Reactivity of Damaged Pyrimidines: DNA Cleavage via Hemiaminal Formation at the C4 Positions of the Saturated Thymine of Spore Photoproduct and Dihydrouridine

Lin, Gan; Jian, Yajun; Dria, Karl J.; Long, Eric C.; Li, Lei

doi:10.1021/ja505407p

Cited by 10 publications

(45 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As a consequence, the original oxygen atom attached with the C4=O moiety only possesses a 50% chance to be retained with the regenerated SP after one reaction cycle, and it can eventually be replaced by an oxygen atom from water if the reaction is allowed to proceed long enough. This possibility is supported by 18 O labeling experiments, where almost all remaining SP molecules carried an 18 O label after a 24‐h reaction using 18 O labeled water at pH 12 . Such an oxygen exchange process mediated by the hemiaminal intermediate is facilitated by basic conditions; however, it also occurs at physiological pH albeit at a slower rate .…”

Section: Impacts Of Sp On the Genomic Dnamentioning

confidence: 85%

“…This possibility is supported by 18 O labeling experiments, where almost all remaining SP molecules carried an 18 O label after a 24‐h reaction using 18 O labeled water at pH 12 . Such an oxygen exchange process mediated by the hemiaminal intermediate is facilitated by basic conditions; however, it also occurs at physiological pH albeit at a slower rate .…”

Section: Impacts Of Sp On the Genomic Dnamentioning

confidence: 85%

See 1 more Smart Citation

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Setlow

2015

Photochem & Photobiology

Self Cite

View full text Add to dashboard Cite

Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV irradiated bacterial spores [Donnellan, J. & Setlow R. (1965) Science, 149, 308–310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A-DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid-soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. SP photoreaction is proved to occur via a unique H-atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP-containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past fifty years, which indicates a very rich SP photobiology that may exist beyond endospores.

show abstract

Section: Impacts Of Sp On the Genomic Dnamentioning

confidence: 85%

Section: Impacts Of Sp On the Genomic Dnamentioning

confidence: 85%

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Setlow

2015

Photochem & Photobiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…the spore photoproduct (SP), activates the C4=O moiety, supporting a water addition reaction to yield a hemiaminal intermediate. 14 In contrast, such a 5 reaction is not observed with an intact thymidine residue. 14 A similar reaction was observed with another damaged pyrimidine: 5,6-dihydro-2′-deoxyuridine (dHdU), 14 suggesting that this reaction may be ascribed as a general property of a saturated pyrimidine residue.…”

Section: Introductionmentioning

confidence: 98%

“…14 In contrast, such a 5 reaction is not observed with an intact thymidine residue. 14 A similar reaction was observed with another damaged pyrimidine: 5,6-dihydro-2′-deoxyuridine (dHdU), 14 suggesting that this reaction may be ascribed as a general property of a saturated pyrimidine residue. Oxidation, alkylation, and other electrophilic reagents acting on nucleobases are known to reduce the electron density from the heterocycle, making the modified nucleobases better leaving groups to form an AP.…”

Section: Introductionmentioning

confidence: 98%

Reactivity of Damaged Pyrimidines: Formation of a Schiff Base Intermediate at the Glycosidic Bond of Saturated Dihydrouridine

