Synthesis of DNA Duplexes Containing Site-Specific Interstrand Cross-Links via Sequential Reductive Amination Reactions Involving Diamine Linkers and Abasic Sites on Complementary Oligodeoxynucleotides

Abstract

Interstrand DNA cross-links are important in biology, medicinal chemistry, and materials science. Accordingly, methods for the targeted installation of interstrand cross-links in DNA duplexes may be useful in diverse fields. Here, a simple procedure is reported for the preparation of DNA duplexes containing site-specific, chemically defined interstrand cross-links. The approach involves sequential reductive amination reactions between diamine linkers and two abasic (apurinic/apyrimidinic, AP) sites on complementary oligodeoxynucleotides. Use of the symmetrical triamine, tris(2-aminoethyl)amine, in this reaction sequence enabled the preparation of a cross-linked DNA duplex bearing a derivatizable aminoethyl group.

Formation and Properties of DNA Adducts Generated by Reactions of Abasic Sites with 1,2-Aminothiols Including Cysteamine, Cysteine Methyl Ester, and Peptides Containing N-Terminal Cysteine Residues

“…64,65 This reagent was expected to reduce the AP- derived iminium ion intermediate 1a to give the corresponding chemically stable alkylamine derivative 3. 59,60,63 Gel electrophoretic analysis of the products generated in the presence of NaBH 3 CN revealed a new band that migrated more slowly than the parent AP-containing oligonucleotide, which is consistent with the reduction of the iminium ion intermediate 1a to the alkylaminothiol adduct 3a (Figure 6). Little strand cleavage was observed under these conditions, suggesting that the AP site was reduced to the corresponding AP-alcohol 4 during the reaction (Scheme 2).…”

“…Amine-catalyzed cleavage of AP sites in DNA typically proceeds via formation of an iminium ion intermediate (e.g., 1 , Scheme ) that increases the acidity of the α-protons adjacent to the C1-carbonyl, thereby facilitating strand scission via β-elimination of the 3′-phosphoryl group from the abasic sugar (Scheme ). ,− Seeking evidence for formation of the putative iminium ion intermediate 1a , we incubated the AP-containing 5′- 32 P-phosphoryl-labeled oligonucleotide B with cysteamine and the water-compatible hydride reducing agent NaBH 3 CN. , This reagent was expected to reduce the AP-derived iminium ion intermediate 1a to give the corresponding chemically stable alkylamine derivative 3 . ,, Gel electrophoretic analysis of the products generated in the presence of NaBH 3 CN revealed a new band that migrated more slowly than the parent AP-containing oligonucleotide, which is consistent with the reduction of the iminium ion intermediate 1a to the alkylaminothiol adduct 3a (Figure ). Little strand cleavage was observed under these conditions, suggesting that the AP site was reduced to the corresponding AP-alcohol 4 during the reaction (Scheme ).…”

Reconsidering the Chemical Nature of Strand Breaks Derived from Abasic Sites in Cellular DNA: Evidence for 3′-Glutathionylation

“…Synthesis of N 5 -((2R)-1-((Carboxymethyl)amino)-1-oxo-3-(((2R)-1,2,5-trihydroxypentan-3-yl)thio)propan-2-yl)-L-glutamine (3). The compound (S,E)-4,5-dihydroxypent-2-enal 1 (25 mg, 0.22 mmol) prepared as described in our previous work 78 was dissolved in water (4 mL) containing potassium carbonate (71 mg, 0.52 mmol) and glutathione (79 mg, 26 mmol). The reaction mixture was stirred for 8 h, followed by addition of sodium borohydride (40 mg, 1.1 mmol) and stirring for an additional 2 h at 24 °C.…”