title: High-throughput analysis and protein engineering using microcapillary arrays.
abstract: We describe a multipurpose technology platform, termed μSCALE (microcapillary single-cell analysis and laser extraction), that enables massively parallel, quantitative biochemical and biophysical measurements on millions of protein variants expressed from yeast or bacteria. μSCALE spatially segregates single cells within a microcapillary array, enabling repeated imaging, cell growth and protein expression. We performed high-throughput analysis of cells and their protein products using a range of fluorescent assays, including binding-affinity measurements and dynamic enzymatic assays. A precise laser-based extraction method allows rapid recovery of live clones and their genetic material from microcapillaries for further study. With μSCALE, we discovered a new antibody against a clinical cancer target, evolved a fluorescent protein biosensor and engineered an enzyme to reduce its sensitivity to its inhibitor. These protein analysis and engineering applications each have unique assay requirements and different host organisms, highlighting the flexibility and technical capabilities of the μSCALE platform.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.
authors.forename: Bob
authors.initials: B
authors.lastname: Chen
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.
authors.forename: Sungwon
authors.initials: S
authors.lastname: Lim
authors.affiliation: Department of Chemical Engineering, Stanford University, Stanford, California, USA.
authors.forename: Arvind
authors.initials: A
authors.lastname: Kannan
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.
authors.forename: Spencer C
authors.initials: SC
authors.lastname: Alford
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California, USA.
authors.forename: Fanny
authors.initials: F
authors.lastname: Sunden
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California, USA.|Department of Chemistry, Stanford University, Stanford, California, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA.
authors.forename: Ivan K
authors.identifier: http://orcid.org/0000-0002-3667-5013
authors.initials: IK
authors.lastname: Dimov
authors.affiliation: Stanford Photonics Research Center, Stanford University, Stanford, California, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Baer
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California, USA.|Department of Chemical Engineering, Stanford University, Stanford, California, USA.
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Cochran
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis*; D015374:Biosensing Techniques / Q000295:instrumentation; D002623:Chemistry Techniques, Analytical / Q000295:instrumentation*; D005434:Flow Cytometry; D005456:Fluorescent Dyes / Q000737:chemistry; D005656:Fungal Proteins / Q000032:analysis*; D015723:Gene Library; D040081:Protein Array Analysis / Q000295:instrumentation*; D011485:Protein Binding; D015202:Protein Engineering / Q000295:instrumentation*; D059010:Single-Cell Analysis / Q000295:instrumentation*
chemical_list: D001426:Bacterial Proteins; D005456:Fluorescent Dyes; D005656:Fungal Proteins