A Graphene-Based Biosensing Platform Based on Regulated Release of an Aptameric DNA Biosensor

A novel biosensing platform was developed by integrating an aptamer-based DNA biosensor with graphene oxide (GO) for rapid and facile detection of adenosine triphosphate (ATP, as a model target). The DNA biosensor, which is locked by GO, is designed to contain two sensing modules that include recognition site for ATP and self-replication track that yields the nicking domain for Nt.BbvCI. By taking advantage of the different binding affinity of single-stranded DNA, double-stranded DNA and aptamer-target complex toward GO, the DNA biosensor could be efficiently released from GO in the presence of target with the help of a complementary DNA strand (CPDNA) that partially hybridizes to the DNA biosensor. Then, the polymerization/nicking enzyme synergetic isothermal amplification could be triggered, leading to the synthesis of massive DNA amplicons, thus achieving an enhanced sensitivity with a wide linear dynamic response range of four orders of magnitude and good selectivity. This biosensing strategy expands the applications of GO-DNA nanobiointerfaces in biological sensing, showing great potential in fundamental research and biomedical diagnosis.

[1]  D. Patel,et al.  Structural analysis of nucleic acid aptamers. , 1997, Current opinion in chemical biology.

[2]  Juewen Liu,et al.  Mechanisms of DNA sensing on graphene oxide. , 2013, Analytical chemistry.

[3]  Itamar Willner,et al.  Spotlighting of cocaine by an autonomous aptamer-based machine. , 2007, Journal of the American Chemical Society.

[4]  Yuehe Lin,et al.  Graphene and graphene oxide: biofunctionalization and applications in biotechnology , 2011, Trends in Biotechnology.

[5]  F. Simmel,et al.  DNA nanodevices. , 2005, Small.

[6]  Charles W Buffington,et al.  Human plasma ATP concentration. , 2007, Clinical chemistry.

[7]  E. Vermaas,et al.  Selection of single-stranded DNA molecules that bind and inhibit human thrombin , 1992, Nature.

[8]  Chengde Mao,et al.  A DNA nanomachine based on a duplex-triplex transition. , 2004, Angewandte Chemie.

[9]  Chun-yang Zhang,et al.  Highly sensitive detection of protein with aptamer-based target-triggering two-stage amplification. , 2012, Analytical chemistry.

[10]  Yamuna Krishnan,et al.  A DNA nanomachine that maps spatial and temporal pH changes inside living cells. , 2009, Nature nanotechnology.

[11]  Hong-Wu Tang,et al.  Low background signal platform for the detection of ATP: when a molecular aptamer beacon meets graphene oxide. , 2011, Biosensors & bioelectronics.

[12]  Itamar Willner,et al.  DNA machines: bipedal walker and stepper. , 2011, Nano letters.

[13]  Guo-Li Shen,et al.  In situ amplification signaling-based autonomous aptameric machine for the sensitive fluorescence detection of cocaine. , 2013, Biosensors & bioelectronics.

[14]  Meng Liu,et al.  A graphene-based biosensing platform based on the release of DNA probes and rolling circle amplification. , 2014, ACS nano.

[15]  杨朝勇.  Aptamers evolved from live cells as effective molecular probes for cancer study , 2006 .

[16]  B. Hong,et al.  Biomedical applications of graphene and graphene oxide. , 2013, Accounts of chemical research.

[17]  Pui Sai Lau,et al.  A general strategy to create RNA aptamer sensors using "regulated" graphene oxide adsorption. , 2014, ACS applied materials & interfaces.

[18]  N. Seeman.  From genes to machines: DNA nanomechanical devices. , 2005, Trends in biochemical sciences.

[19]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[20]  Itamar Willner,et al.  Amplified fluorescence aptamer-based sensors using exonuclease III for the regeneration of the analyte. , 2012, Chemistry.

[21]  O. Urakawa,et al.  Small - , 2007 .

[22]  Jian-hui Jiang,et al.  Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. , 2010, Analytical chemistry.

[23]  A. Govindaraj,et al.  Binding of DNA nucleobases and nucleosides with graphene. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

[24]  R. Ruoff,et al.  The chemistry of graphene oxide. , 2010, Chemical Society reviews.

[25]  Feng Yan,et al.  The use of polyethylenimine-grafted graphene nanoribbon for cellular delivery of locked nucleic acid modified molecular beacon for recognition of microRNA. , 2011, Biomaterials.

[26]  Razvan Nutiu,et al.  In vitro selection of structure-switching signaling aptamers. , 2005, Angewandte Chemie.

[27]  Huang-Hao Yang,et al.  A graphene platform for sensing biomolecules. , 2009, Angewandte Chemie.

[28]  Yuehe Lin,et al.  Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells. , 2010, Journal of the American Chemical Society.

[29]  Guo-Li Shen,et al.  Graphene-DNAzyme based biosensor for amplified fluorescence "turn-on" detection of Pb2+ with a high selectivity. , 2011, Analytical chemistry.

[30]  Arben Merkoçi,et al.  Graphene Oxide as an Optical Biosensing Platform , 2012, Advanced materials.

[31]  D. Patel,et al.  RNA bulges as architectural and recognition motifs. , 2000, Structure.

[32]  Yaping Hu,et al.  Graphene signal amplification for sensitive and real-time fluorescence anisotropy detection of small molecules. , 2013, Analytical chemistry.

[33]  Chunhai Fan,et al.  DNA nanostructure-decorated surfaces for enhanced aptamer-target binding and electrochemical cocaine sensors. , 2011, Analytical chemistry.

[34]  Eun Jeong Cho,et al.  Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. , 2005, Journal of the American Chemical Society.

[35]  Itamar Willner,et al.  Graphene oxide/nucleic-acid-stabilized silver nanoclusters: functional hybrid materials for optical aptamer sensing and multiplexed analysis of pathogenic DNAs. , 2013, Journal of the American Chemical Society.

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

[37]  Itamar Willner,et al.  Multiplexed analysis of genes and of metal ions using enzyme/DNAzyme amplification machineries. , 2014, Analytical chemistry.

[38]  G. Eda,et al.  Graphene oxide as a chemically tunable platform for optical applications. , 2010, Nature chemistry.

[39]  Da Chen,et al.  Graphene oxide: preparation, functionalization, and electrochemical applications. , 2012, Chemical reviews.

[40]  Po-Jung Jimmy Huang,et al.  Molecular beacon lighting up on graphene oxide. , 2012, Analytical chemistry.

[41]  Huang-Hao Yang,et al.  Amplified aptamer-based assay through catalytic recycling of the analyte. , 2010, Angewandte Chemie.

[42]  Ronghua Yang,et al.  Two-photon graphene oxide/aptamer nanosensing conjugate for in vitro or in vivo molecular probing. , 2014, Analytical chemistry.

[43]  Guo-Li Shen,et al.  Fluorescence aptameric sensor for strand displacement amplification detection of cocaine. , 2010, Analytical chemistry.

[44]  Chung-Yuen Hui,et al.  Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy. , 2008, Nano letters.