title: Multiplex single-molecule interaction profiling of DNA-barcoded proteins.
abstract: In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by the number of spectrally non-overlapping chromophores. Here we introduce a single-molecular-interaction sequencing (SMI-seq) technology for parallel protein interaction profiling leveraging single-molecule advantages. DNA barcodes are attached to proteins collectively via ribosome display or individually via enzymatic conjugation. Barcoded proteins are assayed en masse in aqueous solution and subsequently immobilized in a polyacrylamide thin film to construct a random single-molecule array, where barcoding DNAs are amplified into in situ polymerase colonies (polonies) and analysed by DNA sequencing. This method allows precise quantification of various proteins with a theoretical maximum array density of over one million polonies per square millimetre. Furthermore, protein interactions can be measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Two demanding applications, G-protein coupled receptor and antibody-binding profiling, are demonstrated. SMI-seq enables 'library versus library' screening in a one-pot assay, simultaneously interrogating molecular binding affinity and specificity.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Liangcai
authors.initials: L
authors.lastname: Gu
authors.affiliation: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: John
authors.initials: J
authors.lastname: Aach
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
authors.affiliation: 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
mesh_terms: D004247:DNA / Q000737:chemistry*; D018076:DNA, Complementary / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D047468:Immunoprecipitation; D021141:Nucleic Acid Amplification Techniques; D019151:Peptide Library; D012333:RNA, Messenger / Q000737:chemistry
chemical_list: D018076:DNA, Complementary; D019151:Peptide Library; D012333:RNA, Messenger; D004247:DNA