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Protein display NGS

Protein display (PD) can screen millions to billions of amino acid sequences for their binding to an immobilized target. With traditional clone-picking and Sanger-sequencing a few hundred sequences is laborious and vastly underutilises experiment results. Conversely, next-generation DNA sequencing (NGS) can increase experiment resolution to many thousands of amino acid sequences for a high throughput and superior experiment outcome.

Whether investigating peptides, antibodies or other proteins, DNASense has the necessary sequencing techniques and bioinformatic skills to provide actionable results fast. The results allow for extensive investigation of a wide set of target-binding sequences including those in low abundance, qualifying PD selection efficacy, and exploring amino acid sequence clusters and motifs. For suitable samples, the ONT rapid option is excellent and cost-efficient for fast optimization of selection efficacy.

Technology Resolution (total sequences/sample) Protein size Turnaround time List price
Illumina very high (104-106) < 150 aa 4 weeks 3750 EUR
( 10 samples)
ONT rapid kit* moderate (103-104) Any 4 days 3400 EUR
( ≤ 12 samples)
Modified ONT high (104-105) Any 2 weeks 6700 EUR
( ≤ 12 samples)

*requires relative low-diversity samples and a plasmid reference sequence for mapping against.

Technology Resolution (total sequences/sample) Protein size Turnaround time List price
Illumina very high (104-106) < 150 aa 4 weeks 28000 DKK
( 10 samples)
ONT rapid kit* moderate (103-104) Any 4 days 25000 DKK
( ≤ 12 samples)
Modified ONT high (104-105) Any 2 weeks 50000 DKK
( ≤ 12 samples)

*requires relative low-diversity samples and a plasmid reference sequence for mapping against.

Services include: sequencing library preparation from plasmid samples, DNA sequencing, bioinformatics analysis (evaluation of sequencing outcome, DNA/AA sequence quantification, diversity estimations, sequence similarity clustering, aggregated results in excel-files, etc.), online-access to data and result files, a detailed project report, and an optional results online-meeting with a DNASense specialist.

Add-on services include: investigate PD library cloning integrity, explore amino acid motifs of specific sequence clusters, evaluation of experiment background, curation of a target-binding sequences into a selection repertoire.

FAQ

  • Yes, it is possible to use direct sequencing of e.g. eluted phages or yeast cell, although this requires project customization.

  • Yes, but depending on diversity this typically requires analyzing just the one sample with high resolution sequencing. Costs will be comparable to analyzing e.g. a set of 10 selection round samples.

  • Each amino acid sequence is provided with its originating DNA sequence for direct use in ordering DNA fragments for cloning or finished vectors from third party suppliers.

Mads Toft Søndergaard, Ph.D.
Chief Executive Officer

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