Mispair-aligned N3T-alkyl-N3T interstrand cross-linked DNA: Synthesis and characterization of duplexes with interstrand cross-links of variable lengths

Christopher J. Wilds, Anne M. Noronha, Sebastien Robidoux, Paul S. Miller

Research output: Contribution to journalArticlepeer-review


Therapeutic bifunctional alkylating agents generate interstrand cross-links in duplex DNA. As part of our continuing studies on DNA duplexes that contain alkyl interstrand cross-links, we have synthesized a cross-link that bridges the N3 positions of a mismatched thymidine base pair. This cross-link, which is similar to the N3C-alkyl-N3C cross-link that has been observed between mismatched cytosine base pairs, was introduced by first incorporating a cross-linked phosphoramidite unit at the 5′-end of an oligonucleotide chain. Fully cross-linked duplexes were then synthesized using an orthogonal approach to selectively remove protecting groups, thus allowing construction of the cross-linked duplex via conventional solid-phase oligonucleotide synthesis. Short DNA duplexes with alkyl cross-links of various lengths (two, four, and seven methylene units) were prepared, and their physical properties were studied via UV thermal denaturation and circular dichroism spectroscopy. These linkers were found to stabilize the duplexes by 37, 31, and 16 °C for the two-, four-, and seven-carbon linkers, respectively, relative to a non-cross-linked duplex. Circular dichroism spectra suggested that these lesions induce very little deviation in the global structure relative to the non-cross-linked duplex DNA control. Molecular models show that the two-carbon cross-link spans the distance between the N3 atoms of the T-T mismatch without perturbing the helix structure, whereas the longer linkers, particularly the seven-carbon linker, tend to push the thymines apart, creating a local distortion. This perturbation may account for the lower thermal stability of the seven-carbon versus two-carbon cross-linked duplex.

Original languageEnglish (US)
Pages (from-to)9257-9265
Number of pages9
JournalJournal of the American Chemical Society
Issue number30
StatePublished - Aug 4 2004

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry


Dive into the research topics of 'Mispair-aligned N<sup>3</sup>T-alkyl-N<sup>3</sup>T interstrand cross-linked DNA: Synthesis and characterization of duplexes with interstrand cross-links of variable lengths'. Together they form a unique fingerprint.

Cite this