Genomes and Genes
selex aptamer technique
Summary: A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.
- Ulrich H, Wrenger C. Disease-specific biomarker discovery by aptamers. Cytometry A. 2009;75:727-33 pubmed publisher..In this review, we discuss an approach for the development of aptamers targeting parasite-derived surface proteins of Trypanosoma and Plasmodium. ..
- Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, et al. Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus. Nucleic Acids Res. 2009;37:4621-8 pubmed publisher..aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer. ..
- Latulippe D, Szeto K, Ozer A, Duarte F, Kelly C, Pagano J, et al. Multiplexed microcolumn-based process for efficient selection of RNA aptamers. Anal Chem. 2013;85:3417-24 pubmed publisher..The combination of our microcolumns with a multiplex approach and high-throughput sequencing enables the selection of aptamers to multiple targets in a high-throughput and efficient manner. ..
- Song K, Lee S, Ban C. Aptamers and their biological applications. Sensors (Basel). 2012;12:612-31 pubmed publisher..In summary, aptamers are promising materials for diverse areas, not just as alternatives to antibodies, but as the core components of medical and analytical equipment. ..
- Ahmad K, Oh S, Kim S, McClellen F, Xiao Y, Soh H. Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS ONE. 2011;6:e27051 pubmed publisher..To further explore this relationship, we performed selections against PDGF-BB under different pH conditions using the same selection protocol, and report an inverse correlation between protein charge and aptamer K(d). ..
- Park S, Kim S, Yoon H, Kim K, Kalme S, Oh S, et al. Selection of an antiviral RNA aptamer against hemagglutinin of the subtype H5 avian influenza virus. Nucleic Acid Ther. 2011;21:395-402 pubmed publisher..Thus, the RNA aptamer HAS15-5, which acts by blocking and inhibiting the receptor-binding domain of viral HA, can be developed as a novel antiviral agent against type H5 avian influenza virus. ..
- Barbas A, Mi J, Clary B, White R. Aptamer applications for targeted cancer therapy. Future Oncol. 2010;6:1117-26 pubmed publisher..In this article, we review recent developments in the use of aptamers for targeted cancer therapy, particularly focusing on novel applications of aptamers targeting the cell surface. ..
- Miyachi Y, Shimizu N, Ogino C, Fukuda H, Kondo A. Selection of a DNA aptamer that binds 8-OHdG using GMP-agarose. Bioorg Med Chem Lett. 2009;19:3619-22 pubmed publisher..22 DNA aptamer was on the order of 0.1micromol/L. This result suggests that using an analogue will be a useful new SELEX method for obtaining various aptamers that are difficult to immobilize on a matrix. ..
- Chang Y, Kao W, Wang W, Wang W, Yang R, Peck K. Identification and characterization of oligonucleotides that inhibit Toll-like receptor 2-associated immune responses. FASEB J. 2009;23:3078-88 pubmed publisher..The results of functional assays showed that AP177 acted as a TLR2 antagonist and may hold therapeutic potential in the treatment of diseases related to dysregulated TLR2 immune responses. ..
- Teramoto J, Yoshimura S, Takeyasu K, Ishihama A. A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Nucleic Acids Res. 2010;38:3605-18 pubmed publisher..We then propose that YgiP is a novel nucleoid protein of E. coli under anaerobiosis and propose to rename it Dan (DNA-binding protein under anaerobic conditions). ..
- Bing T, Yang X, Mei H, Cao Z, Shangguan D. Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories. Bioorg Med Chem. 2010;18:1798-805 pubmed publisher..The highly variable sequence composition of streptavidin-binding aptamer would make the design of aptameric sensor or device based on streptavidin more flexible and easy. ..
- Sefah K, Shangguan D, Xiong X, O Donoghue M, Tan W. Development of DNA aptamers using Cell-SELEX. Nat Protoc. 2010;5:1169-85 pubmed publisher..The procedure, from design of oligonucleotides to enrichment of the selected pools, takes approximately 3 months. ..
- Wang J, Rudzinski J, Gong Q, Soh H, Atzberger P. Influence of target concentration and background binding on in vitro selection of affinity reagents. PLoS ONE. 2012;7:e43940 pubmed publisher..Finally, we perform a comparative analysis of two different selection methods over multiple rounds of selection, and show that methods with inherently lower background binding offer dramatic advantages in selection efficiency. ..
- Gong Q, Wang J, Ahmad K, Csordas A, Zhou J, Nie J, et al. Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Anal Chem. 2012;84:5365-71 pubmed publisher..Moreover, we show that these aptamer pairs do not interfere with each other's binding and effectively detect the target even in complex mixtures such as undiluted serum. ..
- Lee Y, Han S, Maeng J, Cho Y, Lee S. In vitro selection of Escherichia coli O157:H7-specific RNA aptamer. Biochem Biophys Res Commun. 2012;417:414-20 pubmed publisher..This novel O157:H7-specific aptamer could be of potential application as a diagnostic ligand against the pathogen-related food borne illness. ..
