The Future of Decoding Non-Standard Nucleotides: Leveraging Nanopore Sequencing for Expanded Genetic Codes

Abstract: Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological information encoded in these non-standard nucleotides presents new challenges, as traditional sequencing technologies are unable to recognize or interpret novel base pairings. In this perspective, we explore the potential of nanopore sequencing, which is uniquely suited to decipher both standard and non-standard nucleotides by directly measuring the biophysical properties of nucleic acids. Nanopore technology offers real-time, long-read sequencing without the need for amplification or synthesis, making it particularly advantageous for expanded genetic systems like Artificially Expanded Genetic Information Systems (AEGIS). We discuss how the adaptability of nanopore sequencing and advancements in data processing can unlock the potential of these synthetic genomes and open new frontiers in understanding and utilizing expanded genetic codes.