Emerging isothermal amplification technologies for microRNA biosensing: Applications to liquid biopsies.

The potential of microRNAs (miRNAs) as biomarker candidates in clinical practice for diagnosis, prognosis and treatment response prediction, especially in liquid biopsies, has led to a tremendous demand for techniques that can detect these molecules rapidly and accurately. Hence, numerous achievements have been reported recently in miRNA research. In this review, we discuss the challenges associated with the emerging field of miRNA detection, which are linked to the intrinsic properties of miRNAs, advantages and drawbacks of the currently available technologies and their potential applications in clinical research. We summarize the most promising nucleic acid amplification techniques applied to the in vitro detection of miRNAs, with a particular emphasis on the state of the art for isothermal alternatives to RT-qPCR. We detail the sensitivity, specificity and quantitativity of these approaches, as well as their potential for multiplexing. We also review the different detection formats to which these chemistries have been adapted, including analog readouts such as real-time monitoring, digital counting based on single-molecule amplification in compartments, and surface-based strategies.

[1]  X Chris Le,et al.  Reduction of Background Generated from Template-Template Hybridizations in the Exponential Amplification Reaction. , 2018, Analytical chemistry.

[2]  R. Wong,et al.  Direct quantification of single-molecules of microRNA by total internal reflection fluorescence microscopy. , 2010, Analytical chemistry.

[3]  Ryan T Fuchs,et al.  Small RNA Expression Profiling by High-Throughput Sequencing: Implications of Enzymatic Manipulation , 2012, Journal of nucleic acids.

[4]  M. Tewari,et al.  Droplet digital PCR as a novel detection method for quantifying microRNAs in acute myocardial infarction. , 2018, International journal of cardiology.

[5]  Tian Tian,et al.  Integrated paper-based microfluidic devices for point-of-care testing , 2018 .

[6]  Genxi Li,et al.  Detection of microRNA SNPs with ultrahigh specificity by using reduced graphene oxide-assisted rolling circle amplification. , 2015, Chemical communications.

[7]  Tania Nolan,et al.  The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments. , 2013, Clinical chemistry.

[8]  R. Abramson,et al.  Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Huan Xu,et al.  A label-free electrochemical biosensor for microRNAs detection based on DNA nanomaterial by coupling with Y-shaped DNA structure and non-linear hybridization chain reaction. , 2019, Biosensors & bioelectronics.

[10]  Wei Zhang,et al.  Label-free fluorescence detection of circulating microRNAs based on duplex-specific nuclease-assisted target recycling coupled with rolling circle amplification. , 2019, Talanta.

[11]  Jibin Abraham Punnoose,et al.  DNA nanotechnology approaches for microRNA detection and diagnosis , 2019, Nucleic acids research.

[12]  E. Stickeler,et al.  Universal nucleic acid sequence-based amplification for simultaneous amplification of messengerRNAs and microRNAs. , 2012, Analytica chimica acta.

[13]  M. Rodicio,et al.  Detection methods for microRNAs in clinic practice. , 2013, Clinical biochemistry.

[14]  Zhengping Li,et al.  One-step ultrasensitive detection of microRNAs with loop-mediated isothermal amplification (LAMP). , 2011, Chemical communications.

[15]  Longhua Tang,et al.  Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells. , 2014, Angewandte Chemie.

[16]  Jin Jen,et al.  Quantitative miRNA Expression Analysis Using Fluidigm Microfluidics Dynamic Arrays , 2011, BMC Genomics.

[17]  M. Kubista,et al.  Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification , 2017, Nucleic acids research.

[18]  Y. Guan,et al.  Production of dumbbell probe through hairpin cleavage-ligation and increasing RCA sensitivity and specificity by circle to circle amplification , 2016, Scientific Reports.

[19]  Shusheng Zhang,et al.  Label-free detection of microRNA based on coupling multiple isothermal amplification techniques , 2016, Scientific Reports.

[20]  E. Lander,et al.  Lessons from the Cancer Genome , 2013, Cell.

[21]  Chun-yang Zhang,et al.  Homogeneous and label-free detection of microRNAs using bifunctional strand displacement amplification-mediated hyperbranched rolling circle amplification. , 2014, Analytical chemistry.

[22]  K. Houlind,et al.  Quantification of microRNA levels in plasma – Impact of preanalytical and analytical conditions , 2018, PloS one.

[24]  R. Yuan,et al.  Bio-cleavable nanoprobes for target-triggered catalytic hairpin assembly amplification detection of microRNAs in live cancer cells. , 2018, Nanoscale.

