Aptamer amplification: divide and signal

Bibliography

• Holliger P, Hudson PJ. Engineered antibody fragments and the rise of single domains. Nat Biotech 2005;23:9
   Google Scholar
• Hosse RJ, Rothe A, Power BE. A new generation of protein display scaffolds for molecular recognition. Protein Sci 2006;15:14-27
   PubMed Web of Science ®Google Scholar
• Skerra A. Alternative non-antibody scaffolds for molecular recognition. Curr Opin Biotechnol 2007;18:295-304
   PubMed Web of Science ®Google Scholar
• Stump MT, Binz HK, Amstutz P. DARPins: A new generation of protein therapeutics. Drug Discov Today 2008;13:15-6
   Google Scholar
• Mairal T, Ozalp P, Sanchez PL, et al. Aptamers: molecular tools for analytical applications. Anal Bioanal Chem 2008;390:989-1007
   PubMed Web of Science ®Google Scholar
• Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007;24:381-403
   PubMedGoogle Scholar
• Bunka DH, Stockley PG. Aptamers come of age – at last. Nat Rev Microbiol 2006;4:588-96
   PubMed Web of Science ®Google Scholar
• Fischer NO, Tarasow TM, Tok JB. Protein detection via direct enzymatic amplification of short DNA aptamers. Anal Biochem 2008;373:121-8
   PubMed Web of Science ®Google Scholar
• Jayasena SD. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 1999;45:1628-50
   PubMed Web of Science ®Google Scholar
• Jiang Y, Fang X, Bai C. Signaling aptamer/protein binding by a molecular light switch complex. Anal Chem 2004;76:5230-05
   PubMed Web of Science ®Google Scholar
• Lee JF, Stovall GM, Ellington AD. Aptamer therapeutics advance. Curr Opin Chem Biol 2006;10:282-9
   PubMed Web of Science ®Google Scholar
• Chu T, Ebright J, Ellington AD. Using aptamers to identify and enter cells. Curr Opin Mol Ther 2007;9:137-44
   PubMed Web of Science ®Google Scholar
• Deisingh AK, Thompson M. Biosensors for the detection of bacteria. Can J Microbiol 2004;50:69-77
   PubMed Web of Science ®Google Scholar
• Shamah SM, Healy JM, Cload ST. Complex target SELEX. Acc Chem Res 2008;41:130-8
   PubMed Web of Science ®Google Scholar
• Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007;107:3715-43
   PubMed Web of Science ®Google Scholar
• Nutiu R, Li Y. Structure-switching signaling aptamers. J Am Chem Soc 2003;125:4771-8
   PubMed Web of Science ®Google Scholar
• Wang W, Chen C, Qian M, et al. Aptamer biosensor for protein detection using gold nanoparticles. Anal Biochem 2008;373:213-9
   PubMed Web of Science ®Google Scholar
• Hamaguchi N, Ellington AD, Stanton M. Aptamer beacons for the direct detection of proteins. Anal Biochem 2001;294:126-31
   PubMed Web of Science ®Google Scholar
• Li JJ, Fang X, Tan W. Molecular aptamer beacons for real-time protein recognition. Biochem Biophys Res Commun 2002;292:31-40
   PubMed Web of Science ®Google Scholar
• Missailidis S, Perkins A. Update: aptamers as novel radiopharmaceuticals: their applications and future prospects in diagnosis and therapy. Cancer Biother Radiopharm 2007;22:453-68
   PubMed Web of Science ®Google Scholar
• Navani NK, Li Y. Nucleic acid aptamers and enzymes as sensors. Curr Opin Chem Biol 2006;10:272-81
   PubMed Web of Science ®Google Scholar
• Zhang H, Wang Z, Li XF, et al. Ultrasensitive detection of proteins by amplification of affinity aptamers. Angew Chem Int Ed Engl 2006;45:1576-80
   PubMed Web of Science ®Google Scholar
• Sano T, Smith CL, Cantor CR. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 1992;258:120-2
   PubMed Web of Science ®Google Scholar
• Niemeyer CM, Adler M, Wacker R. Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification. Trends Biotechnol 2005;23:208-16
   PubMed Web of Science ®Google Scholar
