@article{37836c9c1ccb4311bfc850770d3fd04e,
title = "ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes",
abstract = "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.",
keywords = "Biochemistry, Biochemistry applications, Proteomics, Sequence analysis, Transcriptomics",
author = "Hong, {Jessica M.} and Michael Gibbons and Ali Bashir and Diana Wu and Shirley Shao and Zachary Cutts and Mariya Chavarha and Ye Chen and Lauren Schiff and Mikelle Foster and Church, {Victoria A.} and Llyke Ching and Sara Ahadi and {Hieu-Thao Le}, Anna and Alexander Tran and Michelle Dimon and Marc Coram and Brian Williams and Phillip Jess and Marc Berndl and Annalisa Pawlosky",
note = "Funding Information: The authors would like to acknowledge Philip Nelson, John Platt, Erica Brand, Jason Miller, and Patrick Riley for project support and management advice and Tiffany Ly, John Hazard, and Amy Chung-Yu Chou for administrative support. In addition, the authors would like to thank Joshua Cutts, Orion Pritchard, and Samuel Yang for protocol feedback, automation support, and microscopy assistance, as well as Marytheresa Ifediba and Maureen Mckeague for technical discussions. The work presented here was funded through Google Research. Conceptualization, A.P.; methodology, Z.C. J.M.H. D.W. P.J. V.A.C. M. Chavarha, M.G. M.B. B.W, A.P.; software, M.B. B.W. A.B. M. Coram; validation, M.G. D.W. S.S. Z.C. J.M.H. M.F. A.H.-T.L. A.T. P.J. A.P.; formal analysis, B.W. A.B. P.J. D.W. M.G. M.B. A.P.; investigation, M. Chavarha, S.S. Y.C. D.W. J.M.H. M.G. Z.C. M.F. A.H.-T.L. L.S. A.T. P.J. A.P.; writing - original draft, J.M.H. A.B. D.W. S.S. M. Chavarha, Y.C. M.F. V.A.C. L.C. S.A. M.D. B.W. P.J. A.P.; writing - review & editing, J.M.H. V.A.C. L.C. B.W. P.J. A.P.; visualization, S.S. A.B. B.W. D.W. Y.C. J.M.H. L.C. M. Coram, P.J. A.P.; supervision, AP; project administration, AP. A.B. M.D. M.C. B.W. P.J. M.B. and A.P. are employees and shareholders of Alphabet. Google has filed patent applications related to this work, including PCT/US2020/050574, PCT/US2020/053716, PCT/US2020/040130, PCT/US2020/053715. US20210079398A1, US20210079557A1, US20210102248A1, and WO2021051011A1. M.C. is an inventor of US10546650B2. All work was completed while authors were affiliated with Alphabet. Current affiliations for authors who have moved on from Alphabet are the following:, J.H. S.S. Z.C. M.F. L.C. University of California, San Francisco (UCSF); M.G. 10x Genomics; D.W. Genentech, employee and shareholder; Y.C. University of Washington, Seattle; S.A. Alkahest, employee; L.S. Insitro, employee; A.H.-T.L. University of California Los Angeles (UCLA); V.A.C. Washington University School of Medicine, St. Louis. Funding Information: The authors would like to acknowledge Philip Nelson, John Platt, Erica Brand, Jason Miller, and Patrick Riley for project support and management advice and Tiffany Ly, John Hazard, and Amy Chung-Yu Chou for administrative support. In addition, the authors would like to thank Joshua Cutts, Orion Pritchard, and Samuel Yang for protocol feedback, automation support, and microscopy assistance, as well as Marytheresa Ifediba and Maureen Mckeague for technical discussions. The work presented here was funded through Google Research. Publisher Copyright: {\textcopyright} 2021 The Author(s)",
year = "2022",
month = jan,
day = "21",
doi = "10.1016/j.isci.2021.103586",
language = "English",
volume = "25",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier Inc.",
number = "1",
}