Development of an Aptamer-Based Sensing Platform for Metal Ions, Proteins, and Small Molecules through Terminal Deoxynucleotidyl Transferase Induced G-Quadruplex Formation.

We report a label-free, structure-independent luminescent-sensing platform for metal ions, proteins, and small molecules utilizing an Ir(III) complex, terminal deoxynucleotidyl transferase (TdT), and a structure-folding aptamer. A novel G-quadruplex-selective Ir(III) complex was identified to detect the nascent G-quadruplex motifs with an enhanced luminescence response. Unlike most label-free DNA-based assays reported in the literature, this sensing platform does not require a specific secondary structure of aptamer, thus greatly simplifying DNA design. The detection platform was demonstrated by the detection of K(+) ions, thrombin, and cocaine as representative examples of metal ions, proteins, and small molecules.

[1]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[2]  Yong Xue,et al.  Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. , 2007, Journal of the American Chemical Society.

[3]  Dik-Lung Ma,et al.  Group 9 organometallic compounds for therapeutic and bioanalytical applications. , 2014, Accounts of chemical research.

[4]  Wei Feng,et al.  Blue-emissive upconversion nanoparticles for low-power-excited bioimaging in vivo. , 2012, Journal of the American Chemical Society.

[5]  Qian Liu,et al.  A general strategy for biocompatible, high-effective upconversion nanocapsules based on triplet-triplet annihilation. , 2013, Journal of the American Chemical Society.

[6]  R. Wu,et al.  Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase. , 1976, Nucleic acids research.

[7]  Yi Xiao,et al.  i-Motif quadruplex DNA-based biosensor for distinguishing single- and multiwalled carbon nanotubes. , 2009, Journal of the American Chemical Society.

[8]  Qiang Zhao,et al.  Series of new cationic iridium(III) complexes with tunable emission wavelength and excited state properties: structures, theoretical calculations, and photophysical and electrochemical properties. , 2006, Inorganic chemistry.

[9]  Ka-Ho Leung,et al.  Label-free detection of sub-nanomolar lead(II) ions in aqueous solution using a metal-based luminescent switch-on probe. , 2013, Biosensors & bioelectronics.

[10]  Chunhui Huang,et al.  A nonemissive iridium(III) complex that specifically lights-up the nuclei of living cells. , 2011, Journal of the American Chemical Society.

[11]  X. Qu,et al.  Human telomeric G-quadruplex formation and highly selective fluorescence detection of toxic strontium ions. , 2012, Molecular bioSystems.

[12]  C. Fan,et al.  Amplified fluorescent recognition of g-quadruplex folding with a cationic conjugated polymer and DNA intercalator. , 2010, ACS applied materials & interfaces.

[13]  Lianghai Hu,et al.  Aptamer in bioanalytical applications. , 2011, Analytical chemistry.

[14]  Yu-hua Hao,et al.  Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex. , 2004, Journal of the American Chemical Society.

[15]  X. Qu,et al.  Silver metallization engineered conformational switch of G-quadruplex for fluorescence turn-on detection of biothiols. , 2012, Chemical communications.

[16]  Dik-Lung Ma,et al.  Luminescent detection of DNA-binding proteins , 2011, Nucleic acids research.

[17]  C. Fan,et al.  A graphene-based platform for fluorescent detection of SNPs. , 2013, The Analyst.

[18]  Friedrich C Simmel,et al.  Nucleic acid based molecular devices. , 2011, Angewandte Chemie.

[19]  Jie Wu,et al.  Ultrasensitive immunoassay of protein biomarker based on electrochemiluminescent quenching of quantum dots by hemin bio-bar-coded nanoparticle tags. , 2011, Analytical chemistry.

[20]  Photosensitizer-incorporated G-quadruplex DNA-functionalized magnetofluorescent nanoparticles for targeted magnetic resonance/fluorescence multimodal imaging and subsequent photodynamic therapy of cancer. , 2012, Chemical communications.

[21]  S. R. Kushner,et al.  Indirect suppression of recB and recC mutations by exonuclease I deficiency. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Y. Huang,et al.  A power-free microfluidic chip for SNP genotyping using graphene oxide and a DNA intercalating dye. , 2013, Chemical communications.

[23]  Feng Yan,et al.  Highly sensitive rapid chemiluminescent immunoassay using the DNAzyme label for signal amplification. , 2011, The Analyst.

[24]  Xiaocui Zhu,et al.  Simultaneous fluorescence imaging of the activities of DNases and 3' exonucleases in living cells with chimeric oligonucleotide probes. , 2013, Analytical chemistry.

[25]  Xiaogang Qu,et al.  Catalytically active nanomaterials: a promising candidate for artificial enzymes. , 2014, Accounts of chemical research.

[26]  Xinhui Lou,et al.  Label-free fluorescent detection of ions, proteins, and small molecules using structure-switching aptamers, SYBR Gold, and exonuclease I. , 2012, Analytical chemistry.

[27]  Sheng Lin,et al.  Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe† †Electronic supplementary information (ESI) available: Compound characterisation and supplementary data. See DOI: 10.1039/c4sc03319a Click here for additional data file. , 2014, Chemical science.

[28]  S. Yao,et al.  Randomly arrayed G-quadruplexes for label-free and real-time assay of enzyme activity. , 2014, Chemical communications.

[29]  Bingling Li,et al.  "Fitting" makes "sensing" simple: label-free detection strategies based on nucleic acid aptamers. , 2013, Accounts of chemical research.

[30]  Ka-Ho Leung,et al.  Detection of base excision repair enzyme activity using a luminescent G-quadruplex selective switch-on probe. , 2013, Chemical communications.

[31]  X. Qu,et al.  A label-free fluorescent turn-on enzymatic amplification assay for DNA detection using ligand-responsive G-quadruplex formation. , 2011, Chemical communications.

[32]  Chunhai Fan,et al.  DNAzyme-based rolling-circle amplification DNA machine for ultrasensitive analysis of microRNA in Drosophila larva. , 2012, Analytical chemistry.

[33]  N. Smargiasso,et al.  Ligands playing musical chairs with G-quadruplex DNA: a rapid and simple displacement assay for identifying selective G-quadruplex binders. , 2008, Biochimie.

[34]  Lihua Lu,et al.  Luminescent oligonucleotide-based detection of enzymes involved with DNA repair , 2013 .

[35]  Ka-Ho Leung,et al.  Antagonizing STAT3 dimerization with a rhodium(III) complex. , 2014, Angewandte Chemie.

[36]  Fuyou Li,et al.  Cationic iridium(III) complexes for phosphorescence staining in the cytoplasm of living cells. , 2008, Chemical communications.

[37]  D. Choi,et al.  Ion homeostasis and apoptosis. , 2001, Current opinion in cell biology.

[38]  Xiaocui Zhu,et al.  In situ, real-time monitoring of the 3' to 5' exonucleases secreted by living cells. , 2012, Analytical chemistry.