• Barletta JM, Edelman DC, Highsmith WE, et al. Detection of ultra-low levels of pathologic prion protein in scrapie infected hamster brain homogenates using real-time immuno-PCR. J Virol Methods 2005;127:154-64
   PubMed Web of Science ®Google Scholar
• Nam JM, Thaxton CS, Mirkin CA. Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 2003;301:1884-6
   PubMed Web of Science ®Google Scholar
• Niemeyer CM. Semi-synthetic nucleic acid-protein conjugates: applications in life sciences and nanobiotechnology. J Biotechnol 2001;82:47-66
   PubMedGoogle Scholar
• Saito K, Kobayashi D, Sasaki M, et al. Detection of human serum tumor necrosis factor-alpha in healthy donors, using a highly sensitive immuno-PCR assay. Clin Chem 1999;45:665-9
   PubMed Web of Science ®Google Scholar
• Adler M, Wacker R, Niemeyer CM. A real-time immuno-PCR assay for routine ultrasensitive quantification of proteins. Biochem Biophys Res Commun 2003;308:240-50
   PubMed Web of Science ®Google Scholar
• Adler M, Wacker R, Niemeyer CM. Sensitivity by combination: immuno-PCR and related technologies. Analyst 2008;133:702-18
   PubMed Web of Science ®Google Scholar
• Wacker R, Ceyhan B, Alhorn P. Magneto immuno-PCR: a novel immunoassay based on biogenic magnetosome nanoparticles. Biochem Biophys Res Commun 2007;357:391-6
   PubMed Web of Science ®Google Scholar
• Niemeyer CM, Wacker R, Adler M. Combination of DNA-directed immobilization and immuno-PCR: very sensitive antigen detection by means of self-assembled DNA-protein conjugates. Nucleic Acids Res 2003;31:e90
   PubMed Web of Science ®Google Scholar
• Brakmann S. DNA-based barcodes, nanoparticles, and nanostructures for the ultrasensitive detection and quantification of proteins. Angew Chem Int Ed Engl 2004;43:5730-4
   PubMed Web of Science ®Google Scholar
• Nam JM, Wise AR, Groves JT. Colorimetric bio-barcode amplification assay for cytokines. Anal Chem 2005;77:6985-8
   PubMed Web of Science ®Google Scholar
• Fang X, Cao Z, Beck T, et al. Molecular aptamer for real-time oncoprotein platelet-derived growth factor monitoring by fluorescence anisotropy. Anal Chem 2001;73:5752-7
   PubMed Web of Science ®Google Scholar
• Huang CC, Huang YF, Cao Z, et al. Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. Anal Chem 2005;77:5735-41
   PubMed Web of Science ®Google Scholar
• Li W, Wang K, Tan W, et al. Aptamer-based analysis of angiogenin by fluorescence anisotropy. Analyst 2007;132:107-13
   PubMed Web of Science ®Google Scholar
• Niemeyer CM, Adler M, Pignataro B, et al. Self-assembly of DNA-streptavidin nanostructures and their use as reagents in immuno-PCR. Nucleic Acids Res 1999;27:4553-61
   PubMed Web of Science ®Google Scholar
• Fischer NO, Tarasow TM, Tok JB. Aptasensors for biosecurity applications. Curr Opin Chem Biol 2007;11:316-28
   PubMed Web of Science ®Google Scholar
• Langer PR, Waldrop AA, Ward DC. Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci USA 1981;78:6633-7
   PubMed Web of Science ®Google Scholar
• Moriyama K, Kimoto M, Mitsui T, et al. Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs. Nucleic Acids Res 2005;33:e129
   PubMed Web of Science ®Google Scholar
• Fattal E, Bochot A. Antisense oligonucleotides, aptamers and SiRNA: promises for the treatment of ocular diseases. Arch Soc Esp Oftalmol 2006;81:3-4,5-6
   PubMedGoogle Scholar
• Nimjee SM, Rusconi CP, Sullenger BA. Aptamers: an emerging class of therapeutics. Annu Rev Med 2005;56:555-83
   PubMed Web of Science ®Google Scholar
• Yan AC, Bell KM, Breeden MM, et al. Aptamers: prospects in therapeutics and biomedicine. Front Biosci 2005;10:1802-27
   PubMed Web of Science ®Google Scholar
• Schneider DJ, Feigon J, Hostomsky Z, et al. High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 1995;34:9599-610
   PubMed Web of Science ®Google Scholar
