Recent aspects of the photochemistry of nucleic acids and related model compounds

Cadet, Jean; Voituriez, L.; Grand, André; Hruska, Frank E.; Vigny, Paul; Kan, Lou‐Sing

doi:10.1016/s0300-9084(85)80070-5

Cited by 67 publications

(55 citation statements)

References 95 publications

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“…1-4 The (2+2) adduct is the major product obtained both from irradiation of cellular and DNA and model systems. 5 The (6-4) adduct is formed upon thermal ring opening of an unstable oxetane intermediate which is the product of a cycloaddition reaction between the C=O double bond of the 3′-thymine to the C=C double bond of its 5′-neighbor.…”

Section: Introductionmentioning

confidence: 99%

Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 − 4) vs. (2 + 2) adducts

Hariharan

Siegmund

Saurel

et al. 2014

Photochem Photobiol Sci

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The photochemical reactions of eleven synthetic DNA hairpins possessing a single TT step either in a base-paired stem or in a hexanucleotide linker have been investigated. The major reaction products have been identified as the cis-syn (2+2) adduct and the (6-4) adduct on the basis of their spectroscopic properties including 1D and 2D NMR spectra, UV spectra and stability or instability to photochemical cleavage. Product quantum yields and ratios determined by HPLC analysis allow the behaviour of the eleven hairpins to be placed into three groups: Group I in which the the (2+2) adduct is the major product, as is usually the case for DNA, Group II in which comparable amounts of (2+2) and (6-4) adducts are formed, and Group III in which the major product is the (6-4) adduct. The latter behaviour is without precedent in natural or synthetic DNA and appears to be related to the highly fluxional structures of the hairpin reactants. Molecular dynamics simulation of ground state conformations provides quantum yields and product ratios calculated using a single parameter model that are in reasonable agreement with most of the experimental results. Factors which may influence the observed product ratios are discussed.

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Section: Introductionmentioning

confidence: 99%

Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 − 4) vs. (2 + 2) adducts

Hariharan

Siegmund

Saurel

et al. 2014

Photochem Photobiol Sci

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“…In typical cells, the genomic DNA adopts a B-conformation, and thymine photo-dimerization leads to the formation of cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone photoproduct ((6-4) PD) [4]. In contrast, in endospores, the genomic DNA adopts an A-conformation, due to the low water content, as well as the binding of small acid-soluble proteins (SASPs) [6–8].…”

Section: The Unique Photo-damage In Bacterial Endosporesmentioning

confidence: 99%

The Enzyme-Mediated Direct Reversal of a Dithymine Photoproduct in Germinating Endospores

Yang

2013

IJMS

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Spore photoproduct lyase (SPL) repairs a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct, or SP, in germinating endospores. SP is the exclusive DNA photo-damaging product found in endospores; its generation and swift repair by SPL are responsible for the spores’ extremely high UV resistance. Early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair SP in the absence of light. Recently, it has been established that SPL belongs to the radical S-adenosylmethionine (SAM) superfamily. The enzymes in this superfamily utilize a tri-cysteine CXXXCXXC motif to bind a [4Fe-4S] cluster. The cluster provides an electron to the S-adenosylmethionine (SAM) to reductively cleave its C5′-S bond, generating a reactive 5′-deoxyadenosyl (5′-dA) radical. This 5′-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. The H atom donor is suggested to be a conserved cysteine141 in B. subtilis SPL; the resulting thiyl radical likely interacts with a neighboring tyrosine99 before oxidizing the 5′-dA to 5′-dA radical and, subsequently, regenerating SAM. These findings suggest SPL to be the first enzyme in the large radical SAM superfamily (>44,000 members) to utilize a radical transfer pathway for catalysis; its study should shed light on the mechanistic understanding of the SAM regeneration process in other members of the superfamily.

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“…Importantly, such crosslinking could be achieved with relatively low levels of UV-induced strand breakage. In contrast to low intensity UV light which leads to the absorption of single photons by bases to induce formation of the S 1 and T 1 excited states (Cadet and Vigny, 1990; Daniels, 1976; Fisher and Johns, 1976), the higher energy of the pulse laser is thought to allow the absorption of two photons to form the higher activation states of H T and H S (Budowsky et al , 1986; Cadet and Vigny, 1990). Importantly, bases in H T and H S states crosslink more efficiently and may have expanded speci-ficity relative to the excited states produced with low intensity UV (Budowsky et al , 1986).…”

Section: Generation Of Crosslinked Rnasmentioning

confidence: 99%

RNA Crosslinking Methods

Harris

Christian

2009

Methods in Enzymology

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RNA–RNA crosslinking provides a rapid means of obtaining evidence for the proximity of functional groups in structurally complex RNAs and ribonucleoproteins. Such evidence can be used to provide a physical context for interpreting structural information from other biochemical and biophysical methods and for the design of further experiments. The identification of crosslinks that accurately reflect the native conformation of the RNA of interest is strongly dependent on the position of the crosslinking agent, the conditions of the crosslinking reaction, and the method for mapping the crosslink position. Here, we provide an overview of protocols and experimental considerations for RNA–RNA cross-linking with the most commonly used long- and short-range photoaffinity reagents. Specifically, we describe the merits and strategies for random and site-specific incorporation of these reagents into RNA, the crosslinking reaction and isolation of crosslinked products, the mapping crosslinked sites, and assessment of the crosslinking data.

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Recent aspects of the photochemistry of nucleic acids and related model compounds

Cited by 67 publications

References 95 publications

Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 − 4) vs. (2 + 2) adducts

Thymine photodimer formation in DNA hairpins. Unusual conformations favor (6 − 4) vs. (2 + 2) adducts

The Enzyme-Mediated Direct Reversal of a Dithymine Photoproduct in Germinating Endospores

RNA Crosslinking Methods

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