Hybridization-Promoted and Cytidine-Selective Activation for Cross-Linking with the Use of 2-Amino-6-vinylpurine Derivatives

Abstract

Recently, we have proposed a new concept for cross-linking agents with inducible reactivity, in which the highly reactive cross-linking agent, the 2-amino-6-vinylpurine nucleoside analogue (1), can be regenerated in situ from its stable precursors, the phenylsulfide (4) and the phenylsulfoxide (3) derivatives, by a hybridization-promoted activation process with selectivity to cytidine. The phenylsulfide precursor (4) exhibited cross-linking ability despite its high stability toward strong nucleophiles such as amines and thiols. In this study, we investigated the substituent effects of the phenylsulfide group on the cross-linking reaction, and determined the 2-carboxy substituent of the phenylsulfide derivative (11k) as an efficient cross-linking agent with inducible reactivity. Detailed investigations have shown that the phenylsulfoxide (3) and phenylsulfide (4) precursors produce the 2-amino-6-vinylpurine nucleoside (1) as the common reactive species. It has been concluded that the nature of the inducible reactivity of the precursors (3 and 4) is acceleration of their elimination to the 2-amino-6-vinylpurine nucleoside (1) through the selective process in the duplex with the ODN having cytidine at the target site.

Furan‐Oxidation‐Triggered Inducible DNA Cross‐Linking: Acyclic Versus Cyclic Furan‐Containing Building Blocks—On the Benefit of Restoring the Cyclic Sugar Backbone

“…[11] Relying on the inducible reactivity principle, [32] the furan moiety is oxidized selectively, after duplex formation, generating the cross-linking moiety in an environment in which the target nucleophiles are forced into proximity so as to minimize side reactions with non-target nucleophiles. Others have recently picked up this methodology and based on our furanoxidation strategy have shown that such type of furan-containing probes can be used for the diagnosis of adenine-related DNA mutations.…”

Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics

“…The functional group may react spontaneously once annealed to the DNA (facilitated by the increased effective molarity induced by duplex formation, as in the Michael addition shown in the top left of Fig. 14) 130 or in other cases its reactivity can be triggered by an external stimulus such as light (see top right of Fig. 14).…”

Intracellular Inducible Alkylation System That Exhibits Antisense Effects with Greater Potency and Selectivity than the Natural Oligonucleotide

“…[2,16] We recently proposed a new concept of inducible reactivity, in which a phenylsulfide derivative used as a stable precursor to a 2-amino-6-vinylpurine nucleoside analogue is automatically activated in the proximity of the target cytidine residue to form a covalent bond selectively (Scheme 1). [17][18][19][20] The selectivity of this inducible alkylation system for cytidine is so high that a single nucleotide difference can be discriminated in the alkylation. Herein we describe the capacity of the inducible alkylation system to exhibit antisense effects in an intracellular environment with greater potency and selectivity than the corresponding unmodified oligonucleotide.…”

“…[17] The vinyl compound 3 can also be generated selectively from the sulfide precursor 1 in the hybrid with the complementary sequence. In this case it is anticipated that activation from 1 to 3 takes place directly.…”

“…The antisense sequence to firefly-luciferase mRNA (sequence A in Scheme 2) was designed according to a reported technique. [24] The methylsulfide derivative of a 2-amino 6-alkyl purine was incorporated into the natural-type ODN (5 a and 6 a), [17] and was then transformed into the phenylsulfide (5 b, 6 b), 2-carboxyphenylsulfide (5 c, 6 c), 4-carboxyphenylsulfide (5 d, 6 d), and phenylamino derivatives (5 e) by sequential reactions with magnesium monoperphthalate (MMPP) and aqueous NaOH, following the addition of the corresponding thiol or amine. The amino group of the 3' terminus of 5 was modified with N-succimidyl-3-(2-pyridyldithio)propionate (SPDP), followed by reduction with dithiothreitol (DTT) to form the thiol-containing ODN 7.…”