Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning.

ABSTRACT: The discovery of non-canonical bases (NCBs) and development of synthetic xeno-nucleic acids (XNAs) has spawned interest in many applications in viral genomics, synthetic biology and DNA storage. However, inability to do high-throughput sequencing of NCBs has been a significant limitation. We demonstrate that XNAs with NCBs can be robustly sequenced on a MinION system ( > 2.3×10⁶ reads/flowcell) to obtain significantly distinct signals from controls (median fold-change >6×). To enable AI-model training, we synthesized and sequenced a complex pool of 1,024 NCB-containing oligonucleotides with varied 6-mer contexts and high purity ( > 90%). Bootstrapped models assisted in data preparation, and data augmentation with spliced reads provided high context diversity, enabling learning o

SUBMITTER: Perez M 

PROVIDER: S-EPMC12311055 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature