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. 2019 Sep;78(1):e93.
doi: 10.1002/cpnc.93.

Synthesis of N2 -Aryl-2'-Deoxyguanosine Modified Phosphoramidites and Oligonucleotides

Pratibha P Ghodke  1   2 , P I Pradeepkumar  2
Affiliations

Synthesis of N2 -Aryl-2'-Deoxyguanosine Modified Phosphoramidites and Oligonucleotides

Pratibha P Ghodke et al. Curr Protoc Nucleic Acid Chem. 2019 Sep.

Abstract

The N2 -position of 2'-deoxyguanosine (N2 -position in dG) is well known for forming carcinogenic minor groove DNA adducts, which originate from environmental pollutants, chemicals, and tobacco smoke. The N2 -dG DNA adducts have strong implications on biological processes such as DNA replication and repair and may, therefore, result in genomic instability by generating mutations or even cell death. It is crucial to know the role of DNA polymerases when they encounter the N2 -dG damaged site in DNA. To get detailed insights on the in vitro DNA damage tolerance or bypass mechanism, there is a need to synthetically access N2 -dG damaged DNAs. This article describes a detailed protocol of the synthesis of N2 -aryl-dG modified nucleotides using the Buchwald-Hartwig reaction as a main step and incorporation of the modified nucleotides into DNA. In Basic Protocol 1, we focused on the synthesis of five different N2 -dG modified phosphoramidites with varying bulkiness (benzyl to pyrenyl). Basic Protocol 2 describes the details of synthesizing N2 -dG modified oligonucleotides employing the standard solid phase synthesis protocol. This strategy provides robust synthetic access to various modifications at the N2 -position of dG; the modified dGs serve as good substrates to study translesion synthesis and repair pathways. Overall data presented in this article are based on earlier published reports. © 2019 by John Wiley & Sons, Inc.

Keywords: 2′-deoxyguanosine; Buchwald-Hartwig coupling; nucleosides; oligonucleotides; phosphoramidite; solid phase synthesis.

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