Preparation and Purification of Oligodeoxynucleotide Duplexes Containing a Site-Specific, Reduced, Chemically Stable Covalent Interstrand Cross-Link Between a Guanine Residue and an Abasic Site

Methods for the preparation of DNA duplexes containing interstrand covalent cross-links may facilitate research in the fields of biochemistry, molecular biology, nanotechnology, and materials science. Here we report methods for the synthesis and isolation of DNA duplexes containing a site-specific, chemically stable, reduced covalent interstrand cross-link between a guanine residue and an abasic site. The method uses experimental techniques and equipment that are common in most biochemical laboratories and inexpensive, commercially available oligonucleotides and reagents.

Polymerase bypass of N7-guanine monoadducts of cisplatin, diepoxybutane, and epichlorohydrin

DNA oligonucleotides containing site-specific N7-guanine monoadducts of cisplatin, diepoxybutane, and epichlorohydrin were used as templates for DNA synthesis by two bacterial DNA polymerases and human polymerase β. These polymerases were able to bypass the lesions effectively, although the efficiency was decreased, with inhibition increasing with the size of the lesion. Fidelity of incorporation was essentially unaltered, suggesting that N7-guanine monoadducts do not significantly contribute to the mutational spectra of these agents.

A New Cross-Link for an Old Cross-Linking Drug: The Nitrogen Mustard Anticancer Agent Mechlorethamine Generates Cross-Links Derived from Abasic Sites in Addition to the Expected Drug-Bridged Cross-Links

Nitrogen mustard anticancer drugs generate highly reactive aziridinium ions that alkylate DNA. Monoadducts arising from reaction with position N7 of guanine residues are the major DNA adducts generated by these agents. Interstrand cross-links in which the drug bridges position N7 of two guanine residues are formed in low yields relative to those of the monoadducts but are generally thought to be central to medicinal activity. The N7-alkylguanine residues generated by nitrogen mustards are depurinated to yield abasic (Ap) sites in duplex DNA. Here, we show that Ap sites generated by the nitrogen mustard mechlorethamine lead to interstrand cross-links of a type not previously associated with this drug. Gel electrophoretic data were consistent with early evolution of the expected drug-bridged cross-links, followed by the appearance of Ap-derived cross-links. The evidence is further consistent with a reaction pathway involving alkylation of a guanine residue in a 5'-GT sequence, followed by depurination to generate the Ap site, and cross-link formation via reaction of the Ap aldehyde residue with the opposing adenine residue at this site [Price, N. E., Johnson, K. M., Wang, J., Fekry, M. I., Wang, Y., and Gates, K. S. (2014) J. Am. Chem. Soc. 136, 3483-3490]. The monofunctional DNA-alkylating agents 2-chloro-N,N-diethylethanamine 5, (2-chloroethyl)ethylsulfide 6, and natural product leinamycin similarly were found to induce the formation of Ap-derived cross-links in duplex DNA. This work provides the first characterization of Ap-derived cross-links at sequences in which a cytosine residue is located directly opposing the Ap site. Cross-linking processes of this type could be relevant in medicine and biology because Ap sites with directly opposing cytosine residues occur frequently in genomic DNA via spontaneous or enzymatic depurination of guanine and N7-alkylguanine residues.

Can gel concentration gradients improve two-dimensional DNA displays?

The abrupt reduction in gel electrophoretic mobility that is observed when a dsDNA fragment is partially denatured has recently been predicted to exhibit a dependence upon the gel pore size. Using theoretical modeling, we demonstrate that this dependence can be exploited and used to improve the performance of 2D display of DNA. We report experimental evidence of this dependence and propose a new separation system in which a gel porosity gradient is utilized in a way analogous to temperature or denaturant gradients in traditional 2D display. Such gel porosity gradients can also be used in conjunction with denaturant gradients to improve 2D display results. We test these new ideas by modeling the fragment mobilities and computing the final fragment positions to find optimal 2D separation conditions.