Sequence Specific DNA Cross-Linking Triggered by Visible Light

Beeck, Marieke Op de; Madder, Annemieke

doi:10.1021/ja301901p

Cited by 101 publications

(87 citation statements)

References 33 publications

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“…An HPLC comparison with authentic 17 confirmed that the cross-link was predominantly formed with the 6-amino group of dA at acidic pH (Figure 5A). Conversely, Figure 5B clearly shows that the cross-link was formed at the N3 atom of T ( 18 ) at alkaline pH (Figure 5B). These results suggest that the reactivity of the vinyl group of 2 is affected by the pH of the reaction medium.…”

Section: Resultsmentioning

confidence: 99%

“…Cross-link formation is also used to maintain 3D nucleic acid structures (9–11). A variety of functional groups have also been developed to enable interstrand cross-linking, including disulfide bonds (12), benzophenone derivatives (13), carbazoles (14), quinone methides (15,16), phenylselenyl derivatives of pyrimidines (17) and furan derivatives (18). To further advance these studies, an efficient cross-linking method is still desired.…”

Section: Introductionmentioning

confidence: 99%

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4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA

Nishimoto

Jitsuzaki

Onizuka

et al. 2013

Nucleic Acids Research

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The formation of interstrand cross-links in nucleic acids can have a strong impact on biological function of nucleic acids; therefore, many cross-linking agents have been developed for biological applications. Despite numerous studies, there remains a need for cross-linking agents that exhibit both efficiency and selectivity. In this study, a 4-vinyl-substituted analog of thymidine (T-vinyl derivative) was designed as a new cross-linking agent, in which the vinyl group is oriented towards the Watson–Crick face to react with the amino group of an adenine base. The interstrand cross-link formed rapidly and selectively with a uridine on the RNA substrate at the site opposite to the T-vinyl derivative. A detailed analysis of cross-link formation while varying the flanking bases of the RNA substrates indicated that interstrand cross-link formation is preferential for the adenine base on the 5′-side of the opposing uridine. In the absence of a 5′-adenine, a uridine at the opposite position underwent cross-linking. The oligodeoxynucleotides probe incorporating the T-vinyl derivative efficiently formed interstrand cross-links in parallel-type triplex DNA with high selectivity for dA in the homopurine strand. The efficiency and selectivity of the T-vinyl derivative illustrate its potential use as a unique tool in biological and materials research.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA

Nishimoto

Jitsuzaki

Onizuka

et al. 2013

Nucleic Acids Research

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“…This crosslinking chemistry is based on the pronounced propensity of furans to undergo oxidative conversion to highly electrophilic ene‐1,4‐diones in an aqueous environment; these readily react with DNA and RNA nucleobases bearing exocyclic amino groups (Scheme ) 2b. 6 An attractive feature of this reaction sequence is that it can be initiated with singlet oxygen, which can be generated in situ by irradiation of photosensitisers with non‐UV light under aerobic conditions 2a. This enables spatiotemporal control of crosslinking and offers enhanced penetration depths in biological samples.…”

Section: Methodsmentioning

confidence: 99%

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

et al. 2014

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We report the template-free pyrolysis of easily available natural seaweed, Undaria pinnatifida, as a single precursor, which results in "seaweed carbon" (SCup). Interestingly, thus-obtained SCup not only contains heteroatoms such as nitrogen and sulfur in its framework, but it also possesses a well-developed porous structure with high surface area. The heteroatoms in SCup originate from the nitrogen- and sulfur-containing ingredients in seaweed, whereas the porosity is created by removal of salts inherently present in the seaweed. These essential and fundamental properties make seaweed a prime choice as a precursor for heteroatom-containing highly porous carbon as a metal-free efficient electrocatalyst. As-synthesized SCup showed excellent electrocatalytic activity in the oxygen reduction reaction (ORR) in alkaline medium, which can be addressed in terms of the presence of the nitrogen and sulfur heteroatoms, the well-developed porosity, and the electrical conductivity in the carbon framework. The pyrolysis temperature was a key controlling parameter that determined the trade-off between heteroatom doping, surface properties, and electrical conductivity. In particular, SCup prepared at 1000 °C showed the best ORR performance. Additionally, SCup exhibited enhanced durability and methanol tolerance relative to the state of the art commercial Pt catalyst, which demonstrates that SCup is a promising alternative to costly Pt-based catalysts for the ORR.

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“…Since 1 O 2 can be generated by irradiation of photosensitizers with red light, this approach should offer a high penetration depth in complex biological samples and the absence of nucleic acid damaging photoreactions associated with UV light. This chemistry had previously been described and thoroughly characterized in the context of DNA-DNA interstrand crosslink formation and proceeds via a proposed mechanism involving a 2+4 cycloaddition of 1 O 2 to the furan, opening of the resulting ozonide, and ultimately formation of a γ-keto-enal that can build cyclic adducts with A, G, and C nucleobases (Figure 2C) (Op De Beeck and Madder, 2011, 2012). Since this represents a rather nucleic acid-selective crosslinking chemistry that targets only certain nucleobases, it could provide more detailed information on the topology of protein-nucleic acid complexes, potentially including information about the binding mode of protein motifs (backbone- or groove-interaction) and the pairing state of individual nucleobases in complexed RNA or DNA.…”

Section: Genetically Encoded Chemistries For Studying Regulatory Procmentioning

confidence: 97%

Genetic code expansion as a tool to study regulatory processes of transcription

Schmidt¹,

Summerer²

2014

Front. Chem.

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The expansion of the genetic code with non-canonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.

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Sequence Specific DNA Cross-Linking Triggered by Visible Light

Cited by 101 publications

References 33 publications

4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA

4-vinyl-substituted pyrimidine nucleosides exhibit the efficient and selective formation of interstrand cross-links with RNA and duplex DNA

Seaweed‐Derived Heteroatom‐Doped Highly Porous Carbon as an Electrocatalyst for the Oxygen Reduction Reaction

Genetic code expansion as a tool to study regulatory processes of transcription

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