Interstrand DNA-DNA cross-links are highly toxic to cells because these lesions block the extraction of information from the genetic material. The pathways by which cells repair cross-links are important, but not well understood. The preparation of chemically well-defined cross-linked DNA substrates represents a significant challenge in the study of cross-link repair. Here we report a simple method that employs “post-synthetic” modifications of commercially available 2’-deoxyoligonucleotides to install a single cross-link in high yield at a specified location within a DNA duplex. The cross-linking process exploits hydrazone formation between a non-natural N4-amino-2’-deoxycytidine nucleobase and the aldehyde residue of an abasic site in duplex DNA. The resulting cross-link is stable under physiological conditions, but can be readily dissociated and re-formed through heating-cooling cycles.

Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are “unhooked” by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.

The formation of interstrand cross-links in duplex DNA is important in biology, medicine, and biotechnology. Interstrand cross-links arising from the reaction of the aldehyde residue of an abasic (apurinic or AP) site with the exocyclic amino groups of guanine or adenine residues on the opposing strand of duplex DNA have previously been characterized. The canonical nucleobase cytosine has an exocyclic amino group but its ability to form interstrand cross-links by reaction with an AP site has not been characterized before now. Here it is shown that substantial yields of interstrand cross-links are generated in sequences having a mispaired cytosine residue located one nucleotide to the 3′-side of the AP site on the opposing strand (e.g., 5′XA/5′CA, where X = AP). Formation of the dC-AP cross-link is pH-dependent, with significantly higher yields at pH 5 than pH 7. Once formed, the dC-AP cross-link is quite stable, showing less than 5% dissociation over the course of 96 h at pH 7 and 37 °C. No significant yields of cross-link are observed when the cytosine residue is paired with its Watson−Crick partner guanine. It was also shown that a single AP site can engage with multiple nucleobase cross-linking partners in some sequences. Specifically, the dG-AP and dC-AP cross-links coexist in dynamic equilibrium in the sequence 5′CXA/5′CAG (X = AP). In this sequence, the dC-AP cross-link dominates. However, in the presence of NaBH 3 CN, irreversible reduction of small amounts of the dG-AP cross-link present in the mixture shifts the equilibria away from the dC-AP cross-link toward good yields of the dG-AP red cross-link.

The protocol describes the preparation and purification of interstrand DNA-DNA cross-links derived from the reaction of an N4-aminocytidine residue with an abasic site in duplex DNA. The procedures employ inexpensive, commercially-available chemicals and enzymes to carry out post-synthetic modification of commercially-available oligodeoxynucleotides. The yield of cross-linked duplex is typically better than 90%. If purification is required, the cross-linked duplex can be readily separated from single-stranded DNA starting materials by denaturing gel electrophoresis. The resulting covalent hydrazone-based cross-links are stable under physiologically-relevant conditions and may be useful for biophysical studies, structural analyses, DNA repair studies, and materials science applications.

Although cisplatin is considered as an effective anti-cancer agent, it has shown limitations and may produce toxicity in patients. Therefore, we synthesized two cis-dichlorideplatinum(II) compounds (13 and 14) composed of meta- and para-N,N-diphenyl pyridineamine ligands through a reaction of the amine precursors and PtCl2 with respective yields of 16% and 47%. We hypothesized that compounds 13 and 14, with lipophilic ligands, should transport efficiently in cancer cells and demonstrate more effectiveness than cisplatin. When tested for biological activity, compounds 13 and 14 were found to inhibit the growth of MCF 7 and MDA-MB-231 cells (IC50s 1 ± 0.4 μM and 1 ± 0.2 μM for 13 and 14, respectively, and IC50 7.5 ± 1.3 μM for compound 13 and 1 ± 0.3 μM for compound 14). Incidentally, these doses were found to be lower than cisplatin doses (IC50 5 ± 0.7 μM for MCF 7 and 10 ± 1.1 μM for MDA-MB-231). Similar to cisplatin, 13 and 14 interacted with DNA and induced apoptosis. However, unlike cisplatin, they blocked the migration of MDA-MB-231 cells suggesting that in addition to apoptotic and DNA-binding capabilities, these compounds are useful in blocking the metastatic migration of breast cancer cells. To delineate the mechanism of action, computer-aided analyses (DFT calculations) were conducted for compound 13. Results indicate that in vivo, the pyridineamine ligands are likely to dissociate from the complex, forming a platinum DNA adduct with anti-proliferative activity. These results suggest that complexes 13 and 14 hold promise as potential anti-cancer agents.