[25]  Paola Tiberio,et al.  Challenges in Using Circulating miRNAs as Cancer Biomarkers , 2015, BioMed research international.

[26]  C. Bode,et al.  Chip-based digital PCR as a novel detection method for quantifying microRNAs in acute myocardial infarction patients , 2017, Acta Pharmacologica Sinica.

[27]  Christopher M. Hindson,et al.  Absolute quantification by droplet digital PCR versus analog real-time PCR , 2013, Nature Methods.

[28]  Chunhai Fan,et al.  A dumbbell probe-mediated rolling circle amplification strategy for highly sensitive microRNA detection , 2010, Nucleic acids research.

[29]  Wei Ren,et al.  Graphene surface-anchored fluorescence sensor for sensitive detection of microRNA coupled with enzyme-free signal amplification of hybridization chain reaction. , 2012, ACS applied materials & interfaces.

[30]  Zhengping Li,et al.  Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction. , 2016, Analytical chemistry.

[31]  Zong Dai,et al.  Asymmetric exponential amplification reaction on a toehold/biotin featured template: an ultrasensitive and specific strategy for isothermal microRNAs analysis , 2016, Nucleic acids research.

[32]  K. Iczkowski,et al.  Tissue-Specific MicroRNA Expression Patterns in Four Types of Kidney Disease. , 2017, Journal of the American Society of Nephrology : JASN.

[33]  J. Qu,et al.  An improved method for detecting circulating microRNAs with S-Poly(T) Plus real-time PCR , 2015, Scientific Reports.

[34]  Zhengping Li,et al.  Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification. , 2009, Angewandte Chemie.

[35]  A. Krolewski,et al.  Circulating miRNA Profiles Associated With Hyperglycemia in Patients With Type 1 Diabetes , 2018, Diabetes.

[36]  P. Lingor,et al.  Circulating miRNAs as Diagnostic Biomarkers for Parkinson’s Disease , 2018, Front. Neurosci..

[37]  Zhengping Li,et al.  Rolling circle extension-actuated loop-mediated isothermal amplification (RCA-LAMP) for ultrasensitive detection of microRNAs. , 2019, Biosensors & bioelectronics.

[38]  D. Beebe,et al.  The present and future role of microfluidics in biomedical research , 2014, Nature.

[39]  Jaber Aslanzadeh,et al.  Preventing PCR amplification carryover contamination in a clinical laboratory. , 2004, Annals of clinical and laboratory science.

[40]  Lili Wang,et al.  Steps to achieve quantitative measurements of microRNA using two step droplet digital PCR , 2017, PloS one.

[41]  Jiye Shi,et al.  Hybridization chain reaction amplification of microRNA detection with a tetrahedral DNA nanostructure-based electrochemical biosensor. , 2014, Analytical chemistry.

[42]  Yu-Qiang Liu,et al.  One-step, multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification. , 2012, Journal of the American Chemical Society.

[43]  P. Leedman,et al.  Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal , 2018, BMC Biotechnology.

[44]  Y. Sakai,et al.  The Molecular Basis and Therapeutic Potential of Let-7 MicroRNAs against Colorectal Cancer , 2018, Canadian journal of gastroenterology & hepatology.

[45]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[46]  E. Miska,et al.  MicroRNA—implications for cancer , 2007, Virchows Archiv.

[47]  Daniel B. Martin,et al.  Circulating microRNAs as stable blood-based markers for cancer detection , 2008, Proceedings of the National Academy of Sciences.

[48]  S. Deo,et al.  MicroRNA Detection: Current Technology and Research Strategies. , 2015, Annual review of analytical chemistry.

[49]  Jie Chao,et al.  Single-Molecule Analysis of MicroRNA and Logic Operations Using a Smart Plasmonic Nanobiosensor. , 2018, Journal of the American Chemical Society.

[50]  H. Gong,et al.  Ratiometric Fluorescence Sensor for the MicroRNA Determination by Catalyzed Hairpin Assembly. , 2017, ACS sensors.

[51]  J. McCubrey,et al.  Cardiovascular disease-related miRNAs expression: potential role as biomarkers and effects of training exercise , 2018, Oncotarget.

[52]  Zachary B. Abrams,et al.  Alterations in patient plasma microRNA expression profiles following resection of metastatic melanoma , 2018, Journal of surgical oncology.

