Selective Unnatural Base Pairing and Recognition of 2-Hydroxy-2′-deoxyadenosine in DNA Using Pseudo-dC Derivatives

The formation of unnatural base pairs within duplex DNA would facilitate DNA nanotechnology and biotechnology. Iso-2'-deoxyguanosine (iso-dG) forms base pairs with iso-2'-deoxycytidine, and its use as an unnatural base pair was investigated. Iso-dG is one of the tautomers of 2-hydroxy-2'-deoxyadenosine (2-OH-dA), known as an oxidatively damaged nucleobase, and its selective recognition in DNA plays an important role in the diagnosis and pathogenesis of disease. Therefore, we focused on pseudo-dC (psi dC) as a suitable molecule that recognizes 2-OH-dA in DNA. Since 2-OH-dA shows tautomeric structures in DNA, we designed and used psi dC, which also has a tautomeric structure. We successfully synthesized a psi dC phosphoramidite compound for the synthesis of oligonucleotides (ODNs) as well as its triphosphate derivative (psi dCTP). T-m measurements revealed that ODNs including psi dC showed stable base pair formation with ODNs having 2-OH-dA. In contrast, low T-m values were observed for other bases (dG, dA, dC, and T). The results obtained for the single-nucleotide primer extension reaction revealed that psi dCTP was incorporated into the complementary position of 2-OH-dA in template DNA with high selectivity. In addition, the primer elongation reaction was confirmed to proceed in the presence of dNTPs. The present study reports an artificial nucleic acid that selectively and stably forms unnatural base pairs with 2-OH-dA in DNA.

Automated summary

The formation of unnatural base pairs within duplex DNA is important for DNA nanotechnology and biotechnology. In this study, the authors investigated the use of iso-2'-deoxyguanosine (iso-dG) as an unnatural base pair. They focused on pseudo-dC (psi dC) as a molecule that recognizes 2-hydroxy-2'-deoxyadenosine (2-OH-dA) in DNA. Through synthesis and analysis, the authors demonstrated that psi dC can form stable base pairs with 2-OH-dA, suggesting its potential applications in DNA manipulation.