- Miyachi Y, Shimizu N, Ogino C, Kondo A. Selection of DNA aptamers using atomic force microscopy. Nucleic Acids Res. 2010;38:e21 pubmed publisher..AFM-SELEX is, therefore, considered to be an available method for the selection of DNA aptamers that have a high affinity for their target molecules. ..
- Li H, Ding X, Peng Z, Deng L, Wang D, Chen H, et al. Aptamer selection for the detection of Escherichia coli K88. Can J Microbiol. 2011;57:453-9 pubmed publisher..This method of detecting ETEC K88 by aptamers can also be applied to bacteria other than ETEC K88. ..
- Schütze T, Arndt P, Menger M, Wochner A, Vingron M, Erdmann V, et al. A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides. Nucleic Acids Res. 2010;38:e23 pubmed publisher..Direct comparisons of nucleic acid pools obtained from an aptamer selection demonstrate that even highly complex populations can be evaluated by using DiStRO, without the need of complicated calculations. ..
- Kuwahara M, Sugimoto N. Molecular evolution of functional nucleic acids with chemical modifications. Molecules. 2010;15:5423-44 pubmed publisher..This review focuses on the effectiveness of chemical modifications on the evolution of nucleic acids as functional molecules and the outlook for related technologies. ..
- Srisawat C, Engelke D. Selection of RNA aptamers that bind HIV-1 LTR DNA duplexes: strand invaders. Nucleic Acids Res. 2010;38:8306-15 pubmed publisher..The results presented here show that aptamer RNAs can be selected in vitro that strand-invade at preferred DNA duplex sequences to form stable complexes. ..
- Avci Adali M, Paul A, Wilhelm N, Ziemer G, Wendel H. Upgrading SELEX technology by using lambda exonuclease digestion for single-stranded DNA generation. Molecules. 2009;15:1-11 pubmed publisher..We believe that the generation of ssDNA aptamers using this method will greatly improve the success rate of SELEX experiments concerning the recovery of target-specific aptamers. ..
- Kunii T, Ogura S, Mie M, Kobatake E. Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. Analyst. 2011;136:1310-2 pubmed publisher..Our results showed that the DNA aptamer binds to molecules that exist predominantly on target SCLC cell surfaces compared with other types of SCLC cells. ..
- Sun W, Du L, Li M. Advances and perspectives in cell-specific aptamers. Curr Pharm Des. 2011;17:80-91 pubmed..The current review article would like to provide a survey of contemporary developments in cell-specific aptamers, including methodology, applications and optimization of cell-SELEX. ..
- Sefah K, Meng L, Lopez Colon D, Jimenez E, Liu C, Tan W. DNA aptamers as molecular probes for colorectal cancer study. PLoS ONE. 2010;5:e14269 pubmed publisher..The selected aptamers can identify specific biomarkers associated with colorectal cancers. We believe that these probes could be further developed for early disease detection, as well as prognostic markers, of colorectal cancers. ..
- Van Simaeys D, Lopez Colon D, Sefah K, Sutphen R, Jimenez E, Tan W. Study of the molecular recognition of aptamers selected through ovarian cancer cell-SELEX. PLoS ONE. 2010;5:e13770 pubmed publisher..Though binding to other cancer cell lines was observed, these aptamers could lead to identification of biomarkers that are related to cancer. ..
- Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, et al. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer. Anal Chem. 2013;85:4961-7 pubmed publisher
- Paige J, Wu K, Jaffrey S. RNA mimics of green fluorescent protein. Science. 2011;333:642-6 pubmed publisher..Spinach is markedly resistant to photobleaching, and Spinach fusion RNAs can be imaged in living cells. These RNA mimics of GFP provide an approach for genetic encoding of fluorescent RNAs. ..
- Huang C, Lin H, Shiesh S, Lee G. An integrated microfluidic system for rapid screening of alpha-fetoprotein-specific aptamers. Biosens Bioelectron. 2012;35:50-5 pubmed publisher..The screened aptamer was used as a recognition molecule for AFP and has a linear detection range from 12.5 to 800 ng/mL, which was suitable for rapid clinical applications. ..
- Oh S, Qian J, Lou X, Zhang Y, Xiao Y, Soh H. Generation of highly specific aptamers via micromagnetic selection. Anal Chem. 2009;81:5490-5 pubmed publisher..Since a wide spectrum of molecular targets can be readily conjugated to magnetic beads, MMS-based SELEX provides a general platform for rapid generation of specific aptamers. ..
- Fang X, Tan W. Aptamers generated from cell-SELEX for molecular medicine: a chemical biology approach. Acc Chem Res. 2010;43:48-57 pubmed publisher..Importantly, we demonstrate how molecular assemblies can integrate the properties of aptamers and, for example, nanoparticles or microfluidic devices, to improve cancer cell enrichment, detection and therapy. ..