[53]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[54]  Haifeng Dong,et al.  Target-Triggered Catalytic Hairpin Assembly-Induced Core-Satellite Nanostructures for High-Sensitive "Off-to-On" SERS Detection of Intracellular MicroRNA. , 2018, Analytical chemistry.

[55]  Henrik H. J. Persson,et al.  DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets , 2009, Nature.

[56]  Nóra Varga,et al.  Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. , 2004, Nucleic acids research.

[57]  K. Morris,et al.  Profiling microRNA expression with microarrays. , 2008, Trends in biotechnology.

[58]  G. Shin,et al.  Multiplex quantitative analysis of microRNA expression via exponential isothermal amplification and conformation-sensitive DNA separation , 2017, Scientific Reports.

[59]  Bingwen Yu,et al.  Digital PCR on an integrated self-priming compartmentalization chip. , 2014, Lab on a chip.

[60]  Yu Cao,et al.  Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection , 2018, Theranostics.

[61]  Hiroyuki Fujita,et al.  Microfabricated arrays of femtoliter chambers allow single molecule enzymology , 2005, Nature Biotechnology.

[62]  Jinbo B Fan,et al.  Single-molecule catalytic hairpin assembly for rapid and direct quantification of circulating miRNA biomarkers. , 2018, Analytica chimica acta.

[63]  Raffaele Palmirotta,et al.  Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology , 2018, Therapeutic advances in medical oncology.

[64]  Zhiqiang Gao,et al.  A microfluidic-assisted microarray for ultrasensitive detection of miRNA under an optical microscope. , 2011, Lab on a chip.

[65]  Mei Zhao,et al.  Identification of a Circulating MicroRNA Signature for Colorectal Cancer Detection , 2014, PloS one.

[66]  Jianhui Jiang,et al.  A ligation-based loop-mediated isothermal amplification (ligation-LAMP) strategy for highly selective microRNA detection. , 2016, Chemical communications.

[67]  R. Crooks,et al.  Detection of microRNA by Electrocatalytic Amplification: A General Approach for Single-Particle Biosensing. , 2017, Journal of the American Chemical Society.

[68]  Dinh-Tuan Phan,et al.  Ultrahigh-throughput droplet microfluidic device for single-cell miRNA detection with isothermal amplification. , 2018, Lab on a chip.

[69]  F. Slack,et al.  The let-7 family of microRNAs. , 2008, Trends in cell biology.

[70]  Qinyu Ge,et al.  MicroRNA Detection Specificity: Recent Advances and Future Perspective. , 2019, Analytical chemistry.

[71]  R. J. Mitchell,et al.  Locked nucleic acids in PCR primers increase sensitivity and performance. , 2008, Genomics.

[72]  Yannick Rondelez,et al.  Isothermal digital detection of microRNAs using background-free molecular circuit , 2019, Science Advances.

[73]  You-hong Cui,et al.  A novel photoelectrochemical strategy based on an integrative photoactive heterojunction nanomaterial and a redox cycling amplification system for ultrasensitive determination of microRNA in cells. , 2019, Biosensors & bioelectronics.

[74]  K. Zen,et al.  Circulating MicroRNAs: a novel class of biomarkers to diagnose and monitor human cancers , 2012, Medicinal research reviews.

[75]  Chun-yang Zhang,et al.  Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor. , 2012, Analytical chemistry.

[76]  Yuguo Tang,et al.  Electrochemical Detection of miRNA Combining T7 Exonuclease-Assisted Cascade Signal Amplification and DNA-Templated Copper Nanoparticles. , 2018, Analytical chemistry.

[77]  Hong Zhang,et al.  MicroRNA-92a promotes growth, metastasis, and chemoresistance in non-small cell lung cancer cells by targeting PTEN , 2016, Tumor Biology.

[78]  Debin Zhu,et al.  Detection of microRNA in clinical tumor samples by isothermal enzyme-free amplification and label-free graphene oxide-based SYBR Green I fluorescence platform. , 2015, Biosensors & bioelectronics.

[79]  H. Park,et al.  Enzyme-free and label-free miRNA detection based on target-triggered catalytic hairpin assembly and fluorescence enhancement of DNA-silver nanoclusters , 2018 .

[80]  L. Mazutis,et al.  Quantitative and sensitive detection of rare mutations using droplet-based microfluidics. , 2011, Lab on a chip.

[81]  N. Gu,et al.  Phage-mediated counting by the naked eye of miRNA molecules at attomolar concentrations in a Petri dish. , 2015, Nature materials.

