Chemoselective Modification of Vinyl DNA by Triazolinediones

Abstract

A new method for the post-synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step-wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst-free addition between PTAD and the terminal alkene of 5-vinyl-2'-deoxyuridine (VdU) was exceptionally fast, with a second-order rate constant of 2×10 m s . PTAD derivatives selectively reacted with VdU-containing oligonucleotides in a conformation-selective manner, with higher yields observed for G-quadruplex versus duplex DNA. These results demonstrate a new strategy for copper-free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.

A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids

“…[50] To characterize DNA-templated PINK-VdU reactions, we synthesized a VdU-containing 17-mer DNA oligonucleotide "ODN1" (Table S1, Figure S10). The DMT-protected VdU phosphoramidite S4 (Scheme S1, Supporting Information) [51] was incorporated into the oligomer utilizing standard solid phase supported DNA synthesis. ODN1 was purified using reverse-phase HPLC and annealed with a complementary strand to form a duplex (see Supporting Information).…”

Purine Nucleosides with a Reactive (β‐Iodovinyl)sulfone or a (β‐Keto)sulfone Group at the C8 Position and Their Polymerase‐Catalyzed Incorporation into DNA

“…Bioconjugation of the pyrimidine nucleotides bearing reactive groups with an amino acid, peptide or protein have been studied [32–35] . The Hocek group has cross‐linked DNA fragments containing reactive vinylsulfonamide groups to peptides and protein p53 [34] .…”

“…[28][29][30][31] Bioconjugation of the pyrimidine nucleotides bearing reactive groups with an amino acid, peptide or protein have been studied. [32][33][34][35] The Hocek group has cross-linked DNA fragments containing reactive vinylsulfonamide groups to peptides and protein p53. [34] We have previously reported halovinylsulfonation of 5-ethynylpyrimidine nucleosides and the efficient reactions of the resulting 5-(1-halo-2-tosylvinyl) probes with nucleophiles such as amines and thiols, including amino acids, via addition-elimination.…”

Water‐Involved Ring‐Opening of 4‐Phenyl‐1,2,4‐triazoline‐3,5‐dione for “Photo‐Clicked” Access to Carbamoyl Formazan Photoswitches In Situ

“…[25][26][27][28][29][30] Moreover, RTADs were easily attacked by amines to furnish ring-opening species which releases nitrogen to form urea [31,32] or dimerized bicyclic adduct (Figure 1b). [18.33] Engrossingly, the relatively stable PTAD derivatives are able to engage in electrophilic substitution toward electron-rich arenes (Figure 1c) [34][35][36][37] or toward alkene-modified DNA [38] in protonic solvent systems (Figure 1d). The selective modifications toward tyrosine or 2'-deoxy-5-vinyluridine (VdU) meet the stringent prerequisites of a "click" chemistry under very mild conditions.…”

“…The selective modifications toward tyrosine or 2'-deoxy-5-vinyluridine (VdU) meet the stringent prerequisites of a "click" chemistry under very mild conditions. [33][34][35][36][37][38] However, the hydrolysis of PTAD is not negligible and, as a consequence, impeding the applications in water-containing systems. In fact, PTAD derivatives could only be stored for a prolonged period of time in the solid state, and often retained as urazole precursors that require a pre-oxidation prior to use.…”