Bypass of DNA-protein cross-links conjugated to the 7-deazaguanine position of DNA by translesion synthesis polymerases

Susith Wickramaratne, Shaofei Ji, Shivam Mukherjee, Yan Su, Matthew G. Pence, Lee Lior-Hoffmann, Iwen Fu, Suse Broyde, F. Peter Guengerich, Mark Distefano, Orlando D. Schãrer, Yuk Yin Sham, Natalia Tretyakova

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Abstract

DNA-protein cross-links (DPCs) are bulky DNA lesions that form both endogenously and following exposure to bis-electrophiles such as common antitumor agents. The structural and biological consequences of DPCs have not been fully elucidated due to the complexity of these adducts. The most common site of DPC formation in DNA following treatment with bis-electrophiles such as nitrogen mustards and cisplatin is the N7 position of guanine, but the resulting conjugates are hydrolytically labile and thus are not suitable for structural and biological studies. In this report, hydrolytically stable structural mimics of N7-guanine-conjugated DPCs were generated by reductive amination reactions between the Lys and Arg side chains of proteins/peptides and aldehyde groups linked to 7-deazaguanine residues in DNA. These model DPCs were subjected to in vitro replication in the presence of human translesion synthesis DNA polymerases. DPCs containing full-length proteins (11-28 kDa) or a 23-mer peptide blocked human polymerases η and κ. DPC conjugates to a 10-mer peptide were bypassed with nucleotide insertion efficiency 50-100-fold lower than for native G. Both human polymerase (hPol) κ and hPol η inserted the correct base (C) opposite the 10-mer peptide cross-link, although small amounts of T were added by hPol η. Molecular dynamics simulation of an hPol κ ternary complex containing a template-primer DNA with dCTP opposite the 10-mer peptide DPC revealed that this bulky lesion can be accommodated in the polymerase active site by aligning with the major groove of the adducted DNA within the ternary complex of polymerase and dCTP.

Original languageEnglish (US)
Pages (from-to)23589-23603
Number of pages15
JournalJournal of Biological Chemistry
Volume291
Issue number45
DOIs
StatePublished - Nov 4 2016

Bibliographical note

Funding Information:
This work was supported by National Institutes of Health NIEHS Grants R01 ES023350 (to N.T.), R01 ES010546 (to F. P. G.), and R01 ES025987 (to S. B.); NCI, National Institutes of Health Grants R01 CA100670 (to N.T.) and R01 CA75449 (to S. B.); and NIGMS, National Institutes of Health Grant R01 GM084152 (to M. D.) and a Brainstorm Award from the University of Minnesota Masonic Cancer Center. The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Publisher Copyright:
© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

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