Aptamer-based molecular recognition for biosensor development

AbstractNucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production. FigaAptamer-based molecular recognition for analyte detection.

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

[2]  Defa Li,et al.  Ultrasensitive electrochemical detection of proteins by amplification of aptamer-nanoparticle bio bar codes. , 2007, Analytical chemistry.

[3]  Yingfu Li,et al.  Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays , 2008, Sensors.

[4]  M Yarus,et al.  Diversity of oligonucleotide functions. , 1995, Annual review of biochemistry.

[5]  In vitro selection of RNA-based irreversible inhibitors of human neutrophil elastase. , 1995, Chemistry & biology.

[6]  Sheela M. Waugh,et al.  2′-Fluoropyrimidine RNA-based Aptamers to the 165-Amino Acid Form of Vascular Endothelial Growth Factor (VEGF165) , 1998, The Journal of Biological Chemistry.

[7]  G. Tocchini-Valentini,et al.  In vitro selection of dopamine RNA ligands. , 1997, Biochemistry.

[8]  B. Sullenger,et al.  RNA aptamers as reversible antagonists of coagulation factor IXa , 2002, Nature.

[9]  Lingxin Chen,et al.  Nanomaterial-assisted aptamers for optical sensing. , 2010, Biosensors & bioelectronics.

[10]  Sam F. Y. Li,et al.  Molecular aptamer beacon for myotonic dystrophy kinase-related Cdc42-binding kinase alpha. , 2010, Talanta.

[11]  A. Ellington,et al.  Simultaneous detection of diverse analytes with an aptazyme ligase array. , 2003, Analytical biochemistry.

[12]  Juewen Liu,et al.  Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. , 2005, Angewandte Chemie.

[13]  S. Klußmann,et al.  Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. , 2003, Nucleic acids research.

[14]  A. Heeger,et al.  An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. , 2006, Journal of the American Chemical Society.

[15]  Weihong Tan,et al.  Synthetic DNA Aptamers to Detect Protein Molecular Variants in a High‐Throughput Fluorescence Quenching Assay , 2003, Chembiochem : a European journal of chemical biology.

[16]  J C Cox,et al.  Automated selection of anti-protein aptamers. , 2001, Bioorganic & medicinal chemistry.

[17]  A. Aitken,et al.  The Generation and Characterization of Antagonist RNA Aptamers to Human Oncostatin M* , 2000, The Journal of Biological Chemistry.

[18]  D. S. Coffey,et al.  Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. , 2002, Cancer research.

[19]  Chih-Ching Huang,et al.  Aptamer-Functionalized Nano-Biosensors , 2009, Sensors.

[20]  Chunhai Fan,et al.  Aptamer-based biosensors , 2008 .

[21]  Yong Wang,et al.  Structural prediction and binding analysis of hybridized aptamers , 2011, Journal of molecular recognition : JMR.

[22]  Kun Han,et al.  Design Strategies for Aptamer-Based Biosensors , 2010, Sensors.

[23]  Robert Langer,et al.  An aptamer-doxorubicin physical conjugate as a novel targeted drug-delivery platform. , 2006, Angewandte Chemie.

[24]  Stacey L Clark,et al.  Electrochromatographic retention studies on a flavin-binding RNA aptamer sorbent. , 2003, Analytical chemistry.

[25]  A. Ono,et al.  Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. , 2004, Angewandte Chemie.

[26]  Jeong-O Lee,et al.  Aptamers as molecular recognition elements for electrical nanobiosensors , 2007, Analytical and bioanalytical chemistry.

[27]  S. Jayasena.  Aptamers: an emerging class of molecules that rival antibodies in diagnostics. , 1999, Clinical chemistry.

[28]  E. Quandt,et al.  Combination of a SAW-biosensor with MALDI mass spectrometric analysis. , 2008, Biosensors & bioelectronics.

[29]  D. Shangguan,et al.  Aptamers evolved from live cells as effective molecular probes for cancer study , 2006, Proceedings of the National Academy of Sciences.

[30]  J. Gariépy,et al.  DNA aptamers against the MUC1 tumour marker: design of aptamer–antibody sandwich ELISA for the early diagnosis of epithelial tumours , 2008, Analytical and bioanalytical chemistry.

[31]  J. Williamson.  Induced fit in RNA–protein recognition , 2000, Nature Structural Biology.

