Aptamer Selection Technology and Recent Advances

Over the last decade, aptamers have begun to find their way from basic research to diverse commercial applications. The development of diagnostics is even more widespread than clinical applications because aptamers do not have to be extensively modified to enhance their in vivo stability and pharmacokinetics in diagnostic assays. The increasing attention has propelled the technical progress of the in vitro selection technology (SELEX) to enhance the efficiency of developing aptamers for commercially interesting targets. This review highlights recent progress in the technical steps of a SELEX experiment with a focus on high-throughput next-generation sequencing and bioinformatics. Achievements have been made in the optimization of aptamer libraries, separation schemes, amplification of the selected libraries and the identification of aptamer sequences from enriched libraries.

[1]  Gwo-Bin Lee,et al.  An integrated microfluidic system for rapid screening of alpha-fetoprotein-specific aptamers. , 2012, Biosensors & bioelectronics.

[2]  Zhen Liu,et al.  Efficient selection of glycoprotein-binding DNA aptamers via boronate affinity monolithic capillary. , 2013, Analytical chemistry.

[3]  George Georgiou,et al.  Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. , 2002, Nucleic acids research.

[4]  C. Lorenz,et al.  Genomic SELEX: A discovery tool for genomic aptamers , 2010, Methods.

[5]  Gerhard Ziemer,et al.  CELL-SELEX: Novel Perspectives of Aptamer-Based Therapeutics , 2008, International journal of molecular sciences.

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

[7]  M. Bowser,et al.  Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. , 2005, Analytical chemistry.

[8]  Andreas Nitsche,et al.  One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX , 2007, BMC biotechnology.

[9]  J. McNamara,et al.  RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB , 2012, Molecular Pharmacology.

[10]  Michael Musheev,et al.  Non-SELEX selection of aptamers. , 2006, Journal of the American Chemical Society.

[11]  L. Farinelli,et al.  By-passing in vitro screening—next generation sequencing technologies applied to antibody display and in silico candidate selection , 2010, Nucleic acids research.

[12]  Seung Soo Oh,et al.  Generation of highly specific aptamers via micromagnetic selection. , 2009, Analytical chemistry.

[13]  Ge Zhang,et al.  Strategies for combination of aptamer and targeted drug delivery. , 2014, Journal of nanoscience and nanotechnology.

[14]  Michael Blank,et al.  Next-Generation Analysis of Deep Sequencing Data: Bringing Light into the Black Box of SELEX Experiments. , 2016, Methods in molecular biology.

[15]  S. Ohuchi,et al.  Cell-SELEX Technology , 2012, BioResearch open access.

[16]  Paloma H. Giangrande,et al.  Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers , 2012, Nucleic acids research.

[17]  Abhishek Parashar,et al.  Aptamers in Therapeutics. , 2016, Journal of clinical and diagnostic research : JCDR.

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

[19]  J. Burnett,et al.  RNA-based therapeutics: current progress and future prospects. , 2012, Chemistry & biology.

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

[21]  William H. Thiel,et al.  Isolation and Optimization of Murine IL-10 Receptor Blocking Oligonucleotide Aptamers Using High-throughput Sequencing. , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

[22]  Weihong Tan,et al.  In vitro Selection of DNA Aptamers to Glioblastoma Multiforme. , 2011, ACS chemical neuroscience.

[23]  Gwo-Bin Lee,et al.  Influenza A virus-specific aptamers screened by using an integrated microfluidic system. , 2014, Lab on a chip.

[24]  Zasha Weinberg,et al.  R2R - software to speed the depiction of aesthetic consensus RNA secondary structures , 2011, BMC Bioinformatics.

[25]  Johan T den Dunnen,et al.  Phage display screening without repetitious selection rounds. , 2012, Analytical biochemistry.

[26]  James W. Brown,et al.  The RNA structure alignment ontology. , 2009, RNA.

[27]  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.

[28]  Gwo-Bin Lee,et al.  Integrated microfluidic system for rapid screening of CRP aptamers utilizing systematic evolution of ligands by exponential enrichment (SELEX). , 2010, Biosensors & bioelectronics.

[29]  A. Hüttenhofer,et al.  In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S. Klußmann,et al.  In vitro selection using a dual RNA library that allows primerless selection , 2006, Nucleic acids research.

[31]  Christoph E. Dumelin,et al.  High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries , 2008, Proceedings of the National Academy of Sciences.

[32]  Juan M. Vaquerizas,et al.  Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. , 2010, Genome research.

[33]  R. Stewart,et al.  Quantitative selection and parallel characterization of aptamers , 2013, Proceedings of the National Academy of Sciences.

[34]  M. Bowser,et al.  In vitro selection of aptamers with affinity for neuropeptide Y using capillary electrophoresis. , 2005, Journal of the American Chemical Society.

