Synthesis and Characterization of Oligonucleotides Containing the C4′‐Oxidized Abasic Site Produced by Bleomycin and Other DNA Damaging Agents

Kim, Jaeseung; Gil, José María Mengual; Greenberg, Marc M.

doi:10.1002/anie.200352102

Cited by 46 publications

(55 citation statements)

References 36 publications

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“…40 DNA lesions also cleave faster in single stranded material. 41, 42 In contrast, cleavage from 5,6-dihydrouridin-6-yl radical ( 2 ) ( k Cleave ) was less than 100 s −1 in either single or double stranded RNA and strand scission was faster in the latter substrate. 10 The dependency of k Cleave on secondary structure indicated that C2'-radical ( 4 ) cleavage could not be the rate limiting step.…”

Section: Resultsmentioning

confidence: 99%

Direct Strand Scission in Double Stranded RNA via a C5-Pyrimidine Radical

et al. 2012

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Nucleobase radicals are the major family of reactive intermediates produced when nucleic acids are exposed to γ-radiolysis. 5,6-Dihydrouridin-5-yl radical (1), the formal product of hydrogen atom addition and a model for hydroxyl radical addition was independently generated from a ketone precursor via Norrish Type I photocleavage in single stranded, and double stranded RNA. Radical 1 produces direct strand breaks at the 5'-adjacent nucleotide and only minor amounts of strand scission are observed at the initial site of radical generation. Strand scission occurs preferentially in double stranded RNA and in the absence of O2. The dependence of strand scission efficiency from 5,6-dihydrouridin-5-yl radical (1) on secondary structure under anaerobic conditions suggests that this reactivity may be useful for extracting additional RNA structural information from hydroxyl radical reactions. Varying the identity of the 5'-adjacent nucleotide has little effect on strand scission. Internucleotidyl strand scission occurs via β-elimination of the 3'-phosphate following C2'-hydrogen atom abstraction by 1. The subsequently formed olefin cation radical yields RNA fragments containing 3'-phosphate or 3'-deoxy-2'-ketonucleotide termini from competing deprotonation pathways. The ketonucleotide end group is favored in the presence of low concentrations of thiol, presumably by reducing the cation radical to the enol. Competition studies with thiol show that strand scission from 5,6-dihydrouridin-5-yl radical (1) is significantly faster than from 5,6-dihydrouridin-6-yl radical (2) and is consistent with computational studies using the G3B3 approach that predict the latter to be more stable than 1 by 2.8 kcal/mol.

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Section: Resultsmentioning

confidence: 99%

Direct Strand Scission in Double Stranded RNA via a C5-Pyrimidine Radical

et al. 2012

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“…Consequently, we and other groups have developed methods for independently producing C4-AP from stable precursors in chemically synthesized oligonucleotides. 4,28–31 In this study, C4-AP was generated on an as needed basis from the photolabile precursor ( 5 ), which was incorporated into oligonucleotides from phosphoramidite 4 during solid-phase DNA synthesis (Scheme 1). 4 The general sequence in 1 is part of a restriction fragment from pBR322, which possesses a hot-spot for cleavage by bleomycin.…”

Section: Resultsmentioning

confidence: 99%

Probing DNA interstrand cross-link formation by an oxidized abasic site using nonnative nucleotides

Sczepanski

Hiemstra

Greenberg

2011

Bioorganic & Medicinal Chemistry

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The C4'-oxidized abasic site (C4-AP) forms two types of interstrand cross-links with the adjacent nucleotides in DNA. Previous experiments revealed that dG does not react with the lesion and that formation of one type of cross-link is catalyzed by the opposing dA. Iso-guanosine•dC and 2-aminopurine•dT base pairs were used to determine why dG does not cross-link with C4-AP despite its well known reactivity with other bis-electrophiles. 7-Deaza-2'-deoxyadenosine was used to probe the role of the nucleotide opposite C4-AP in the catalysis of interstrand cross-link formation.

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“…General Approach for Synthesizing Oligonucleotides Containing DOB Using the synthesis of the respective C4-AP phosphoramidite as a guide, we viewed 11 (Scheme 6) as a key synthetic intermediate. 11 Stereocontrolled synthesis of 11 was initially pursued by attempted nucleophilic substitution of the protected glycerol derivatives (14, 15) (Scheme 5). The stereochemistry was set using the asymmetric dihydroxylation of the pmethoxybenzoate of allyl alcohol (12).…”

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Preparation and Analysis of Oligonucleotides Containing Lesions Resulting from C5‘-Oxidation

Kodama

Greenberg

2005

J. Org. Chem.

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[reaction: see text] Hydrogen atom abstraction from the C5'-position of nucleotides in DNA results in direct strand scission. The newly formed 5'-termini of the cleaved DNA consists of alkali-labile fragments of the oxidized nucleotide. One terminus contains a 5'-aldehyde as part of an otherwise undamaged nucleotide (T-al). A second more structurally distinct product that is produced in lower yields results from cleavage of the C4'-C5' carbon-carbon bond. The 1,4-dioxo-2-phosphorylbutane (DOB) is a precursor of the alkylating agent but-2-ene-1,4-dial. To facilitate studies on these lesions, methods for synthesizing oligodeoxynucleotides containing DOB or T-al at their 5'-termini were developed. The effects of these lesions on the UV-melting temperatures of duplex DNA, and their cleavage labilities were determined. T-al cleaves very slowly (t(1/2) = 100.7 h), whereas DOB has a half-life at 37 degrees C (pH 7.2) of less than 11 h. In addition, DOB forms a stable adduct very efficiently with Tris, which protects the abasic site against cleavage.

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Synthesis and Characterization of Oligonucleotides Containing the C4′‐Oxidized Abasic Site Produced by Bleomycin and Other DNA Damaging Agents

Cited by 46 publications

References 36 publications

Direct Strand Scission in Double Stranded RNA via a C5-Pyrimidine Radical

Direct Strand Scission in Double Stranded RNA via a C5-Pyrimidine Radical

Probing DNA interstrand cross-link formation by an oxidized abasic site using nonnative nucleotides

Preparation and Analysis of Oligonucleotides Containing Lesions Resulting from C5‘-Oxidation

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