favorable C2′-carbon–hydrogen BDE in RNA than DNA (Table 1) plays a role.…”

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

confidence: 90%

“…The product distribution obtained upon irradiating BrdU and/or IdU in DNA has been used by Sugiyama to probe nucleic acid structure. 99 As discussed below, the chemistry is different still in RNA 100 …”

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

confidence: 99%

Reactivity of Nucleic Acid Radicals

Greenberg

2016

Advances in Physical Organic Chemistry

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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.

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“…8a). CGrepeated sequence-containing RNA can adopt a Z-form structure (55,56). In this structure, the uracil radical abstracts the C2 0 aH of ribose, resulting in the formation of the keto product (Fig.…”

Section: Formation Of the Ribose Residuementioning

confidence: 99%

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

Tashiro

Sugiyama

2021

Photochem & Photobiology

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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 structuredependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groovebinder/DNA and protein/DNA complexes using a 5bromouracil-based electron transfer system is also described.

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Photoreactivities of 5-Bromouracil-containing RNAs

Cited by 6 publications

References 32 publications

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Reactivity of Nucleic Acid Radicals

Photoreaction of DNA Containing 5‐Halouracil and its Products^†

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Photoreactivities of 5-Bromouracil-containing RNAs

Cited by 6 publications

References 32 publications

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Mechanistic Studies on RNA Strand Scission from a C2′-Radical

Reactivity of Nucleic Acid Radicals

Photoreaction of DNA Containing 5‐Halouracil and its Products†

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Product

Resources

About

Photoreaction of DNA Containing 5‐Halouracil and its Products^†