Structure Of A Stable Interstrand Dna Cross-Link Involving A Beta-N-Glycosyl Linkage Between An N-6-Da Amino Group And An Abasic Site

Abasic (AP) sites are one of the most common forms of DNA damage. The deoxyribose ring of AP sites undergoes anomerization between alpha and beta configurations, via an electrophilic aldehyde intermediate. In sequences where an adenine residue is located on the opposing strand and offset 1 nt to the 3' side of the AP site, the nucleophilic N-6-dA amino group can react with the AP aldehyde residue to form an interstrand cross-link (ICL). Here, we present an experimentally determined structure of the dA-AP ICL by NMR spectroscopy. The ICL was constructed in the oligodeoxynucleotide 5'-d(T(1)A(2)T(3)G(4)T(5)C(6)T(7)A(8)A(9)-G(10)T(11)T(12)C(13)A(14)T(15)C(16)T(17)A(18)) - 3' : 5'-(T(19)A(20)G(21)A(22)T(23)G(24)A(25)A(26)C(27)X(28)T(29)A(30)G(31)A(32)C(33)A(34)T(35)A(36))-3' (X=AP site), with the dA-AP ICL forming between A(8) and X-28. The NMR spectra indicated an ordered structure for the cross-linked DNA duplex and afforded detailed spectroscopic resonance assignments. Structural refinement, using molecular dynamics calculations restrained by NOE data (rMD), revealed the structure of the ICL. In the dA-AP ICL, the 2'-deoxyribosyl ring of the AP site was ring-closed and in the beta configuration. Juxtapositioning the N-6-dA amino group and the aldehydic C1 of the AP site within bonding distance while simultaneously maintaining two flanking unpaired A(9) and T-29 bases stacked within the DNA is accomplished by the unwinding of the DNA at the ICL. The structural data is discussed in the context of recent studies describing the replication-dependent unhooking of the dA-AP ICL by the base excision repair glycosylase NEIL3.