{
  "abstract": "Nanopore-based DNA sequencing technology has achieved remarkable success in sequencing increasingly long DNA strands (e.g., over a million nucleotides long) for genomics research and biotechnology applications. However, the same level of progress has not been achieved for DNA oligonucleotides (usually ≤ 300 nucleotides long). Oligonucleotides play a crucial role in genome engineering efforts through oligo library generation and in DNA data storage, where they are used to encode computer information, such as binary (digital) data in DNA libraries. To enable these applications, accurate sequencing of oligonucleotides in a way that allows to assess for sequence variability, quality and length is essential. But sequencing solutions for oligonucleotides — particularly DNA primers for PCR, oligo DNA libraries used for mutagenesis or cDNA libraries used in gene expression analysis — remain inadequate. To address this gap, OligoSeq is presented as an innovative approach that integrates two complementary techniques: AmpliSeq (based on PCR) and RevSeq (based on reverse complementation with sequence-specific or random primers) to facilitate sequencing of single-stranded oligonucleotides using reference sequence anchor matches of more than ≥ 90% identity spanning from about 70% to 10% with AmpliSeq or RevSeq with random nonamers, respectively, and resolving the final reference sequence based on the most likely candidate from basecall frequencies, regardless of length and double-stranding method. OligoSeq can be integrated with nanopore sequencing technology pipelines and can be used as a reference for other sequencing platforms requiring double-stranded adapters, offering a practical and scalable alternative for standard quality control in single-stranded oligonucleotide synthesis. The use of nanopore technology, compatible with the double-stranding methods showcased, is shown to be the most cost-effective method for resolving original DNA sequences of different length and quality, and to assess its sequence variability, compared to other methods such as Illumina, PacBio or HPLC/MS.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Computing, Faculty of Engineering, Imperial College London, London, Great Britain, United Kingdom",
    "London Biofoundry, Translation and Innovation Hub (I-HUB), Imperial College London, London, Great Britain, United Kingdom",
    "New England Biolabs (UK) Ltd., Hitchin, Great Britain, United Kingdom"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Robert Ramirez-Garcia"
    },
    {
      "affs": [
        1
      ],
      "name": "Akashaditya Das"
    },
    {
      "affs": [
        2
      ],
      "name": "Patrycja Sokolowska"
    },
    {
      "name": "Thomas Heinis"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/48ahkxs5m7z69.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0355056",
  "fulltext_url": null,
  "id": "48ahkxs5m7z69",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0355056",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA libraries"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA synthesis"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleotides/Oligonucleotides"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/DNA-binding proteins/Polymerases/DNA polymerase"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/DNA/DNA libraries"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/DNA/DNA synthesis"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Sequencing techniques/DNA sequencing"
    ],
    [
      "plos",
      "/Research and analysis methods/Chemical synthesis/Biosynthetic techniques/Nucleic acid synthesis/DNA synthesis"
    ],
    [
      "plos",
      "/Research and analysis methods/Chemical synthesis/Biosynthetic techniques/Nucleic acid synthesis/Oligonucleotide synthesis"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Bioinformatics/Sequence analysis/Sequence alignment"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/DNA sequencing"
    ]
  ],
  "openalex": "W4411193383",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0355056&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-03",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/48ahkxs5m7z69.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:56Z",
      "native_id": "10.1371/journal.pone.0355056",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0355056"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "plos:molecular biology",
      "subfield": "molecular-biology"
    },
    {
      "field": "biology",
      "origin": "plos:bioinformatics",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "OligoSeq: Rapid nanopore-sequencing of single-stranded oligonucleotides",
  "title_text": "OligoSeq: Rapid nanopore-sequencing of single-stranded oligonucleotides",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:56Z",
  "url": "https://research.draconitic.com/paper/48ahkxs5m7z69",
  "venue": "PLOS One",
  "versions": []
}