- Thiel K, Giangrande P. Therapeutic applications of DNA and RNA aptamers. Oligonucleotides. 2009;19:209-22 pubmed publisher..This review highlights those aptamers and aptamer-based approaches with particular likelihood of achieving therapeutic application. ..
- Glökler J, Schütze T, Konthur Z. Automation in the high-throughput selection of random combinatorial libraries--different approaches for select applications. Molecules. 2010;15:2478-90 pubmed publisher..In this review we will discuss several concepts of combinatorial libraries and provide information as what to expect from these depending on the given context. ..
- Bunka D, Platonova O, Stockley P. Development of aptamer therapeutics. Curr Opin Pharmacol. 2010;10:557-62 pubmed publisher..We will also mention a few of the growing number of aptamer therapeutics in various stages of preclinical and clinical trial. ..
- Shigdar S, Qiao L, Zhou S, Xiang D, Wang T, Li Y, et al. RNA aptamers targeting cancer stem cell marker CD133. Cancer Lett. 2013;330:84-95 pubmed publisher..These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging. ..
- Jolma A, Yan J, Whitington T, Toivonen J, Nitta K, Rastas P, et al. DNA-binding specificities of human transcription factors. Cell. 2013;152:327-39 pubmed publisher..We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA. ..
- Kasahara Y, Irisawa Y, Ozaki H, Obika S, Kuwahara M. 2',4'-BNA/LNA aptamers: CE-SELEX using a DNA-based library of full-length 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides. Bioorg Med Chem Lett. 2013;23:1288-92 pubmed publisher..2',4'-BNA/LNA aptamers of groups V and VI bound human thrombin with K(d) values in the range of several 10 nanomolar levels. ..
- Dwivedi H, Smiley R, Jaykus L. Selection and characterization of DNA aptamers with binding selectivity to Campylobacter jejuni using whole-cell SELEX. Appl Microbiol Biotechnol. 2010;87:2323-34 pubmed publisher..jejuni strains (exclusivity). Whole-cell SELEX is a promising technique to design aptamer-based molecular probes for microbial pathogens without tedious isolation and purification of complex markers or targets. ..
- Thiel K, Hernandez L, Dassie J, Thiel W, Liu X, Stockdale K, et al. Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers. Nucleic Acids Res. 2012;40:6319-37 pubmed publisher..The future refinement of this technology may promote the widespread use of RNA-based reagents for targeted therapeutic applications. ..
- Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M, et al. Probing the SELEX process with next-generation sequencing. PLoS ONE. 2011;6:e29604 pubmed publisher..Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts. ..
- Ahn J, Jo M, Dua P, Lee D, Kim S. A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selection. Oligonucleotides. 2011;21:93-100 pubmed publisher..Additionally, we show that sol-gel embedded protein arrays can be used as a high-throughput assay for quantifying binding affinities of aptamers. ..
- Zhao Z, Xu L, Shi X, Tan W, Fang X, Shangguan D. Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst. 2009;134:1808-14 pubmed publisher..The aptamers are expected to be new molecular probes for the investigation of the molecular bases of different NSCLC subtypes and their biological heterogeneity, which is valuable for advancing NSCLC diagnosis and treatment. ..
- Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 2010;20:861-73 pubmed publisher..Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers. ..
- Zhang K, Sefah K, Tang L, Zhao Z, Zhu G, Ye M, et al. A novel aptamer developed for breast cancer cell internalization. ChemMedChem. 2012;7:79-84 pubmed publisher..These results indicate that KMF2-1a is a promising agent for cell-type-specific intracellular delivery with both diagnostic and therapeutic implications. ..
- Hwang S, Sun H, Lee K, Oh B, Cha Y, Kim B, et al. 5'-Triphosphate-RNA-independent activation of RIG-I via RNA aptamer with enhanced antiviral activity. Nucleic Acids Res. 2012;40:2724-33 pubmed publisher..Based on these data, we propose that RIG-I aptamer has strong potential to be an antiviral agent that specifically boosts the RIG-I-dependent signaling cascade. ..
- Cho M, Xiao Y, Nie J, Stewart R, Csordas A, Oh S, et al. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci U S A. 2010;107:15373-8 pubmed publisher..Given that many biocombinatorial libraries are encoded with nucleic acids, we extrapolate that our method may be extended to other types of libraries for a range of molecular functions. ..
- Cerchia L, Esposito C, Jacobs A, Tavitian B, de Franciscis V. Differential SELEX in human glioma cell lines. PLoS ONE. 2009;4:e7971 pubmed publisher..Differential whole cell SELEX reveals an exciting strategy widely applicable to cancer cells that permits generation of highly specific ligands for cancer biomarkers. ..
- Dastjerdi K, Tabar G, Dehghani H, Haghparast A. Generation of an enriched pool of DNA aptamers for an HER2-overexpressing cell line selected by Cell SELEX. Biotechnol Appl Biochem. 2011;58:226-30 pubmed publisher..This method would also be useful in other experiments using live cell enzyme-linked immunosorbent assay on adherent cells. ..