[35]  Primer-free aptamer selection using a random DNA library. , 2010, Methods in molecular biology.

[36]  J. DeStefano,et al.  A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase. , 2011, Analytical biochemistry.

[37]  Meng Jing,et al.  Isolation of DNA aptamers using micro free flow electrophoresis. , 2011, Lab on a chip.

[38]  Dirk Labudde,et al.  Selection of a DNA aptamer against norovirus capsid protein VP1. , 2014, FEMS microbiology letters.

[39]  Sean R. Eddy,et al.  Infernal 1.0: inference of RNA alignments , 2009, Bioinform..

[40]  Jonathan Scolnick,et al.  Aptamer selection by high-throughput sequencing and informatic analysis. , 2011, BioTechniques.

[41]  Emmanuel Dias-Neto,et al.  Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis , 2009, PloS one.

[42]  G. Wallukat,et al.  Aptamer Neutralization of Beta1-Adrenoceptor Autoantibodies Isolated From Patients With Cardiomyopathies , 2011, Circulation research.

[43]  B. Sullenger,et al.  Aptamers: an emerging class of therapeutics. , 2005, Annual review of medicine.

[44]  Sam F. Y. Li,et al.  Selection of aptamers for signal transduction proteins by capillary electrophoresis , 2010, Electrophoresis.

[45]  Sean R. Eddy,et al.  Infernal 1.0: inference of RNA alignments , 2009, Bioinform..

[46]  M. Kuwahara,et al.  In vitro selection of BNA (LNA) aptamers , 2013, Artificial DNA, PNA & XNA.

[47]  Zoltán Konthur,et al.  Probing the SELEX Process with Next-Generation Sequencing , 2011, PloS one.

[48]  Emily Mastronardi,et al.  Smart Materials Based on DNA Aptamers: Taking Aptasensing to the Next Level , 2014, Sensors.

[49]  John Quackenbush,et al.  What would you do if you could sequence everything? , 2008, Nature Biotechnology.

[50]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[51]  David R. Latulippe,et al.  RAPID-SELEX for RNA Aptamers , 2013, PLoS ONE.

[52]  Weihong Tan,et al.  Selection of DNA ligands for protein kinase C-delta. , 2006, Chemical communications.

[53]  Yi Xiao,et al.  Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. , 2011, Analytical chemistry.

[54]  Nadia Nikolaus,et al.  Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics , 2012, Journal of analytical methods in chemistry.

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

[56]  Tracy R. Keeney,et al.  Aptamer-based multiplexed proteomic technology for biomarker discovery , 2010, Nature Precedings.

[57]  Jijun Tang,et al.  The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods , 2006, Electrophoresis.

[58]  Seung Soo Oh,et al.  Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing , 2010, Proceedings of the National Academy of Sciences.

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

[60]  Thomas Bair,et al.  Rapid Identification of Cell-Specific, Internalizing RNA Aptamers with Bioinformatics Analyses of a Cell-Based Aptamer Selection , 2012, PloS one.

[61]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[62]  Yi Xiao,et al.  Probing the Limits of Aptamer Affinity with a Microfluidic SELEX Platform , 2011, PloS one.

[63]  M. Bowser,et al.  Capillary electrophoresis-SELEX selection of catalytic DNA aptamers for a small-molecule porphyrin target. , 2013, Analytical chemistry.

[64]  Jon Ashley,et al.  Selection of bovine catalase aptamers using non‐SELEX , 2012, Electrophoresis.

[65]  Wenli Li,et al.  Applications of Aptasensors in Clinical Diagnostics , 2012, Sensors.

[66]  Letha J. Sooter,et al.  Automated acquisition of aptamer sequences. , 2002, Combinatorial chemistry & high throughput screening.

[67]  Mark P. McPike,et al.  Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep Sequencing , 2011, PloS one.

[68]  Nadia Nikolaus,et al.  DNA-Aptamers Binding Aminoglycoside Antibiotics , 2014, Sensors.

[69]  Christopher A. Bottoms,et al.  High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase , 2012, Nucleic acids research.

[70]  Larry Gold,et al.  Beyond antibodies: New affinity reagents to unlock the proteome , 2014, Proteomics.

[71]  Yoon-Sik Lee,et al.  RNA aptamers: a review of recent trends and applications. , 2013, Advances in biochemical engineering/biotechnology.

[72]  Sergey N Krylov,et al.  Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides , 2006, Nature Protocols.

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

[74]  David G. Gorenstein,et al.  Aptamers and the next generation of diagnostic reagents , 2012, Proteomics. Clinical applications.

[75]  J. KlugS,et al.  特異な延長因子SelBに結合する新規mRNAモチーフのin vitro及びin vivoにおける性質 , 1997 .

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

[77]  Omid C. Farokhzad,et al.  Current Progress of Aptamer-Based Molecular Imaging , 2014, The Journal of Nuclear Medicine.