ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes

Jessica M. Hong, Michael Gibbons, Ali Bashir, Diana Wu, Shirley Shao, Zachary Cutts, Mariya Chavarha, Ye Chen, Lauren Schiff, Mikelle Foster, Victoria A. Church, Llyke Ching, Sara Ahadi, Anna Hieu-Thao Le, Alexander Tran, Michelle Dimon, Marc Coram, Brian Williams, Phillip Jess, Marc BerndlAnnalisa Pawlosky

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


We demonstrate early progress toward constructing a high-throughput, single-molecule protein sequencing technology utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip. DNA binders deposit unique, amino acid-identifying barcodes on the chip. The end goal is that, over multiple binding cycles, a sequential chain of DNA barcodes will identify the amino acid sequence of a peptide. Toward this, we demonstrate successful target identification with two sets of target-binder pairs: DNA-DNA and Peptide-Protein. For DNA-DNA binding, we show assembly and sequencing of DNA barcodes over six consecutive binding cycles. Intriguingly, our computational simulation predicts that a small set of semi-selective DNA binders offers significant coverage of the human proteome. Toward this end, we introduce a binder discovery pipeline that ultimately could merge with the chip assay into a technology called ProtSeq, for future high-throughput, single-molecule protein sequencing.

Original languageEnglish
Article number103586
Issue number1
StatePublished - 21 Jan 2022
Externally publishedYes


  • Biochemistry
  • Biochemistry applications
  • Proteomics
  • Sequence analysis
  • Transcriptomics


Dive into the research topics of 'ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes'. Together they form a unique fingerprint.

Cite this