Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation

Abstract

Modified nucleosides in natural RNA molecules are essential for their functions. Non-natural nucleoside analogues have been introduced into RNA to manipulate its structure and function. We have recently developed a new strategy for the in situ modification of RNA based on the functionality transfer reaction between an oligodeoxynucleotide probe and an RNA substrate. 2′-Deoxy-6-thioguanosine (6-thio-dG) was used as the platform to anchor the transfer group. In this study, a pyridinyl vinyl ketone moiety was newly designed as the transfer group with the expectation that a metal cation would form a chelate complex with the pyridinyl-2-keto group. It was demonstrated that the (E)-pyridinyl vinyl keto group was efficiently and specifically transferred to the 4-amino group of the opposing cytosine in RNA in the presence of NiCl2 with more than 200-fold accelerated rate compared with the previous system with the use of the diketo transfer group. Detailed mechanistic studies suggested that NiCl2 forms a bridging complex between the pyridinyl keto moiety and the N7 of the purine residue neighboring the cytosine residue of the RNA substrate to bring the groups in close proximity.

Synthesis of Nucleobase‐Modified Oligonucleotides by Post‐Synthetic Modification in Solution

“…Transformation of nitrosyl, 2-vinyliden-1,3-diketo, and pyridinyl-keto vinyl groups, which are attached to 6thioguanosine, into the 4-amino group of the cytosine base under neutral conditions produced the corresponding oligonucleotides 22 a-c (Scheme 7). [25][26][27]…”

Development of Novel Functional Molecules Targeting DNA and RNA

“…15) This more efficient guanine modification was applied to the site-specific labelling of RNA 16) and O 6 -methyl guanosine-containing DNA. 17) Next, a pyridinyl-keto vinyl group (5) was designed to attain inducible reactivity. First, the pyridinyl-keto part was expected to form a complex with a divalent metal cation to enhance the reactivity for nucleophiles by an electron-withdrawing effect 18) (Fig.…”

Targeting duplex DNA with the reversible reactivity of quinone methides

“…Ultimately, the most broadly applicable method will likely include an induction method as simple and universal as target binding. 27,28 Self-adducts of QMs have the potential to satisfy this desire as efficient transfer of QMs has only been detected within target complexes and, if alternative reaction occurs, their reversibility will still support final accumulation at the thermodynamically favored site. 12 The utility of oligomer-QM self-adducts in triplex recognition and reaction was not directly apparent from earlier models that relied on Watson–Crick base pairing.…”