[32]  J. Blalock,et al.  Bidirectional Communication between the Neuroendocrine and Immune Systems Common Hormones and Hormone Receptors , 1990, Annals of the New York Academy of Sciences.

[33]  A. Heeger,et al.  Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. , 2005, Angewandte Chemie.

[34]  Eun Jeong Cho,et al.  Applications of aptamers as sensors. , 2009, Annual review of analytical chemistry.

[35]  Yun Xiang,et al.  Quantum-dot/aptamer-based ultrasensitive multi-analyte electrochemical biosensor. , 2006, Journal of the American Chemical Society.

[36]  E. Westhof,et al.  RNA structure: bioinformatic analysis. , 2007, Current opinion in microbiology.

[37]  S. Soper,et al.  Effect of linker structure on surface density of aptamer monolayers and their corresponding protein binding efficiency. , 2008, Analytical chemistry.

[38]  S Tombelli,et al.  Development of an optical RNA-based aptasensor for C-reactive protein , 2008, Analytical and bioanalytical chemistry.

[39]  Isao Karube,et al.  A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm , 2005, Nucleic acids research.

[40]  Ciara K O'Sullivan,et al.  Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor. , 2006, Journal of the American Chemical Society.

[41]  Shigeori Takenaka,et al.  A novel potassium sensing in aqueous media with a synthetic oligonucleotide derivative. Fluorescence resonance energy transfer associated with Guanine quartet-potassium ion complex formation. , 2002, Journal of the American Chemical Society.

[42]  W. James,et al.  Structural Determinants of Conformationally Selective, Prion-binding Aptamers*[boxs] , 2004, Journal of Biological Chemistry.

[43]  Siqing Shan,et al.  Inhibition of rat corneal angiogenesis by a nuclease-resistant RNA aptamer specific for angiopoietin-2 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Jacques Vergne,et al.  Adenine-Aptamer Complexes , 2002, The Journal of Biological Chemistry.

[45]  Akon Higuchi,et al.  Preparation of a DNA aptamer-Pt complex and its use in the colorimetric sensing of thrombin and anti-thrombin antibodies. , 2008, Analytical chemistry.

[46]  F. Luo,et al.  Aptamer from whole-bacterium SELEX as new therapeutic reagent against virulent Mycobacterium tuberculosis. , 2007, Biochemical and biophysical research communications.

[47]  Xiaobo Yu,et al.  Label-free electrochemical detection for aptamer-based array electrodes. , 2005, Analytical chemistry.

[48]  E. Alocilja,et al.  Aptasensors for detection of microbial and viral pathogens , 2008, Biosensors and Bioelectronics.

[49]  L. Gold,et al.  In vitro selection of RNA ligands to substance P. , 1995, Biochemistry.

[50]  Koji Sode,et al.  Novel electrochemical sensor system for protein using the aptamers in sandwich manner. , 2005, Biosensors & bioelectronics.

[51]  Guo-Li Shen,et al.  Electrochemical aptameric recognition system for a sensitive protein assay based on specific target binding-induced rolling circle amplification. , 2010, Analytical chemistry.

[52]  John G. Bruno,et al.  DNA aptamers developed against a soman derivative cross‐react with the methylphosphonic acid core but not with flanking hydrophobic groups , 2009, Journal of molecular recognition : JMR.

[53]  Weihong Tan,et al.  Optimization and Modifications of Aptamers Selected from Live Cancer Cell Lines , 2007, Chembiochem : a European journal of chemical biology.

[54]  Giridharan Gokulrangan,et al.  DNA aptamer-based bioanalysis of IgE by fluorescence anisotropy. , 2005, Analytical chemistry.

[55]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[56]  E. Ferapontova,et al.  An RNA aptamer-based electrochemical biosensor for detection of theophylline in serum. , 2008, Journal of the American Chemical Society.

[57]  Günter Mayer,et al.  Monitoring the progression of the in vitro selection of nucleic acid aptamers by denaturing high-performance liquid chromatography , 2008, Analytical and bioanalytical chemistry.

[58]  C. Mirkin,et al.  Nanoparticle-Based Bio-Bar Codes for the Ultrasensitive Detection of Proteins , 2003, Science.

[59]  Aptameric enzyme subunit for biosensing based on enzymatic activity measurement. , 2006, Analytical chemistry.

