title: Locking-to-unlocking system is an efficient strategy to design DNA/silver nanoclusters (AgNCs) probe for human miRNAs.
abstract: MicroRNAs (miRNAs), small non-coding RNA molecules, are important biomarkers for research and medical purposes. Here, we describe the development of a fast and simple method using highly fluorescent oligonucleotide-silver nanocluster probes (DNA/AgNCs) to efficiently detect specific miRNAs. Due to the great sequence diversity of miRNAs in humans and other organisms, a uniform strategy for miRNA detection is attractive. The concept presented is an oligonucleotide-based locking-to-unlocking system that can be endowed with miRNA complementarity while maintaining the same secondary structure. The locking-to-unlocking system is based on fold-back anchored DNA templates that consist of a cytosine-rich loop for AgNCs stabilization, an miRNA recognition site and an overlap region for hairpin stabilization. When an miRNA is recognized, fluorescence in the visible region is specifically extinguished in a concentration-dependent manner. Here, the exact composition of the fold-back anchor for the locking-to-unlocking system has been systematically optimized, balancing propensity for loop-structure formation, encapsulation of emissive AgNCs and target sensitivity. It is demonstrated that the applied strategy successfully can detect a number of cancer related miRNAs in RNA extracts from human cancer cell lines.
authors.affiliation: UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark.
authors.forename: Pratik
authors.initials: P
authors.lastname: Shah
authors.affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark.
authors.forename: Suk Won
authors.initials: SW
authors.lastname: Choi
authors.affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark.
authors.forename: Ho-Jin
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark.
authors.forename: Seok Keun
authors.initials: SK
authors.lastname: Cho
authors.affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark.
authors.forename: Yong-Joo
authors.initials: YJ
authors.lastname: Bhang
authors.affiliation: UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark.
authors.forename: Moon Young
authors.initials: MY
authors.lastname: Ryu
authors.affiliation: Seoulin Bioscience Co. Ltd. 4F. #A, KOREA BIO PARK, 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea pwt@chem.ku.dk.
authors.forename: Peter Waaben
authors.initials: PW
authors.lastname: Thulstrup
authors.affiliation: Seoulin Bioscience Co. Ltd. 4F. #A, KOREA BIO PARK, 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Korea mobj@chem.ku.dk.
authors.forename: Morten Jannik
authors.initials: MJ
authors.lastname: Bjerrum
authors.affiliation: UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Korea swyang@plen.ku.dk.
authors.forename: Seong Wook
authors.initials: SW
authors.lastname: Yang
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D045744:Cell Line, Tumor; D002851:Chromatography, High Pressure Liquid; D002942:Circular Dichroism; D003596:Cytosine / Q000737:chemistry; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry*; D006801:Humans; D053768:Metal Nanoparticles / Q000737:chemistry* / Q000648:ultrastructure; D035683:MicroRNAs / Q000032:analysis* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry*; D012334:RNA, Neoplasm / Q000032:analysis* / Q000378:metabolism; D012834:Silver / Q000737:chemistry; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D035683:MicroRNAs; D015345:Oligonucleotide Probes; D012334:RNA, Neoplasm; D012834:Silver; D003596:Cytosine