[82]  Enrico Gratton,et al.  Digital quantification of miRNA directly in plasma using integrated comprehensive droplet digital detection. , 2015, Lab on a chip.

[83]  Yongqiang Cheng,et al.  Ultrasensitive detection of microRNAs by exponential isothermal amplification. , 2010, Angewandte Chemie.

[84]  Zhengping Li,et al.  One-step detection of microRNA with high sensitivity and specificity via target-triggered loop-mediated isothermal amplification (TT-LAMP). , 2017, Chemical communications.

[85]  T. Patel,et al.  Comparison of miRNA quantitation by Nanostring in serum and plasma samples , 2017, PloS one.

[86]  M. Behlke,et al.  Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3′-MicroRNA Isoforms , 2018, Front. Genet..

[87]  Sai Bi,et al.  Dumbbell probe-mediated cascade isothermal amplification: a novel strategy for label-free detection of microRNAs and its application to real sample assay. , 2013, Analytica chimica acta.

[88]  Zhengping Li,et al.  A simple molecular beacon with duplex-specific nuclease amplification for detection of microRNA. , 2016, The Analyst.

[89]  D. Ichikawa,et al.  Circulating MicroRNAs: A Next-Generation Clinical Biomarker for Digestive System Cancers , 2016, International journal of molecular sciences.

[90]  Phenix-Lan Quan,et al.  dPCR: A Technology Review , 2018, Sensors.

[91]  G. Berchem,et al.  Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material , 2016, Scientific Reports.

[92]  Chad A Mirkin,et al.  Scanometric microRNA array profiling of prostate cancer markers using spherical nucleic acid-gold nanoparticle conjugates. , 2012, Analytical chemistry.

[93]  Jesper Tegnér,et al.  Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR , 2015, Briefings Bioinform..

[94]  N. Hildebrandt,et al.  Simple, Amplified, and Multiplexed Detection of MicroRNAs Using Time-Gated FRET and Hybridization Chain Reaction. , 2019, Analytical chemistry.

[95]  Niko Hildebrandt,et al.  A Rapid, Amplification-Free, and Sensitive Diagnostic Assay for Single-Step Multiplexed Fluorescence Detection of MicroRNA. , 2015, Angewandte Chemie.

[96]  Li Liang,et al.  Isothermally sensitive detection of serum circulating miRNAs for lung cancer diagnosis. , 2013, Analytical chemistry.

[97]  Š. Pospíšilová,et al.  MicroRNA isolation and stability in stored RNA samples. , 2009, Biochemical and biophysical research communications.

[98]  P. Carroll,et al.  Microfluidic-based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in the sera of prostate cancer patients. , 2011, Cancer research.

[99]  Maria Chiara Giuffrida,et al.  Integration of isothermal amplification methods in microfluidic devices: Recent advances. , 2017, Biosensors & bioelectronics.

[100]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[101]  Valérie Taly,et al.  Detecting biomarkers with microdroplet technology. , 2012, Trends in molecular medicine.

[102]  V. Taly,et al.  Liquid Biopsy: General Concepts , 2019, Acta Cytologica.

[103]  Yingdong Zhao,et al.  Strengths and Limitations of Laboratory Procedures for MicroRNA Detection , 2010, Cancer Epidemiology, Biomarkers & Prevention.

[104]  Valérie Taly,et al.  Development of digital PCR molecular tests for clinical practice: principles, practical implementation and recommendations. , 2018, Annales de biologie clinique.

[105]  K. Kinzler,et al.  Digital PCR. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[106]  C. Lawrie,et al.  New Concepts in Cancer Biomarkers: Circulating miRNAs in Liquid Biopsies , 2016, International journal of molecular sciences.

[107]  Y. Urano,et al.  High-throughput single-molecule bioassay using micro-reactor arrays with a concentration gradient of target molecules. , 2018, Lab on a chip.

[108]  Chun-yang Zhang,et al.  Rapid and label-free monitoring of exonuclease III-assisted target recycling amplification. , 2012, Analytical chemistry.

[109]  Kemin Wang,et al.  A DNA nanowire based localized catalytic hairpin assembly reaction for microRNA imaging in live cells† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc02943a , 2018, Chemical science.

[110]  E. Fokas,et al.  Circulating miRNAs as non-invasive biomarkers to predict aggressive prostate cancer after radical prostatectomy , 2019, Journal of Translational Medicine.

[111]  F. Liu,et al.  Branched rolling circle amplification method for measuring serum circulating microRNA levels for early breast cancer detection , 2018, Cancer science.

