Abstract
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.
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References
Schärer OD (2005) DNA interstrand crosslinks: natural and drug-induced DNA adducts that induce unique cellular responses. Chembiochem 6:27–32
Clauson C, Schärer OD, Niedernhofer LJ (2013) Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. Cold Spring Harb Perspect Biol 5. a012732/012731-a012732/012725
Imani-Nejad M, Johnson KM, Price NE, Gates KS (2016) 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. Biochemistry 55:7033–7041
Stone MP, Cho YJ, Huang H, Kim HY, Kozekov ID, Kozekova A, Wang H, Minko IG, Lloyd RS, Harris TM, Rizzo CJ (2008) Interstrand cross-links induced by α,β-unsaturated aldehydes derived from lipid peroxidation and environmental sources. Acc Chem Res 41:793–804
Greenberg MM (2014) Abasic and oxidized abasic site reactivity in DNA: enzyme inhibition, cross-linking, and nucleosome-catalyzed reactions. Acc Chem Res 47:646–655
Rajski SR, Williams RM (1998) DNA cross-linking agents as antitumor drugs. Chem Rev 98:2723–2795
Yang Z, Price NE, Johnson KM, Wang Y, Gates KS (2017) Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA. Nucleic Acids Res 45:6275–6283
Catalano MJ, Liu S, Andersen N, Yang Z, Johnson KM, Price NA, Wang Y, Gates KS (2015) Chemical structure and properties of the interstrand cross-link formed by the reaction of guanine residues with abasic sites in duplex DNA. J Am Chem Soc 137:3933–3945
Price NE, Catalano MJ, Liu S, Wang Y, Gates KS (2015) Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residue in duplex DNA. Nucleic Acids Res 43:3434–3441
Kato N, Kawasoe Y, Williams HL, Coates E, Roy U, Shi Y, Beese LS, Schärer OD, Yan H, Gottesman ME, Takahashi TS, Gautier J (2017) Sensing and processing of DNA interstrand crosslinks by the mismatch repair pathway. Cell Rep 21:1375–1385
Yang Z, Nejad MI, Gamboa Varela J, Price NE, Wang Y, Gates KS (2017) A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand cross-links derived from psoralen and abasic sites. DNA Repair 52:1–11
Semlow DR, Zhang J, Budzowska M, Drohat AC, Walter JC (2016) Replication-dependent unhooking of DNA interstrand cross-links by the NEIL3 glycosylase. Cell 167:498–511
Huang J-C, Liu S, Bellani MA, Thazhathveetil AK, Ling C, de Winter JP, Wang Y, Wang W, Seidman MM (2013) The DNA translocase FANCM/MHF promotes replication traverse of DNA interstrand cross-links. Mol Cell 52:434–446
Tomás-Gamasa M, Serdjukow S, Su M, Müller M, Carell T (2014) "Post-it" type connected DNA created with a reversible covalent cross-link. Angew Chem Int Ed Eng 53:796–800
Imani-Nejad M, Shi R, Zhang X, Gu L-Q, Gates KS (2017) Sequence-specific covalent capture coupled with high-contrast nanopore detection of a disease-derived nucleic acid sequence. Chembiochem 18:1383–1386
Vieregg JR, Nelson HM, Stoltz BM, Pierce NA (2013) Selective nucleic acid capture with shielded covalent probes. J Am Chem Soc 135:9691–9699
Peng X, Greenberg MM (2008) Facile SNP detection using bifunctional cross-linking oligonucleotide probes. Nucleic Acids Res 36:e31
Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T (2013) Details of the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside: cis-trans isomeric effect and the application for SNP-based genotyping. J Am Chem Soc 135:16161–16167
Rajendran A, Endo M, Katsuda Y, Hidaka K, Sugiyama H (2011) Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. J Am Chem Soc 133:14488–14491
Chen W, Schuster GB (2013) Structural stabilization of DNA-templated nanostructures: cross-linking with 2,5-bis(2-thienyl)-pyrrole monomers. Org Biomol Chem 11:35–40
Dutta S, Chowdhury G, Gates KS (2007) Interstrand crosslinks generated by abasic sites in duplex DNA. J Am Chem Soc 129:1852–1853
Johnson KM, Price NE, Wang J, Fekry MI, Dutta S, Seiner DR, Wang Y, Gates KS (2013) On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an Abasic site with the opposing guanine residue of 5’-CAp sequences in duplex DNA. J Am Chem Soc 135:1015–1025
Gamboa Varela J, Gates KS (2015) A simple, high-yield synthesis of DNA duplexes containing a covalent, thermally-reversible interstrand cross-link at a defined location Angew. Chem Int Ed Eng 54:7666–7669
Price NE, Johnson KM, Wang J, Fekry MI, Wang Y, Gates KS (2014) Interstrand DNA−DNA cross-link formation between adenine residues and Abasic sites in duplex DNA. J Am Chem Soc 136:3483–−3490
Price NE, Li L, Gates KS, Wang Y (2017) Replication and repair of a reduced 2′-deoxyguanosine-abasic site cross-link in human cells. Nucleic Acids Res 45:6486–6493
Gamboa Varela J, Gates KS (2016) Simple, high-yield syntheses of DNA duplexes containing interstrand DNA-DNA cross-links between an N4-aminocytidine residue and an abasic site. Curr Protoc Nucleic Acid Chem 65:5.16.11–15.16.15
Varshney U, van de Sande JH (1991) Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase. Biochemistry 30:4055–4061
Borch RF, Hassid AI (1972) A new method for the methylation of amines. J Org Chem 37:1673–1674
Romero RM, Rojsittisak P, Haworth IS (2013) Electrophoretic mobility of duplex DNA cross-linked by mechlorethamine at a cytosine-cytosine mismatch pair. Electrophoresis 34:917–924
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a lab manual. Cold Spring Harbor Press, Cold Spring Harbor, NY
Tataurov AV, You Y, Owczarzy R (2008) Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys Chem 133:66–70
Melton D, Lewis CD, Price NE, Gates KS (2014) Covalent adduct formation between the antihypertensive drug hydralazine and abasic sites in double- and single-stranded DNA. Chem Res Toxicol 27:2113–2118
Maxam AM, Gilbert W (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol 65:499–560
Gates KS (2009) An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals. Chem Res Toxicol 22:1747–1760
Gates KS, Nooner T, Dutta S (2004) Biologically relevant chemical reactions of N7-alkyl-2′-deoxyguanosine adducts in DNA. Chem Res Toxicol 17:839–856
Shi Y-B, Hearst JE (1986) Thermostability of double-stranded deoxyribonucleic acids: effects of covalent additions of a psoralen. Biochemistry 25:5895–5902
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We are grateful to the National Institutes of Health for supporting this work (ES021007).
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Nejad, M.I. et al. (2019). 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. In: Shank, N. (eds) Non-Natural Nucleic Acids. Methods in Molecular Biology, vol 1973. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9216-4_10
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DOI: https://doi.org/10.1007/978-1-4939-9216-4_10
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