Oxidative Nucleobase Modifications Leading to Strand Scission

Burrows, Cynthia J.; Muller, James G.

doi:10.1021/cr960421s

Cited by 1,689 publications

(1,672 citation statements)

References 417 publications

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“…[68][69][70][71] Indeed, the cleavage with artificial metallo-nucleases is following either an oxidative or a hydrolytic mechanism. 67,[72][73][74] The former is observed with redox-active metal complexes while the latter one is based on the Lewis-acidity of metal ions. At this point, we emphasise that we will cover only work in which PNAs are covalently linked to a metal complex and act as a recognition fragment for a complementary DNA or RNA sequence.…”

Section: Metal-containing Pnas As Artificial Nucleasesmentioning

confidence: 99%

“…A serious drawback of the oxidative cleavage is the generation of products with unnatural termini, whereas the cleaving products of hydrolytical nucleases can be further processed by enzymes. 72,73 Therefore, the hydrolytic cleavage of linear DNA 67 and RNA 65, 66, 78 using PNAzymes is generally preferred. Although most of the examples concern the cleavage of RNA, which is known to be more susceptible to hydrolysis than DNA, 74 Zelder, Mokhir and Krämer demonstrated that the sequencespecific DNA strand cleavage was possible.…”

Section: Metal-containing Pnas As Artificial Nucleasesmentioning

confidence: 99%

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Metal-containing peptide nucleic acid conjugates

2011

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Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physicochemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metalconjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA˙DNA hybrid stability, and last but not least as probes for molecular and cell biology.

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Section: Metal-containing Pnas As Artificial Nucleasesmentioning

confidence: 99%

Section: Metal-containing Pnas As Artificial Nucleasesmentioning

confidence: 99%

Metal-containing peptide nucleic acid conjugates

2011

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“…In gel electrophoresis experiments, oxidatively modified bases are cleaved by hot piperidine or enzymatic treatments. 31 This step can also contribute to the observed strand cleavage patterns because not all guanine lesions may be hot alkali -labile, e.g., 8-oxoguanine, 56 or may be partially labile like 5-guanidino-4-nitroimidazole. 57 …”

Section: Effects Of Base Sequence Context: Insights Into Relationshipmentioning

confidence: 99%

Oxidation of Guanine in G, GG, and GGG Sequence Contexts by Aromatic Pyrenyl Radical Cations and Carbonate Radical Anions: Relationship between Kinetics and Distribution of Alkali-Labile Lesions

et al. 2008

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Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotdes with noncontiguous guanines G, and grouped as contiguous GG and GGG sequences, were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd: Yag laser pulses, the DNA-bound BPT molecules were photoionized to BPT •+ radicals by a consecutive two-photon ionization mechanism. The BPT •+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron transfer reactions, and the rate constants of these reactions follow the trend 5′-..GGG.. > 5′-..GG.. > 5′-..G… In the case of CO 3 •− radicals, the oxidation of guanine occurs by intermolecular collision pathways and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO 3 •− radicals, as well as by BPT •+ , is base sequence context-dependent and is greater than in isolated guanines at the 5′-G in 5′-…GG… sequences, and the first two 5′-guanines in the 5′-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkalilabile guanine products. In the case of the intermolecular one-electron oxidant CO 3 •− , the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA bound oxidant BPT •+ , the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.

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“…A photooxidative DNA cleavage at the G residue occurs via the addition of oxygen and solvent to the G radical cation intermediate; 39,40 therefore, the cleavage at GG 2 in Triplex II may be prevented by steric hindrance of the triplex-forming strand. In a separate experiment, upon 365 nm photoirradiation of a mixture of Duplex I and mismatched third-strand ODN 4, we detected efficient DNA cleavage at the GG 3 site, which was of a similar magnitude to that observed for Duplex I alone ( Figure S2).…”

Section: Resultsmentioning

confidence: 99%

Stepwise regulation of hole transport in DNA by control of triplex formation

Haruna

Iida

Nishimoto

et al. 2013

Bioorganic & Medicinal Chemistry

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A functionality for regulating hole transport efficiency is a prerequisite for the utilization of DNA duplexes as nanodevices. Herein, we report the regulation of hole transport in anthraquinone-tethered DNA with dual triplex forming sites. Long-range photooxidation experiments showed that hole transport was effectively suppressed by the formation of triplex at low temperature, while it was recovered by dissociation to the duplex at higher temperature.Variation of temperature induced the formation and dissociation of the third strand at each triplex region individually, leading to the stepwise regulation of hole transport in DNA.

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Oxidative Nucleobase Modifications Leading to Strand Scission

Cited by 1,689 publications

References 417 publications

Metal-containing peptide nucleic acid conjugates

Metal-containing peptide nucleic acid conjugates

Oxidation of Guanine in G, GG, and GGG Sequence Contexts by Aromatic Pyrenyl Radical Cations and Carbonate Radical Anions: Relationship between Kinetics and Distribution of Alkali-Labile Lesions

Stepwise regulation of hole transport in DNA by control of triplex formation

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