A fluorescent aptasensor with product-triggered amplification by exonuclease III digestion for highly sensitive ATP detection

Here we proposed a conceptually new amplified ATP assay by combination of exonuclease III (Exo III) with an allosteric aptasensor triggered by ATP with graphene oxide (GO) assistance. The assay needs only one single fluorophore-labelled DNA probe, which was designed having the fluorescence labelled nucleotide and enzymatic substrate sequence away from the ATP recognition aptamer sequence to avoid the hindrance of the target recognition and enzymatic cleavage. The signal amplification mechanism is based on the binding ability of the produced dAMP to the ATP aptamer. In every cycle, the ATP can trigger the assay probe to be digested by the Exo III. The digestion product includes 3 dAMPs, which also can trigger the assay probe. The limit of detection as low as 31 nM was achieved, which is very competitive compared to those of other aptasensors with a signal amplification strategy for ATP detection. We envision that this principle could facilitate the design and development of other aptamer-based ATP sensors using different nucleases and find their potential applications in biological and environmental fields in the future.

[1]  M. Billaud,et al.  Mechanisms of ATP release and signalling in the blood vessel wall. , 2012, Cardiovascular research.

[2]  Anthony K. Au,et al.  Ultrarapid detection of pathogenic bacteria using a 3D immunomagnetic flow assay. , 2014, Analytical chemistry.

[3]  Shirmir D. Branch,et al.  GOx signaling triggered by aptamer-based ATP detection. , 2012, Chemical communications.

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

[5]  Ping Yu,et al.  Dual recognition unit strategy improves the specificity of the adenosine triphosphate (ATP) aptamer biosensor for cerebral ATP assay. , 2015, Analytical chemistry.

[6]  Wei Wang,et al.  A general chemiluminescence strategy for measuring aptamer-target binding and target concentration. , 2014, Analytical chemistry.

[7]  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.

[8]  Jinmao You,et al.  A novel aptamer-functionalized MoS2 nanosheet fluorescent biosensor for sensitive detection of prostate specific antigen , 2014, Analytical and Bioanalytical Chemistry.

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

[10]  M. Strano,et al.  A luciferase/single-walled carbon nanotube conjugate for near-infrared fluorescent detection of cellular ATP. , 2010, Angewandte Chemie.

[11]  A universal amplified strategy for aptasensors: enhancing sensitivity through allostery-triggered enzymatic recycling amplification. , 2012, Biosensors & bioelectronics.

[12]  H. Noda,et al.  Attomol-level ATP bioluminometer for detecting single bacterium. , 2017, Luminescence : the journal of biological and chemical luminescence.

[13]  Song Li,et al.  A Graphene-Based Biosensing Platform Based on Regulated Release of an Aptameric DNA Biosensor , 2015, Sensors.

[14]  Deqing Zhang,et al.  Continuous on-site label-free ATP fluorometric assay based on aggregation-induced emission of silole. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[15]  M. Eck.  ATP-binding cassette transporter A1: key player in cardiovascular and metabolic disease at local and systemic level. , 2014 .

[16]  Yi Lu,et al.  Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules. , 2012, Analytical chemistry.

[17]  Lei Wang,et al.  A novel enzyme-free and label-free fluorescence aptasensor for amplified detection of adenosine. , 2013, Biosensors & bioelectronics.

[18]  P. Okunieff,et al.  Cystic Fibrosis Transmembrane Conductance Regulator and Adenosine Triphosphate , 1997, Science.

[19]  Yingfu Li,et al.  Structure-switching signaling aptamers. , 2003, Journal of the American Chemical Society.

[20]  Y. Huang,et al.  Free-labelled fluorescent method for ATP detection assisted by T4 DNA ligase , 2017 .

[21]  Chen Chen,et al.  Possible Involvement of F1F0-ATP synthase and Intracellular ATP in Keratinocyte Differentiation in normal skin and skin lesions , 2017, Scientific Reports.