[112]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[113]  Yongxin Li,et al.  Selective Single Molecule Nanopore Sensing of microRNA Using PNA Functionalized Magnetic Core-Shell Fe3O4-Au Nanoparticles. , 2019, Analytical chemistry.

[114]  H. Park,et al.  Universal, colorimetric microRNA detection strategy based on target-catalyzed toehold-mediated strand displacement reaction , 2018, Nanotechnology.

[115]  Ping Wang,et al.  Highly sensitive detection of microRNAs based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme. , 2013, Biosensors & bioelectronics.

[116]  Jørgen Kjems,et al.  A microRNA detection system based on padlock probes and rolling circle amplification. , 2006, RNA.

[117]  Jing Wang,et al.  Fe₃O₄@Ag magnetic nanoparticles for microRNA capture and duplex-specific nuclease signal amplification based SERS detection in cancer cells. , 2016, Biosensors & bioelectronics.

[118]  Trieu Nguyen,et al.  MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics , 2018, Laboratory Investigation.

[119]  Youping Yin,et al.  Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri , 2016, PloS one.

[120]  Ru-Qin Yu,et al.  A highly sensitive target-primed rolling circle amplification (TPRCA) method for fluorescent in situ hybridization detection of microRNA in tumor cells. , 2014, Analytical chemistry.

[121]  M. Trau,et al.  Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction , 2016, Scientific Reports.

[122]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[123]  J. Qin,et al.  Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis , 2017, BMC Molecular Biology.

[124]  Y. Chai,et al.  Target recycling amplification for sensitive and label-free impedimetric genosensing based on hairpin DNA and graphene/Au nanocomposites. , 2011, Chemical communications.

[125]  Yuan-Jie Fan,et al.  High-throughput and ultra-sensitive single-cell profiling of multiple microRNAs and identification of human cancer. , 2019, Chemical communications.

[126]  Yang Li,et al.  An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe , 2005, Nucleic acids research.

[127]  Yudie Sun,et al.  Composition-Tunable Hollow Au/Ag SERS Nanoprobes Coupled with Target-Catalyzed Hairpin Assembly for Triple-Amplification Detection of miRNA. , 2018, Analytical chemistry.

[128]  N. Pierce,et al.  Multiplexed miRNA northern blots via hybridization chain reaction , 2016, Nucleic acids research.

[129]  Sai Bi,et al.  Programmable strand displacement-based magnetic separation for simultaneous amplified detection of multiplex microRNAs by chemiluminescence imaging array. , 2017, Biosensors & bioelectronics.

[130]  P. Laurent-Puig,et al.  Validation of miR-31-3p Expression to Predict Cetuximab Efficacy When Used as First-Line Treatment in RAS Wild-Type Metastatic Colorectal Cancer , 2018, Clinical Cancer Research.

[131]  Yanyan Yu,et al.  Ultrasensitive electrochemical detection of microRNA based on an arched probe mediated isothermal exponential amplification. , 2014, Analytical chemistry.

[132]  Jinghua Yu,et al.  Sensitive and rapid detection of microRNAs using hairpin probes-mediated exponential isothermal amplification. , 2017, Biosensors & bioelectronics.

[133]  Vladimir Benes,et al.  Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. , 2010, Methods.

[134]  Mattias Strömberg,et al.  Optomagnetic Detection of MicroRNA Based on Duplex-Specific Nuclease-Assisted Target Recycling and Multilayer Core-Satellite Magnetic Superstructures. , 2017, ACS nano.

[135]  Jeff Mellen,et al.  High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number , 2011, Analytical chemistry.

[136]  Longhua Guo,et al.  Direct visualization of sub-femtomolar circulating microRNAs in serum based on the duplex-specific nuclease-amplified oriented assembly of gold nanoparticle dimers. , 2016, Chemical communications.

[137]  Y. Chai,et al.  Versatile and Ultrasensitive Electrochemiluminescence Biosensor for Biomarker Detection Based on Nonenzymatic Amplification and Aptamer-Triggered Emitter Release. , 2019, Analytical chemistry.

[138]  P. Laurent-Puig,et al.  Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective , 2018, Expert review of molecular diagnostics.

[139]  Xiaobo Zhang,et al.  Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc02641e , 2015, Chemical science.

[140]  Guohua Zhou,et al.  Exponential amplification of DNA with very low background using graphene oxide and single-stranded binding protein to suppress non-specific amplification , 2015, Microchimica Acta.

