Abstract

The expansion of the genetic alphabet through the development of unnatural base pairs (UBPs) has the potential to revolutionize synthetic biology and biotechnology. However, the replication of the UBPs by eukaryotic DNA polymerases is largely unexplored and the sequencing of the UBPs remains challenging. Herein, we explored and demonstrated the activity of human DNA polymerase β (Pol β) for the efficient and specific synthesis and extension of a panel of representative UBPs, including dNaM–dTPT3, dCNMO–dTPT3, and their functionalized derivatives. Based on this, we established a method for the sequencing of DNAs containing different unnatural bases, involving stalled primer extension mediated by Pol β, selective conversion of an unnatural nucleotide into two different natural ones in parallel and further primer extension mediated by Taq DNA polymerase, and Sanger or deep sequencing of the produced natural DNAs to locate the unnatural bases. The precision, universality, and potential for high-throughput applications of this method were demonstrated by the successful sequencing of various DNAs containing one or multiple of different unnatural bases. This work suggests the possibility of integrating the UBPs into the eukaryotic DNA replication systems and provides a technical foundation for the robust sequencing of DNAs with an expanded genetic alphabet.