[22]  S. Dong,et al.  Double-strand DNA-templated formation of copper nanoparticles as fluorescent probe for label-free aptamer sensor. , 2011, Analytical chemistry.

[23]  Fengli Qu,et al.  Niche nanoparticle-based FRET assay for bleomycin detection via DNA scission. , 2016, Biosensors & bioelectronics.

[24]  Feng Liu,et al.  A simple and sensitive aptasensor for colorimetric detection of adenosine triphosphate based on unmodified gold nanoparticles. , 2017, Talanta.

[25]  S. G. Rogers,et al.  Exonuclease III of Escherichia coli K-12, an AP endonuclease. , 1980, Methods in enzymology.

[26]  Weihong Tan,et al.  A ligation-triggered DNAzyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal. , 2011, Journal of the American Chemical Society.

[27]  E. Kazerooni,et al.  Bacterial Contamination of CT Equipment: Use of ATP Detection and Culture Results to Target Quality Improvement. , 2017, Academic radiology.

[28]  R. Kennedy,et al.  Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. , 2001, Analytical chemistry.

[29]  Zhi Zhu,et al.  A label-free fluorescence strategy for sensitive detection of ATP based on the ligation-triggered super-sandwich. , 2015, Biosensors & bioelectronics.

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

[31]  Hongje Jang,et al.  A Graphene‐Based Platform for the Assay of Duplex‐DNA Unwinding by Helicase† , 2010, Angewandte Chemie.

[32]  Meng Liu,et al.  Label-free fluorescent detection of Cu(II) ions based on DNA cleavage-dependent graphene-quenched DNAzymes. , 2011, Chemical communications.

[33]  C. Yang,et al.  Carbon nanoparticle-protected aptamers for highly sensitive and selective detection of biomolecules based on nuclease-assisted target recycling signal amplification. , 2014, Chemical communications.

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

[35]  Y. Chai,et al.  Target-induced structure switching of hairpin aptamers for label-free and sensitive fluorescent detection of ATP via exonuclease-catalyzed target recycling amplification. , 2014, Biosensors & bioelectronics.

[36]  Yuanyang Zhao,et al.  Detection of adenosine triphosphate in HeLa cell using capillary electrophoresis-laser induced fluorescence detection based on aptamer and graphene oxide. , 2016, Colloids and surfaces. B, Biointerfaces.

[37]  Zhaohui Li,et al.  A label-free aptasensor for highly sensitive ATP detection by using exonuclease I and oligonucleotide-templated fluorescent copper nanoparticles , 2017 .

[38]  M. J. Pérez de Lara,et al.  Presence and release of ATP from the retina in an Alzheimer's disease model. , 2014, Journal of Alzheimer's disease : JAD.

[39]  I. Willner,et al.  Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations. , 2012, ACS nano.

[40]  Y. Urano,et al.  A fluorescent anion sensor that works in neutral aqueous solution for bioanalytical application. , 2002, Journal of the American Chemical Society.

[41]  Fengfu Fu,et al.  An enzyme-free and label-free fluorescent biosensor for small molecules by G-quadruplex based hybridization chain reaction. , 2015, Talanta.

[42]  Minghui Yang,et al.  Graphene oxide quantum dots@silver core-shell nanocrystals as turn-on fluorescent nanoprobe for ultrasensitive detection of prostate specific antigen. , 2015, Biosensors & bioelectronics.

[43]  Yuyang Jiang,et al.  Label-free fluorescent assays based on aptamer-target recognition. , 2012, The Analyst.

[44]  J. Szostak,et al.  A DNA aptamer that binds adenosine and ATP. , 1995, Biochemistry.

[45]  Fengli Qu,et al.  An amplified fluorescence detection of T4 polynucleotide kinase activity based on coupled exonuclease III reaction and a graphene oxide platform. , 2015, The Analyst.