[141]  Jinfang Shi,et al.  Use of Luminex xMAP bead-based suspension array for detecting microRNA in NSCLC tissues and its clinical application , 2012, Tumori.

[142]  Yongsheng Shi,et al.  Alternative polyadenylation: new insights from global analyses. , 2012, RNA.

[143]  Chunhai Fan,et al.  Lab in a tube: ultrasensitive detection of microRNAs at the single-cell level and in breast cancer patients using quadratic isothermal amplification. , 2013, Journal of the American Chemical Society.

[144]  S H Neoh,et al.  Quantitation of targets for PCR by use of limiting dilution. , 1992, BioTechniques.

[145]  Robert M. Dirks,et al.  An autonomous polymerization motor powered by DNA hybridization , 2007, Nature Nanotechnology.

[146]  K. Witwer,et al.  Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid , 2013, Front. Genet..

[147]  Guiqing Jia,et al.  Droplet digital PCR-based circulating microRNA detection serve as a promising diagnostic method for gastric cancer , 2018, BMC Cancer.

[148]  Shu-Jen Chen,et al.  Optimized Collection Protocol for Plasma MicroRNA Measurement in Patients with Cardiovascular Disease , 2016, BioMed research international.

[149]  G. Yousef,et al.  Droplet digital PCR improves urinary exosomal miRNA detection compared to real-time PCR. , 2019, Clinical biochemistry.

[150]  V. Taly,et al.  Droplet-Based Digital PCR: Application in Cancer Research. , 2017, Advances in clinical chemistry.

[151]  D. Dendukuri,et al.  A focus on microfluidics and nanotechnology approaches for the ultra sensitive detection of microRNA. , 2014, MicroRNA.

[152]  E. Kool,et al.  Amplified microRNA detection by templated chemistry , 2012, Nucleic acids research.

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

[154]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

[155]  D. Noonan,et al.  A comparison between quantitative PCR and droplet digital PCR technologies for circulating microRNA quantification in human lung cancer , 2016, BMC Biotechnology.

[156]  Jian-hui Jiang,et al.  Ultrasensitive detection of microRNAs using catalytic hairpin assembly coupled with enzymatic repairing amplification. , 2016, Chemical communications.

[157]  C. Perou,et al.  A custom microarray platform for analysis of microRNA gene expression , 2004, Nature Methods.

[158]  D. Schadendorf,et al.  The validity of circulating microRNAs in oncology: Five years of challenges and contradictions , 2014, Molecular oncology.

[159]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[160]  Chun-yang Zhang,et al.  Integration of isothermal amplification with quantum dot-based fluorescence resonance energy transfer for simultaneous detection of multiple microRNAs† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00832a , 2018, Chemical science.

[161]  J. Compton,et al.  Nucleic acid sequence-based amplification , 1991, Nature.

[162]  M. Yamamura,et al.  Leak-free million-fold DNA amplification with locked nucleic acid and targeted hybridization in one pot. , 2019, Organic & biomolecular chemistry.

[163]  Amar S Basu,et al.  Digital Assays Part I: Partitioning Statistics and Digital PCR , 2017, SLAS technology.

[164]  G. Calin,et al.  Clinical relevance of circulating cell-free microRNAs in cancer , 2014, Nature Reviews Clinical Oncology.

[165]  Ruijie Deng,et al.  Target-fueled DNA walker for highly selective miRNA detection† †Electronic supplementary information (ESI) available: DNA strand structure and sequences, assembly of DNA strands as noted in the text. See DOI: 10.1039/c5sc02784e Click here for additional data file. , 2015, Chemical science.

[166]  Pengbo Zhang,et al.  Multiplex ligation-dependent probe amplification (MLPA) for ultrasensitive multiplexed microRNA detection using ribonucleotide-modified DNA probes. , 2013, Chemical communications.

[167]  Jingli Yan,et al.  Ultrasensitive quantification of mature microRNAs by real-time PCR based on ligation of a ribonucleotide-modified DNA probe. , 2011, Chemical communications.

[168]  Mattias Strömberg,et al.  On-Particle Rolling Circle Amplification-Based Core-Satellite Magnetic Superstructures for MicroRNA Detection. , 2018, ACS applied materials & interfaces.

[169]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[170]  Jing Zhang,et al.  An immobilization-free electrochemical impedance biosensor based on duplex-specific nuclease assisted target recycling for amplified detection of microRNA. , 2016, Biosensors & bioelectronics.

[171]  D. Bartel MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[172]  H. Ju,et al.  Fluorescence hydrogel array based on interfacial cation exchange amplification for highly sensitive microRNA detection. , 2019, Analytica chimica acta.

