title: Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.
abstract: Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis.
authors.affiliation: Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210046, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chao
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Li
authors.affiliation: Pulmonary Medcine Department, Zhongshan Hospital, 180 Fenglin Road, Shanghai 200032, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China.
authors.forename: Hongzhen
authors.initials: H
authors.lastname: Peng
authors.affiliation: Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210046, China.
authors.forename: Shao
authors.initials: S
authors.lastname: Su
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Li
authors.affiliation: Pulmonary Medcine Department, Zhongshan Hospital, 180 Fenglin Road, Shanghai 200032, China.
authors.forename: Changfeng
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Zuo
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China.
authors.forename: Shiping
authors.initials: S
authors.lastname: Song
authors.affiliation: Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210046, China.
authors.forename: Lianhui
authors.initials: L
authors.lastname: Wang
authors.affiliation: Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China. Electronic address: wanglihua@sinap.ac.cn.
authors.forename: Lihua
authors.initials: L
authors.lastname: Wang
mesh_terms: D020137:Base Pair Mismatch; D004247:DNA / Q000032:analysis* / Q000235:genetics; D003911:Dextrans / Q000737:chemistry*; D004867:Equipment Design; D005453:Fluorescence; D057230:Limit of Detection; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*
chemical_list: D003911:Dextrans; D004247:DNA
keywords: DNA detection; Dextran substrate; HCR amplification; High signal to noise ratio; Microarrays