Programmable site-selective labeling of oligonucleotides based on carbene catalysis

Yang-Ha Lee,Eunsoo Yu,Cheol-Min Park

doi:10.1038/s41467-021-21839-4

Yang-Ha Lee, Eunsoo Yu + Show 1 more

Open Access

https://doi.org/10.1038/s41467-021-21839-4

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Abstract

Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.

Highlights

Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology
In our efforts to develop a catalytic system that allows siteselective modification among multiple Gs embedded in structurally complex oligonucleotides, we aim to address the two fundamental selectivities toward substrates; chemo- and regioselectivity
We describe the post-synthetic modification of oligonucleotides at unpaired Gs in a chemo- and regio-selective manner based on rhodium(I)-carbene catalysis

Summary

Introduction

Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. High regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates. Fused to the proteins of interest and DNA probes linked to the corresponding tags[8] These indispensable methods for the study of DNA-binding proteins require chemical modification of natural nucleic acids to introduce functional handles, often with more than one functionalities for sophisticated manipulations including cross-linking and detection. Proximity-driven modifications by hybridizing opposite strands bearing reactive groups have been reported[25,26,27] Enzymes such as methyltransferase and tRNA-guanine transglycosylase have been employed for selective modification[28,29], which necessitates specific sequences for enzyme recognition and laborious engineering of enzymes/cofactors. 2′-OH modification of RNAs has been shown by using acyl imidazole reagents[30,31] and SELEXbased ribozymes[32]

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