[60]  Yusuke Ohtani,et al.  Bis-pyrene labeled DNA aptamer as an intelligent fluorescent biosensor. , 2003, Bioorganic & medicinal chemistry letters.

[61]  B. Sullenger,et al.  In vivo selection of tumor-targeting RNA motifs , 2009, Nature chemical biology.

[62]  Tibor Hianik,et al.  Detection of aptamer-protein interactions using QCM and electrochemical indicator methods. , 2005, Bioorganic & medicinal chemistry letters.

[63]  Ioanis Katakis,et al.  Aptamers: molecular tools for analytical applications , 2008, Analytical and bioanalytical chemistry.

[64]  Jeffrey B.-H. Tok,et al.  Massively Parallel Interrogation of Aptamer Sequence, Structure and Function , 2008, PloS one.

[65]  Katsunori Horii,et al.  Antibody-specific aptamer-based PCR analysis for sensitive protein detection , 2009, Analytical and bioanalytical chemistry.

[66]  J. Keene,et al.  U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts. , 1991, Nucleic acids research.

[67]  Eun Jeong Cho,et al.  Real-time rolling circle amplification for protein detection. , 2007, Analytical chemistry.

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

[69]  Yi Xiao,et al.  Aptamer-functionalized Au nanoparticles for the amplified optical detection of thrombin. , 2004, Journal of the American Chemical Society.

[70]  M. Oda,et al.  Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. , 2008, Biochemistry.

[71]  Aptamer-based biosensors: biomedical applications. , 2006, Handbook of experimental pharmacology.

[72]  J. Kiel,et al.  Anti-Francisella tularensis DNA aptamers detect tularemia antigen from different subspecies by Aptamer-Linked Immobilized Sorbent Assay , 2006, Laboratory Investigation.

[73]  Joonhyung Lee,et al.  Diffractometric detection of proteins using microbead-based rolling circle amplification. , 2010, Analytical chemistry.

[74]  S. Soper,et al.  Surface immobilization methods for aptamer diagnostic applications , 2008, Analytical and bioanalytical chemistry.

[75]  Su Jin Lee,et al.  ssDNA aptamer-based surface plasmon resonance biosensor for the detection of retinol binding protein 4 for the early diagnosis of type 2 diabetes. , 2008, Analytical chemistry.

[76]  Ciara K O'Sullivan,et al.  Reusable impedimetric aptasensor. , 2005, Analytical chemistry.

[77]  L. Jaeger,et al.  The architectonics of programmable RNA and DNA nanostructures. , 2006, Current opinion in structural biology.

[78]  D. Kell,et al.  Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape , 2008, Nucleic acids research.

[79]  Kemin Wang,et al.  FRET-based aptamer probe for rapid angiogenin detection. , 2008, Talanta.

[80]  Kenzo Maehashi,et al.  Label-free protein biosensor based on aptamer-modified carbon nanotube field-effect transistors. , 2007, Analytical chemistry.

[81]  M. Stojanović,et al.  Aptamer-based folding fluorescent sensor for cocaine. , 2001, Journal of the American Chemical Society.

[82]  Arica A Lubin,et al.  Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic, electrochemical aptamer-based sensor. , 2009, Journal of the American Chemical Society.

[83]  E. Wang,et al.  Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes. , 2007, Chemical communications.

[84]  G. Shen,et al.  Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. , 2007, Analytical chemistry.

[85]  Alastair W Wark,et al.  Fabricating RNA microarrays with RNA-DNA surface ligation chemistry. , 2005, Analytical chemistry.

[86]  A. Heeger,et al.  Micromagnetic selection of aptamers in microfluidic channels , 2009, Proceedings of the National Academy of Sciences.

[87]  Guilherme N M Ferreira,et al.  Acoustic wave biosensors: physical models and biological applications of quartz crystal microbalance. , 2009, Trends in biotechnology.

[88]  Weihong Tan,et al.  Molecular aptamer beacons for real-time protein recognition. , 2002, Biochemical and biophysical research communications.

[89]  Jin-Ming Lin,et al.  Aptamer based electrochemical assay for the determination of thrombin by using the amplification of the nanoparticles. , 2010, Biosensors & bioelectronics.

[90]  Daoben Zhu,et al.  Fluorescent amplifying recognition for DNA G-quadruplex folding with a cationic conjugated polymer: a platform for homogeneous potassium detection. , 2005, Journal of the American Chemical Society.

