title: DNA-Templated Aptamer Probe for Identification of Target Proteins.
abstract: Using aptamers as molecular probes for biomarker discovery has attracted a great deal of attention in recent years. However, it is still a big challenge to accurately identify those protein markers that are targeted by aptamers under physiological conditions due to weak and noncovalent aptamer-protein interactions. Herein, we developed an aptamer based dual-probe using DNA-templated chemistry and photo-cross-linking technique for the identification of target proteins that are recognized by aptamers. In this system, the aptamer was modified by a single strand DNA as binding probe (BP), and another complementary DNA with a photoactive group and reporter group was modified as capture probe (CP). BP was first added to recruit the binding protein via aptamer recognition, and subsequently CP was added to let the cross-linker close to the target via DNA self-assembly, and then a covalent bond between CP and its binding protein was achieved via photo-cross-linking reaction. The captured protein can be detected or affinity enrichment using the tag, finally identified by MS. By use of lysozyme as a model substrate, we demonstrated that this multiple functionalized probe can be utilized for a successful labeling and enrichment of target protein even under a complicated and real environment. Thus, a novel method to precisely identify the aptamer-targeted proteins has been developed and it has a potential application for discovery of aptamer-based biomarkers.
authors.affiliation: Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Bi
authors.affiliation: Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Bai
authors.affiliation: Department of Chemistry, Nankai University , Tianjin 300071, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Gao
authors.affiliation: Department of Chemistry, Nankai University , Tianjin 300071, China.
authors.forename: Congcong
authors.initials: C
authors.lastname: Lu
authors.affiliation: Department of Chemistry, Nankai University , Tianjin 300071, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China.
authors.forename: Guijin
authors.initials: G
authors.lastname: Zhai
authors.affiliation: Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Tian
authors.affiliation: Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg , 79104 Freiburg, Germany.|Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College , Beijing 100005, China.
authors.forename: Enguo
authors.initials: E
authors.lastname: Fan
authors.affiliation: Department of Chemistry, Nankai University , Tianjin 300071, China.|Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.
authors.forename: Yukui
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University , Tianjin 300070, China.
authors.forename: Kai
authors.identifier: 0000-0003-2800-0531
authors.initials: K
authors.lastname: Zhang
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004529:Egg White / Q000737:chemistry; D009113:Muramidase / Q000032:analysis* / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D015342:DNA Probes; D004277:DNA, Single-Stranded; D009113:Muramidase