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Updated: Jun 15, 2026
DNAzyme-dependent Analysis of rRNA 2’-O-Methylation
Published on: September 16, 2019
Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA
Lianghua Lu1, Chengqi Yi, Xing Jian
1Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA.
Abstract:
N(1)-meA and N(3)-meC are cytotoxic DNA base methylation lesions that can accumulate in the genomes of various organisms in the presence of S(N)2 type methylating agents. We report here the structural characterization of these base lesions in duplex DNA using a cross-linked protein-DNA crystallization system. The crystal structure of N(1)-meA:T pair shows an unambiguous Hoogsteen base pair with a syn conformation adopted by N(1)-meA, which exhibits significant changes in the opening, roll and twist angles as compared to the normal A:T base pair. Unlike N(1)-meA, N(3)-meC does not establish any interaction with the opposite G, but remains partially intrahelical. Also, structurally characterized is the N(6)-meA base modification that forms a normal base pair with the opposite T in duplex DNA. Structural characterization of these base methylation modifications provides molecular level information on how they affect the overall structure of duplex DNA. In addition, the base pairs containing N(1)-meA or N(3)-meC do not share any specific characteristic properties except that both lesions create thermodynamically unstable regions in a duplex DNA, a property that may be explored by the repair proteins to locate these lesions.
Insights
Cytotoxic DNA base methylation lesions, N(1)-meA and N(3)-meC, were structurally characterized. These lesions destabilize DNA, potentially aiding repair protein detection.
Area of Science:
- Molecular Biology
- Structural Biology
- Genetics
Background:
- Cytotoxic DNA base methylation lesions, N(1)-meA and N(3)-meC, can accumulate in genomes.
- These lesions arise from exposure to S(N)2 type methylating agents.
Purpose of the Study:
- To structurally characterize N(1)-meA and N(3)-meC base lesions in duplex DNA.
- To understand how these modifications affect DNA structure at a molecular level.
Main Methods:
- Utilized a cross-linked protein-DNA crystallization system.
- Determined crystal structures of DNA duplexes containing base methylation lesions.
Main Results:
- N(1)-meA forms a Hoogsteen base pair with a syn conformation, altering DNA geometry.
- N(3)-meC remains partially intrahelical, without pairing with the opposite base.
- N(6)-meA forms a normal Watson-Crick base pair.
- Both N(1)-meA and N(3)-meC create thermodynamically unstable DNA regions.
Conclusions:
- Structural insights into DNA base methylation lesions N(1)-meA and N(3)-meC.
- These lesions induce significant structural distortions in duplex DNA.
- DNA instability caused by these lesions may be recognized by repair mechanisms.