[173]  Hongying Liao,et al.  The regulatory and predictive functions of miR-17 and miR-92 families on cisplatin resistance of non-small cell lung cancer , 2015, BMC Cancer.

[174]  A. Bhomra,et al.  Comprehensive RNA-Sequencing Analysis in Serum and Muscle Reveals Novel Small RNA Signatures with Biomarker Potential for DMD , 2018, Molecular therapy. Nucleic acids.

[175]  Thean-Hock Tang,et al.  Biases in small RNA deep sequencing data , 2013, Nucleic acids research.

[176]  D. Richman,et al.  Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[177]  D. Walt,et al.  Digital direct detection of microRNAs using single molecule arrays , 2017, Nucleic acids research.

[178]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[179]  M. Kramer Stem‐Loop RT‐qPCR for miRNAs , 2011, Current protocols in molecular biology.

[180]  Y. Zhu,et al.  Integrating PDA microtube waveguide system with heterogeneous CHA amplification strategy towards superior sensitive detection of miRNA. , 2019, Biosensors & bioelectronics.

[181]  PolyA RT-PCR-based quantification of microRNA by using universal TaqMan probe , 2012, Biotechnology Letters.

[182]  Gebert Lfr,et al.  Regulation of microRNA function in animals , 2019 .

[183]  M. Soleimani,et al.  Analysis of microRNA signatures using size-coded ligation-mediated PCR , 2011, Nucleic acids research.

[184]  Gurman Singh Pall,et al.  Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot , 2007, Nucleic acids research.

[185]  T. Ørntoft,et al.  Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs , 2011, BMC Genomics.

[186]  Yongqiang Cheng,et al.  Recent advances in microRNA detection. , 2018, The Analyst.

[187]  Guonan Chen,et al.  A rolling circle amplification-based DNA machine for miRNA screening coupling catalytic hairpin assembly with DNAzyme formation. , 2014, Chemical communications.

[188]  Chao Yang,et al.  A simple G-quadruplex molecular beacon-based biosensor for highly selective detection of microRNA. , 2017, Biosensors & bioelectronics.

[189]  Huang-Hao Yang,et al.  Enzyme-free amplified detection of microRNA using target-catalyzed hairpin assembly and magnesium ion-dependent deoxyribozyme , 2015, Science China Chemistry.

[190]  D. Huo,et al.  An enzyme-free sensitive electrochemical microRNA-16 biosensor by applying a multiple signal amplification strategy based on Au/PPy-rGO nanocomposite as a substrate. , 2019, Talanta.

[191]  R. Corn,et al.  Multiplexed detection methods for profiling microRNA expression in biological samples. , 2008, Angewandte Chemie.

[192]  Jim F Huggett,et al.  Evaluation of digital PCR for absolute DNA quantification. , 2011, Analytical chemistry.

[193]  J. Posfai,et al.  Sensitive and specific miRNA detection method using SplintR Ligase , 2016, Nucleic acids research.

[194]  Muneesh Tewari,et al.  Kinetic fingerprinting to identify and count single nucleic acids , 2015, Nature Biotechnology.

[195]  Wei Cheng,et al.  A simple electrochemical biosensor for highly sensitive and specific detection of microRNA based on mismatched catalytic hairpin assembly. , 2015, Biosensors & bioelectronics.

[196]  X. Le,et al.  Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. , 2014, Chemical Society reviews.

[197]  Zhaoxin Li,et al.  Simple colorimetric DNA detection based on hairpin assembly reaction and target-catalytic circuits for signal amplification. , 2012, Analytical biochemistry.

[198]  S. Lukyanov,et al.  A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. , 2002, Genome research.

[199]  Zhiqiang Gao,et al.  A highly sensitive and selective homogenous assay for profiling microRNA expression. , 2014, Biosensors & bioelectronics.

[200]  Christopher D. Spicer,et al.  Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot–DNA Conjugates , 2018, ACS applied materials & interfaces.

[201]  M. Yigit,et al.  Reprogrammable multiplexed detection of circulating oncomiRs using hybridization chain reaction. , 2016, Chemical communications.

[202]  Yasuyoshi Mori,et al.  Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products , 2008, Nature Protocols.

[203]  Jim F Huggett,et al.  Considerations for digital PCR as an accurate molecular diagnostic tool. , 2015, Clinical chemistry.

