Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors.
Bottom Line: Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA.Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines.Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure-activity relationships in ICL repair.
Affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.Show MeSH
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Mentions: We used oligonucleotides with 7-deazaguanine residues having alkyl aldehyde chains of different lengths (C1, C2, C3) at the 7 position and studied ICL formation with ammonia, hydrazine and DMEDA using a reductive amination reaction. The efficiency of ICL formation was found to be correlated with the length of the ICL and the reactivity of the amine (summarized in Figure 5). We were able to form ICLs with bridge lengths ranging from 7.2 Å, for which our molecular modeling studies predict a bend of about 20° in the DNA duplex (22), to those of 10.8 Å and more, which our preliminary nuclear magnetic resonance (NMR) experiments show are free of distortion (AG, T. Zaliznyak, C. de los Santos, ODS, unpublished data). ICL formation was found to be most efficient with nondistorting ICLs (10.8–13.2 Å), followed by those with minor (8.4–9.6 Å) and moderate distortion (7.2–8.4 Å) (Figure 5). The higher nucleophilicity and reactivity of hydrazine allowed for the formation of more distorted ICLs. The major groove ICLs reported here inducing no, minor and moderate distortion in DNA duplexes (Figure 6) will be invaluable for advancing studies elucidating structure–function relationships in ICL repair.
Affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.