Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 Å resolution

Matthew C. Swenson, Shanthi R. Paranawithana, Paul S. Miller, Clara L. Kielkopf

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Chemotherapeutic alkylating agents, such as bifunctional nitrogen mustards and cisplatins, generate interstrand DNA cross-links that inhibit cell proliferation by arresting DNA transcription and replication. A synthetic N 4C-ethyl-N4C interstrand cross-link between opposing cytidines mimics the DNA damage produced by this class of clinically important compounds and can be synthesized in large quantities to study the repair, physical properties, and structures of these DNA' adducts. The X-ray structure of a DNA duplex d(CCAAC*GTTGG)2 containing a synthetic N 4C-ethyl-N4C interstrand cross-link between the cytosines of the central CpG step (*) has been determined at 1.65 Å resolution. This structure reveals that the ethyl cross-link in the CpG major groove does not significantly disrupt the B-form DNA helix. Comparison of the N4C-ethyl-N4C cross-linked structure with the structure of an un-cross-linked oligonucleotide of the same sequence reveals that the cross-link selectively stabilizes a preexisting alternative conformation. The conformation preferred by the cross-linked DNA is constrained by the geometry of the ethyl group bridging the cytosine amines. Characteristics of the cross-linked CpG step include subtle differences in the roll of the base pairs, optimized Watson-Crick hydrogen bonds, and loss of a divalent cation binding site. Given that the N4C-ethyl-N4C cross-link stabilizes a preexisting conformation of the CpG step, this synthetically accessible substrate presents an ideal model system for studying the genomic effects of covalently coupling the DNA strands, independent of gross alterations in DNA structure.

Original languageEnglish (US)
Pages (from-to)4545-4553
Number of pages9
Issue number15
StatePublished - Apr 17 2007
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry


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