• Wang XL, Li F, Su YH, et al. Ultrasensitive detection of protein using an aptamer-based exonuclease protection assay. Anal Chem 2004;76:5605-10
   PubMed Web of Science ®Google Scholar
• Li Y, Zhou X, Ye D. Molecular beacons: an optimal multifunctional biological probe. Biochem Biophys Res Commun 2008;373:457-61
   PubMed Web of Science ®Google Scholar
• Muller S, Strohbach D, Wolf J. Sensors made of RNA: tailored ribozymes for detection of small organic molecules, metals, nucleic acids and proteins. IEE Proc Nanobiotechnol 2006;153:31-40
   PubMedGoogle Scholar
• Bayer TS, Smolke CD. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 2005;23:337-43
   PubMed Web of Science ®Google Scholar
• Wu ZS, Guo MM, Zhang SB, et al. Reusable electrochemical sensing platform for highly sensitive detection of small molecules based on structure-switching signaling aptamers. Anal Chem 2007;79:2933-9
   PubMed Web of Science ®Google Scholar
• Yamamoto R, Baba T, Kumar PK. Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells 2000;5:389-96
   PubMed Web of Science ®Google Scholar
• Yang L, Ellington AD. Real-time PCR detection of protein analytes with conformation-switching aptamers. Anal Biochem 2008;380:164-73
   PubMed Web of Science ®Google Scholar
• Baker BR, Lai RY, Wood MS, et al. An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. J Am Chem Soc 2006;128:3138-9
   PubMed Web of Science ®Google Scholar
• He P, Shen L, Cao Y, et al. Ultrasensitive electrochemical detection of proteins by amplification of aptamer-nanoparticle bio bar codes. Anal Chem 2007;79:8024-9
   PubMed Web of Science ®Google Scholar
• Gullberg M, Fredriksson S, Taussig M, et al. A sense of closeness: protein detection by proximity ligation. Curr Opin Biotechnol 2003;14:82-6
   PubMed Web of Science ®Google Scholar
• Gustafsdottir SM, Schallmeiner E, Fredriksson S, et al. Proximity ligation assays for sensitive and specific protein analyses. Anal Biochem 2005;345:2-9
   PubMed Web of Science ®Google Scholar
• Landegren U, Schallmeiner E, Nilsson M, et al. Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes. J Mol Recognit 2004;17:194-7
   PubMed Web of Science ®Google Scholar
• Cao Y, Cao R, Hedlund EM. R Regulation of tumor angiogenesis and metastasis by FGF and PDGF signaling pathways. J Mol Med 2008;86:785-9
   PubMed Web of Science ®Google Scholar
• Fredriksson S, Gullberg M, Jarvius J, et al. Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol 2002;20:473-7
   PubMed Web of Science ®Google Scholar
• Gullberg M, Gustafsdottir SM, Schallmeiner E, et al. Cytokine detection by antibody-based proximity ligation. Proc Natl Acad Sci USA 2004;101:8420-44
   PubMed Web of Science ®Google Scholar
• Soderberg O, Leuchowius KJ, Gullberg M, et al. Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay. Methods 2008;45:227-32
   PubMed Web of Science ®Google Scholar
• Fredriksson S, Dixon W, Ji H, et al. Multiplexed protein detection by proximity ligation for cancer biomarker validation. Nat Methods 2007;4:327-9
   PubMed Web of Science ®Google Scholar
• Fredriksson S, Horecka J, Brustugun OT, et al. Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer. Clin Chem 2008;54:582-9
   PubMed Web of Science ®Google Scholar
• Gustafsdottir SM, Nordengrahn A, Fredriksson S, et al. Detection of individual microbial pathogens by proximity ligation. Clin Chem 2006;52:1152-60
   PubMed Web of Science ®Google Scholar
• Pai S, Ellington AD, Levy M. Proximity ligation assays with peptide conjugate ‘burrs’ for the sensitive detection of spores. Nucleic Acids Res 2005;33:e162
   PubMed Web of Science ®Google Scholar
• Pai S, Ellington AD. Using RNA Aptamers and the Proximity Ligation Assay (PLA) for the Detection of Cell Surface Antigens, In Methods in Biotechnology. New Jersey: Humana Press, 2008; In press
