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Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.

Publication ,  Journal Article
Xu, Y; Manghrani, A; Liu, B; Shi, H; Pham, U; Liu, A; Al-Hashimi, HM
Published in: J Biol Chem
November 20, 2020

As the Watson-Crick faces of nucleobases are protected in dsDNA, it is commonly assumed that deleterious alkylation damage to the Watson-Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. However, damage to the Watson-Crick faces of nucleobases has been reported in dsDNA in vitro through mechanisms that are not understood. In addition, the extent of protection from methylation damage conferred by dsDNA relative to ssDNA has not been quantified. Watson-Crick base pairs in dsDNA exist in dynamic equilibrium with Hoogsteen base pairs that expose the Watson-Crick faces of purine nucleobases to solvent. Whether this can influence the damage susceptibility of dsDNA remains unknown. Using dot-blot and primer extension assays, we measured the susceptibility of adenine-N1 to methylation by dimethyl sulfate (DMS) when in an A-T Watson-Crick versus Hoogsteen conformation. Relative to unpaired adenines in a bulge, Watson-Crick A-T base pairs in dsDNA only conferred ∼130-fold protection against adenine-N1 methylation, and this protection was reduced to ∼40-fold for A(syn)-T Hoogsteen base pairs embedded in a DNA-drug complex. Our results indicate that Watson-Crick faces of nucleobases are accessible to alkylating agents in canonical dsDNA and that Hoogsteen base pairs increase this accessibility. Given the higher abundance of dsDNA relative to ssDNA, these results suggest that dsDNA could be a substantial source of cytotoxic damage. The work establishes DMS probing as a method for characterizing A(syn)-T Hoogsteen base pairs in vitro and also lays the foundation for a sequencing approach to map A(syn)-T Hoogsteen and unpaired adenines genome-wide in vivo.

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Published In

J Biol Chem

DOI

EISSN

1083-351X

Publication Date

November 20, 2020

Volume

295

Issue

47

Start / End Page

15933 / 15947

Location

United States

Related Subject Headings

  • Sulfuric Acid Esters
  • DNA Methylation
  • DNA
  • Biochemistry & Molecular Biology
  • Base Pairing
  • 34 Chemical sciences
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

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Xu, Y., Manghrani, A., Liu, B., Shi, H., Pham, U., Liu, A., & Al-Hashimi, H. M. (2020). Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. J Biol Chem, 295(47), 15933–15947. https://doi.org/10.1074/jbc.RA120.014530
Xu, Yu, Akanksha Manghrani, Bei Liu, Honglue Shi, Uyen Pham, Amy Liu, and Hashim M. Al-Hashimi. “Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.J Biol Chem 295, no. 47 (November 20, 2020): 15933–47. https://doi.org/10.1074/jbc.RA120.014530.
Xu Y, Manghrani A, Liu B, Shi H, Pham U, Liu A, et al. Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. J Biol Chem. 2020 Nov 20;295(47):15933–47.
Xu, Yu, et al. “Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.J Biol Chem, vol. 295, no. 47, Nov. 2020, pp. 15933–47. Pubmed, doi:10.1074/jbc.RA120.014530.
Xu Y, Manghrani A, Liu B, Shi H, Pham U, Liu A, Al-Hashimi HM. Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage. J Biol Chem. 2020 Nov 20;295(47):15933–15947.

Published In

J Biol Chem

DOI

EISSN

1083-351X

Publication Date

November 20, 2020

Volume

295

Issue

47

Start / End Page

15933 / 15947

Location

United States

Related Subject Headings

  • Sulfuric Acid Esters
  • DNA Methylation
  • DNA
  • Biochemistry & Molecular Biology
  • Base Pairing
  • 34 Chemical sciences
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences
  • 11 Medical and Health Sciences
  • 06 Biological Sciences