The Structure of the Uridine Dimer Produced by UV Irradiation of Uridine

Fahr, Egon; Fürst, Gerhard; Dörhöfer, Günther; Popp, H.

doi:10.1002/anie.196702502

Cited by 8 publications

(3 citation statements)

References 2 publications

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“…While the exact mechanisms of peptide-nucleotide adduct formation through base stacking are yet to be established, possible mechanisms have been proposed 23 . We note that it has been known for decades that UV can induce the formation of U-U or U-C dimers for nucleotide bases stacked together 49 , probably through similar mechanisms.…”

Section: Discussionmentioning

confidence: 76%

Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes

Feng

Liu

et al. 2022

Preprint

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UV crosslinking of protein-RNA complexes in direct contacts has been widely used to map protein-RNA interactions and yet the underlying mechanisms of photo-crosslinking are poorly understood. This knowledge gap is due to the challenge to precisely map the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we developed a computational method named PxR3D-map to analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped by different assays with experimentally resolved 3D structures of protein-RNA complexes. PxR3D-map can reliably predict crosslink sites using structural information characterizing protein-RNA interaction interfaces. Amino acid-nucleotide crosslinking is strongly associated with and likely facilitated by several structural features. Importantly, we found that base stacking facilitating protein-RNA crosslinking can occur not only with aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms underlie crosslinking of RNA with different types of RNA-binding domains. Our work suggests protein-RNA photo-crosslinking in the cellular environment is highly selective, which can be utilized to better interpret data generated based on UV-crosslinking and guide further technology development to map and characterize protein-RNA complexes.

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Section: Discussionmentioning

confidence: 76%

Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes

Feng

Liu

et al. 2022

Preprint

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show abstract

“…While the exact mechanisms of peptide-nucleotide adduct formation through base stacking are yet to be established, possible mechanisms have been proposed 23 . We note that it has been known for decades that UV light can induce the formation of U-U or U-C dimers for nucleotide bases stacked together 52 , probably through similar mechanisms.…”

Section: Discussionmentioning

confidence: 78%

Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes

Feng,

Lu,

Maji

et al. 2024

Nat Commun

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UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.

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“…Uridine is reduced photochemically in the presence of bisulfite [7] and sodium borohydride [8] to the dihydro derivative. A symmetric dimer bonded at C (5) and C(6) has been prepared photochemically [9].…”

Section: And Discussionmentioning

confidence: 99%

Electrochemical reduction of uridine in dimethyl sulfoxide: effect of the ribose group

Bresnahan

Cummings

Elving

1981

Electrochimica Acta

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Adam-The easier electrochemical reduction of uridme (I-/LLLtibofirranosylumcil) in dimethyl sulfoxide as compared to uracil (2, 4dihydroxypyrimidine) by ca. 0.1 V is exphcable on the basii of the electronwithdrawing effect of the ribose group. This effect and possible steric hindrance by the ribose group markedly affect the reaction sequence following the initial one-electron reduction to generate a radical anion, which abstracts a proton from the parent uridine (father-son reaction) to form the neutral uridine free radical and the uridme anion. With increasing &dine concentration, Further reduction and protonstion reactions are favored, resulting in an increase in the effective faradaic n from CLI. 0.5 to 0.8. The availability of only one proton-donating site on uridine, ie, that on N(3). allows explication of the behavior of other hydroxypyrimidiues such as uracil.

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The Structure of the Uridine Dimer Produced by UV Irradiation of Uridine

Cited by 8 publications

References 2 publications

Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes

Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes

Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes

Electrochemical reduction of uridine in dimethyl sulfoxide: effect of the ribose group

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