[204]  Kai Zhang,et al.  Sensitive detection of microRNA in complex biological samples by using two stages DSN-assisted target recycling signal amplification method. , 2017, Biosensors & bioelectronics.

[205]  H. Ju,et al.  Chemiluminescence imaging for microRNA detection based on cascade exponential isothermal amplification machinery. , 2016, Analytica chimica acta.

[206]  T. Notomi,et al.  Accelerated reaction by loop-mediated isothermal amplification using loop primers. , 2002, Molecular and cellular probes.

[207]  Zissimos Mourelatos,et al.  Microarray-based, high-throughput gene expression profiling of microRNAs , 2004, Nature Methods.

[208]  Zuhong Lu,et al.  miRNA in Plasma Exosome is Stable under Different Storage Conditions , 2014, Molecules.

[209]  Xiaobing Fu,et al.  A Facile and Specific Assay for Quantifying MicroRNA by an Optimized RT-qPCR Approach , 2012, PloS one.

[210]  Patrick S Doyle,et al.  Ultrasensitive multiplexed microRNA quantification on encoded gel microparticles using rolling circle amplification. , 2011, Analytical chemistry.

[211]  Kaixiang Zhang,et al.  Isothermal Amplification for MicroRNA Detection: From the Test Tube to the Cell. , 2017, Accounts of chemical research.

[212]  Jiashu Sun,et al.  Quantitative Detection of MicroRNA in One Step via Next Generation Magnetic Relaxation Switch Sensing. , 2016, ACS nano.

[213]  Jun Wu,et al.  Label-free and enzyme-free colorimetric detection of microRNA by catalyzed hairpin assembly coupled with hybridization chain reaction. , 2016, Biosensors & bioelectronics.

[214]  Cheng Zhang,et al.  Backbone-modified molecular beacons for highly sensitive and selective detection of microRNAs based on duplex specific nuclease signal amplification. , 2013, Chemical communications.

[215]  Zhengping Li,et al.  Digital quantitative analysis of microRNA in single cell based on ligation-depended polymerase colony (Polony). , 2017, Biosensors & bioelectronics.

[216]  Luke P. Lee,et al.  Digital LAMP in a sample self-digitization (SD) chip. , 2012, Lab on a chip.

[217]  D. Xing,et al.  High-specific microRNA detection based on dual-recycling cascade reaction and nicking endonuclease signal amplification , 2018, Sensors and Actuators B: Chemical.

[218]  Teruo Fujii,et al.  Boosting functionality of synthetic DNA circuits with tailored deactivation , 2016, Nature Communications.

[219]  Jinghong Li,et al.  Carbon nanotube enhanced label-free detection of microRNAs based on hairpin probe triggered solid-phase rolling-circle amplification. , 2015, Nanoscale.

[220]  S. Kääb,et al.  Stability of Circulating Blood-Based MicroRNAs – Pre-Analytic Methodological Considerations , 2017, PloS one.

[221]  C. Foy,et al.  A comparison of miRNA isolation and RT-qPCR technologies and their effects on quantification accuracy and repeatability. , 2013, BioTechniques.

[222]  Qian Wang,et al.  High specific and ultrasensitive isothermal detection of microRNA by padlock probe-based exponential rolling circle amplification. , 2013, Analytical chemistry.

[223]  K. Komiya,et al.  Measurement of microRNA with isothermal DNA amplification on fully automated immunoassay analyzers , 2019, Analytical and Bioanalytical Chemistry.

[224]  Sanjay Tyagi,et al.  Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. , 2006, Clinica chimica acta; international journal of clinical chemistry.

[225]  F. Slack,et al.  Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue. , 2018, Analytical chemistry.

[226]  I. Martín-Burriel,et al.  Stability of Circulating Exosomal miRNAs in Healthy Subjects , 2018, Scientific Reports.

[227]  E. Ng,et al.  Differential expression of microRNAs in plasma of patients with colorectal cancer: a potential marker for colorectal cancer screening , 2009, Gut.

[228]  Huangxian Ju,et al.  MicroRNA: function, detection, and bioanalysis. , 2013, Chemical reviews.

[229]  Zong Dai,et al.  Isothermal Amplification on a Structure-Switchable Symmetric Toehold Dumbbell-Template: A Strategy Enabling MicroRNA Analysis at the Single-Cell Level with Ultrahigh Specificity and Accuracy. , 2018, Analytical chemistry.

[230]  Pier Paolo Pompa,et al.  Absolute and direct microRNA quantification using DNA-gold nanoparticle probes. , 2014, Journal of the American Chemical Society.