The rate of formation and stability of abasic site interstrand crosslinks in the DNA duplex

Hušková, Andrea; Landová, Barbora; Bouřa, Evžen; Šilhán, Jan

doi:10.1016/j.dnarep.2022.103300

Cited by 6 publications

(7 citation statements)

References 65 publications

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“…Other than the observations provided above, the effects of local sequence on the ICL yield generated in duplexes containing the dA-AP sequence motif are cryptic. Nonetheless, our findings, alongside earlier results ,,,, clearly demonstrate that the dA-AP ICL can form in a wide variety of sequence contexts. Indeed, the majority of the sequences examined here generated equilibrium ICL yields of 15% or more, and relatively few sequences produced ICL yields below 5%.…”

Section: Resultssupporting

confidence: 86%

“…In most previous studies, formation of the dA-AP ICL was carried out in HEPES buffer (50 mM, pH 7.4) containing 100 mM NaCl. ,,− Here we examined time-courses for cross-link formation in several different buffers and at pH values between 5 and 8.…”

Section: Resultsmentioning

confidence: 99%

“…Our previous work characterized formation of the dA-AP ICL in eight different sequences. ,,, A recent study measured cross-link formation in an additional 13 sequences . Here we used gel electrophoretic analysis to measure the yield of slowly migrating ICL bands generated in more than 40 different sequence contexts containing the core dA-AP cross-linking motif 5′-XN/5′AN (where N is any nucleobase and X = AP site).…”

Section: Resultsmentioning

confidence: 99%

“… 14 , 27 , 37 , 91 A recent study measured cross-link formation in an additional 13 sequences. 38 Here we used gel electrophoretic analysis to measure the yield of slowly migrating ICL bands generated in more than 40 different sequence contexts containing the core dA-AP cross-linking motif 5′-XN/5′AN (where N is any nucleobase and X = AP site). We varied the identity of the nucleobases neighboring and opposing the AP site ( Figures 9 and S12 ).…”

Section: Resultsmentioning

confidence: 99%

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Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA

et al. 2022

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The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg 2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH 3 CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA

et al. 2022

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“…An aldehyde group of the ring-opened ribose at C1′ forms an N -glycosidic bond with an amine group of a base in the opposite DNA strand ( 9 , 10 ). It is noteworthy that a stable and specific Ap-ICL forms between an Ap site and an adenine in the opposite strand within the 5′-Ap-dT-3′ sequence ( 11 , 12 ).…”

Section: Introductionmentioning

confidence: 99%

Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model

Hušková

Dinesh

Srb

et al. 2022

Nucleic Acids Research

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Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block the replication machinery that can cause a genomic instability. Ubiquitous abasic DNA sites are particularly susceptible to spontaneous cross-linking with a base from the opposite DNA strand. Detection of a crosslink induces the DNA helicase ubiquitination that recruits NEIL3, a DNA glycosylase responsible for the lesion removal. NEIL3 utilizes several zinc finger domains indispensable for its catalytic NEI domain repairing activity. They recruit NEIL3 to the repair site and bind the single-stranded DNA. However, the molecular mechanism underlying their roles in the repair process is unknown. Here, we report the structure of the tandem zinc-finger GRF domain of NEIL3 and reveal the molecular details of its interaction with DNA. Our biochemical data indicate the preferential binding of the GRF domain to the replication fork. In addition, we obtained a structure for the catalytic NEI domain in complex with the DNA reaction intermediate that allowed us to construct and validate a model for the interplay between the NEI and GRF domains in the recognition of an interstrand cross-link. Our results suggest a mechanism for recognition of the DNA replication X-structure by NEIL3, a key step in the interstrand cross-link repair.

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Repair of genomic interstrand crosslinks

Bellani,

Shaik,

Majumdar

et al. 2024

DNA Repair

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The rate of formation and stability of abasic site interstrand crosslinks in the DNA duplex

Cited by 6 publications

References 65 publications

Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA

Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA

Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model

Repair of genomic interstrand crosslinks

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