   Google Scholar
• Chen HW, Medley CD, Sefah K, et al. Molecular recognition of small-cell lung cancer cells using aptamers. ChemMedChem 2008;3:991-1001
   PubMed Web of Science ®Google Scholar
• Mallikaratchy P, Tang Z, Kwame S, et al. Aptamer directly evolved from live cells recognizes membrane bound immunoglobin heavy mu chain in Burkitt's lymphoma cells. Mol Cell Proteomics 2007;6:2230-8
   PubMed Web of Science ®Google Scholar
• Shangguan D, Tang Z, Mallikaratchy Z, et al. Optimization and modifications of aptamers selected from live cancer cell lines. Chembiochem 2007;8:603-6
   PubMed Web of Science ®Google Scholar
• Demidov VV. Rolling-circle amplification in DNA diagnostics: the power of simplicity. Expert Rev Mol Diagn 2002;2:542-8
   PubMedGoogle Scholar
• Zhao MMAW, Brook MA, Li Y. Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed 2008;47:6330-7
   PubMed Web of Science ®Google Scholar
• Zhang D, Wu J, Ye F, et al. Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clin Chim Acta 2006;363:61-70
   PubMed Web of Science ®Google Scholar
• Fischer NO, Tarasow TM, Tok JBH. Protein detection via direct enzymatic amplification of short DNA aptamers. Anal Biochem 2008;373:121-8
   PubMed Web of Science ®Google Scholar
• Cho EJ, Yang L, Levy M, et al. Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. J Am Chem Soc 2005;127:2022-3
   PubMed Web of Science ®Google Scholar
• Di Giusto DA, King GC. Construction, stability, and activity of multivalent circular anticoagulant aptamers. J Biol Chem 2004;279:46483-9
   PubMed Web of Science ®Google Scholar
• Schweitzer B, Kingsmore S. Combining nucleic acid amplification and detection. Curr Opin Biotechnol 2001;12:21-7
   PubMed Web of Science ®Google Scholar
• Zhou L, Ou LJ, Chu X, et al. Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein. Anal Chem 2007;79:7492-500
   PubMed Web of Science ®Google Scholar
• Furukawa K, Abe H, Abe N, et al. Fluorescence generation from tandem repeats of a malachite green RNA aptamer using rolling circle transcription. Bioorg Med Chem Lett 2008;18:4562-5
   PubMed Web of Science ®Google Scholar
• Cheglakov Z, Weizmann Y, Basnar B, et al. Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes. Org Biomol Chem 2007;5:223-5
   PubMed Web of Science ®Google Scholar
• Yang L, Fung CW, Cho EJ, et al. Real-time rolling circle amplification for protein detection. Anal Chem 2007;79:3320-9
   PubMed Web of Science ®Google Scholar
• Levy M, Ellington AD. ATP-dependent allosteric DNA anzymes. Chem Biol 2002;9:417-26
   PubMed Web of Science ®Google Scholar
• Di Giusto DA, Wlassoff WA, Gooding JJ, et al. Proximity extension of circular DNA aptamers with real-time protein detection. Nucl Acids Res 2005;33:e64
   PubMed Web of Science ®Google Scholar
• Niu W, Jiang N, Hu Y. Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. Anal Biochem 2007;362:126-35
   PubMed Web of Science ®Google Scholar
• Pelzer H, Schwarz A, Heimburger N. Determination of human thrombin-antithrombin III complex in plasma with an enzyme-linked immunosorbent assay. Thromb Haemost 1988;59:101-6
   PubMed Web of Science ®Google Scholar
• Gersuk G, Carmel R, Pattengale P. Platelet-derived growth factor concentrations in platelet-poor plasma and urine from patients with myeloproliferative disorders. Blood 1989;74:2330-4
   PubMed Web of Science ®Google Scholar
• German I, Buchanan DD, Kennedy RT. Aptamers as ligands in affinity probe capillary electrophoresis. Anal Chem 1998;70:4540-5
   PubMed Web of Science ®Google Scholar
• Jhaveri S, Rajendran M, Ellington AD. In vitro selection of signaling aptamers. Nat Biotechnol 2000;18:1293-7
   PubMed Web of Science ®Google Scholar