et al. 2015

Self Cite

View full text Add to dashboard Cite

DNA glycosylases catalyze the first step of the base excision repair (BER) pathway. The chemistry used by these enzymes for deglycosylation has been largely considered as the chemistry of the oxocarbenium ion, e.g., direct rupture of the C1'-N1 bond resulting in an oxocarbenium ion intermediate. Here we present mechanistic studies revealing the 2'-deoxyribose isomerization and subsequent deglycosylation processes in two pyrimidine lesions: 5,6-dihydro-2'-deoxyuridine (dHdU) and 5,6-dihydrothymidine (dHT), formed via ionizing radiation damage to 2'-deoxycytidine and thymidine, respectively, under anoxic conditions. Acid or heat treatment of these two lesions leads to the production of two pairs of C1' epimers containing a pyranose and a furanose, respectively, indicating that both lesions favor the rupture of the C1'-O4' bond, resulting in a Schiff base intermediate at the N-glycosidic bond. Such a Schiff base intermediate was trapped and characterized by either Pd-catalyzed hydrogenation or thiol-mediated addition reaction. In contrast, in undamaged 2'-deoxyuridine and thymidine, reactions at elevated temperatures lead to the release of nucleobases most likely via the traditional oxocarbenium ion pathway. DFT calculations further support the experimental findings, suggesting that the oxocarbenium ion intermediate is responsible for the deglycosylation process if the integrity of the pyrimidine ring is maintained, while the Schiff base intermediate is preferred if the C5═C6 bond is saturated. Currently, the oxocarbenium ion pathway is indicated to be solely responsible for the deglycosylation in BER enzymes, however our results suggest an alternative Schiff base mechanism which may be responsible for the repair of saturated pyrimidine damages.

show abstract

“…Dihyropyrimidines are non-coding bases that have lost their planar structure as a consequence of the saturation of the C5-C6 double bound (Lindahl, 1993). Above physiological pH, and more slowly at physiological pH, these saturated bases can further decompose into fragments of bases (Lin et al, 2014). Some decomposition products could be genotoxic.…”

Section: Discussionmentioning

confidence: 99%

Dihydropyrimidinase protects from DNA replication stress caused by cytotoxic metabolites.

Basbous

Aze

Chaloin

et al. 2018

Preprint

View full text Add to dashboard Cite

Imbalance in the level of the pyrimidine degradation products dihydrouracil and dihydrothymine is associated with cellular transformation and cancer progression. Dihydropyrimidines are degraded by dihydropyrimidinase (DHP), a zinc metalloenzyme that is upregulated in solid tumors but not in the corresponding normal tissues. How dihydropyrimidine metabolites affect cellular phenotypes remains elusive. Here we show that the suppression of DHP in cancer cell lines is cytotoxic. An increase in the level of dihydropyrimidines induced DNA replication and transcriptional stress. Cells lacking DHP accumulated DNA-protein crosslinks (DPCs), including covalently trapped DNA polymerase . Furthermore, we show that the plant flavonoid dihydromyricetin inhibits human DHP activity. Cellular exposure to dihydromyricetin triggered DPCs-dependent DNA replication stress in cancer cells. This study defines dihydropyrimidines as potentially cytotoxic metabolites that may offer an opportunity for therapeutic-targeting of DHP activity in solid tumors. high in human carcinomas of the lung, colon, pancreas, salivary gland and stomach (Naguib et al., 1985). Here we show that suppression of DHP in cancer cell lines induces DNA replication stress, as revealed by the accumulation of single-stranded DNA, by the induction of ATR/Chk1 signaling and by the slowing of replication fork progression. Depletion of DHP also attenuates transcription activity, stabilizes p53 and eventually blocks cell proliferation. The addition of dihydropyrimidines to Xenopus egg-extracts induces the formation of abnormal DNA replication products. IN DHP depleted cells, DNA replication and transcriptional stress correlates with the accumulation of DNA-protein crosslinks (DPCs). Thus, we suggest that dihydropyrimidines yield DPCs that directly interferes with DNA-templated processes. We found that the flavonoid dihydromyricetin inhibits the activity of purified human dihydropyrimidinase. Addition of dihydromyricetin in the cell culture medium induces the accumulation of DNA-protein crosslinks and interferes with the progression of replication forks. These findings indicate that unless degraded by dihydropyimidinase, the amount of dihydropyrimidines produced in cancer cell cultures is sufficient to block DNA templated processes.

show abstract

Reactivity of Damaged Pyrimidines: DNA Cleavage via Hemiaminal Formation at the C4 Positions of the Saturated Thymine of Spore Photoproduct and Dihydrouridine

Cited by 10 publications

References 31 publications

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Reactivity of Damaged Pyrimidines: Formation of a Schiff Base Intermediate at the Glycosidic Bond of Saturated Dihydrouridine

Dihydropyrimidinase protects from DNA replication stress caused by cytotoxic metabolites.

Contact Info

Product

Resources

About