[91]  S. Han,et al.  Aptamer biosensor for lable-free detection of human immunoglobulin E based on surface plasmon resonance , 2009 .

[92]  A label-free fluorescence sensor for probing the interaction of oligonucleotides with target molecules. , 2009, Analytica chimica acta.

[93]  Chih-Ming Ho,et al.  Aptamer-based electrochemical biosensor for Botulinum neurotoxin , 2009, Analytical and bioanalytical chemistry.

[94]  Kurt V Gothelf,et al.  Effect of serum on an RNA aptamer-based electrochemical sensor for theophylline. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[95]  Glen Hybarger,et al.  A microfluidic SELEX prototype , 2006, Analytical and bioanalytical chemistry.

[96]  S. Manalis,et al.  Micromechanical detection of proteins using aptamer-based receptor molecules. , 2004, Analytical chemistry.

[97]  Danke Xu,et al.  Characterizing the interaction between aptamers and human IgE by use of surface plasmon resonance , 2008, Analytical and bioanalytical chemistry.

[98]  P. Schuster.  Prediction of RNA secondary structures: from theory to models and real molecules , 2006 .

[99]  Xiaofang Hu,et al.  Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. , 2006, Chemical communications.

[100]  B. Eisenstein,et al.  The polymerase chain reaction. A new method of using molecular genetics for medical diagnosis. , 1990, The New England journal of medicine.

[101]  Andrew D Ellington,et al.  Aptamer therapeutics advance. , 2006, Current opinion in chemical biology.

[102]  Yang Xiang,et al.  Aptamer-based piezoelectric quartz crystal microbalance biosensor array for the quantification of IgE. , 2009, Biosensors & bioelectronics.

[103]  Andrew D Ellington,et al.  Selection of fluorescent aptamer beacons that light up in the presence of zinc , 2008, Analytical and bioanalytical chemistry.

[104]  R. Buhmann,et al.  Aptamers—basic research, drug development, and clinical applications , 2005, Applied Microbiology and Biotechnology.

[105]  Juewen Liu,et al.  Preparation of aptamer-linked gold nanoparticle purple aggregates for colorimetric sensing of analytes , 2006, Nature Protocols.

[106]  R. Corn,et al.  Detection of protein biomarkers using RNA aptamer microarrays and enzymatically amplified surface plasmon resonance imaging. , 2007, Analytical chemistry.

[107]  A. Pardi,et al.  High-resolution molecular discrimination by RNA. , 1994, Science.

[108]  D. Anderson,et al.  In Vitro Selection of Bacteriophage φ29 Prohead RNA Aptamers for Prohead Binding* , 1998, The Journal of Biological Chemistry.

[109]  Yi Lu,et al.  Smart Nanomaterials Responsive to Multiple Chemical Stimuli with Controllable Cooperativity , 2006 .

[110]  G. Hicks,et al.  The Enzyme Electrode , 1967, Nature.

[111]  M. Mascini,et al.  Aptamer-based detection of plasma proteins by an electrochemical assay coupled to magnetic beads. , 2007, Analytical chemistry.

[112]  Hao Yan,et al.  Self-Assembled Water-Soluble Nucleic Acid Probe Tiles for Label-Free RNA Hybridization Assays , 2008, Science.

[113]  L. Gold,et al.  Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[114]  Chunhai Fan,et al.  A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP. , 2007, Journal of the American Chemical Society.

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

[116]  I. Ruzic,et al.  Electron transfer kinetics of an adsorbed redox couple by double potential-step chronocoulometry: Methylene blue/leucomethylene blue , 1984 .

[117]  J. Justin Gooding,et al.  Proximity extension of circular DNA aptamers with real-time protein detection , 2005, Nucleic acids research.

[118]  M. Mascini,et al.  Aptamer-based biosensors for the detection of HIV-1 Tat protein. , 2005, Bioelectrochemistry.

[119]  Ciara K O'Sullivan,et al.  Real-time apta-PCR for 20 000-fold improvement in detection limit. , 2009, Molecular bioSystems.

[120]  Nebojsa Janjic,et al.  Inhibitory DNA ligands to platelet-derived growth factor B-chain. , 1996, Biochemistry.

[121]  Yuanyuan Li,et al.  Ultrasensitive densitometry detection of cytokines with nanoparticle-modified aptamers. , 2007, Clinical chemistry.