151
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Quantitative selection and parallel characterization of aptamers. Proc Natl Acad Sci U S A 2013; 110:18460-5. [PMID: 24167271 DOI: 10.1073/pnas.1315866110] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aptamers are promising affinity reagents that are potentially well suited for high-throughput discovery, as they are chemically synthesized and discovered via completely in vitro selection processes. Recent advancements in selection, sequencing, and the use of modified bases have improved aptamer quality, but the overall process of aptamer generation remains laborious and low-throughput. This is because binding characterization remains a critical bottleneck, wherein the affinity and specificity of each candidate aptamer are measured individually in a serial manner. To accelerate aptamer discovery, we devised the Quantitative Parallel Aptamer Selection System (QPASS), which integrates microfluidic selection and next-generation sequencing with in situ-synthesized aptamer arrays, enabling simultaneous measurement of affinity and specificity for thousands of candidate aptamers in parallel. After using QPASS to select aptamers for the human cancer biomarker angiopoietin-2 (Ang2), we in situ synthesized arrays of the selected sequences and obtained equilibrium dissociation constants (Kd) for every aptamer in parallel. We thereby identified over a dozen high-affinity Ang2 aptamers, with Kd as low as 20.5 ± 7.3 nM. The same arrays enabled us to quantify binding specificity for these aptamers in parallel by comparing relative binding of differentially labeled target and nontarget proteins, and by measuring their binding affinity directly in complex samples such as undiluted serum. Finally, we show that QPASS offers a compelling avenue for exploring structure-function relationships for large numbers of aptamers in parallel by coupling array-based affinity measurements with next-generation sequencing data to identify nucleotides and motifs within the aptamer that critically affect Ang2 binding.
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152
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Ameta S, Winz ML, Previti C, Jäschke A. Next-generation sequencing reveals how RNA catalysts evolve from random space. Nucleic Acids Res 2013; 42:1303-10. [PMID: 24157838 PMCID: PMC3902939 DOI: 10.1093/nar/gkt949] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Catalytic RNAs are attractive objects for studying molecular evolution. To understand how RNA libraries can evolve from randomness toward highly active catalysts, we analyze the original samples that led to the discovery of Diels-Alderase ribozymes by next-generation sequencing. Known structure-activity relationships are used to correlate abundance with catalytic performance. We find that efficient catalysts arose not just from selection for reactivity among the members of the starting library, but from improvement of less potent precursors by mutations. We observe changes in the ribozyme population in response to increasing selection pressure. Surprisingly, even after many rounds of enrichment, the libraries are highly diverse, suggesting that potential catalysts are more abundant in random space than generally thought. To highlight the use of next-generation sequencing as a tool for in vitro selections, we also apply this technique to a recent, less characterized ribozyme selection. Making use of the correlation between sequence evolution and catalytic activity, we predict mutations that improve ribozyme activity and validate them biochemically. Our study reveals principles underlying ribozyme in vitro selections and provides guidelines to render future selections more efficient, as well as to predict the conservation of key structural elements, allowing the rational improvement of catalysts.
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Affiliation(s)
- Sandeep Ameta
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120-Heidelberg, Germany and High Throughput Sequencing Core Facility, German Cancer Research Center (DKFZ), 69120-Heidelberg, Germany
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153
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Savory N, Takahashi Y, Tsukakoshi K, Hasegawa H, Takase M, Abe K, Yoshida W, Ferri S, Kumazawa S, Sode K, Ikebukuro K. Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development. Biotechnol Bioeng 2013; 111:454-61. [PMID: 24018905 DOI: 10.1002/bit.25111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/27/2013] [Accepted: 09/03/2013] [Indexed: 01/23/2023]
Abstract
In silico evolution with an in vitro system can facilitate the development of functional aptamers with high specificity and affinity. Although a general technique known as systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method for aptamer selection, it sometimes fails to identify aptamers with sufficient binding properties. We have previously developed in silico maturation (ISM) to improve functions of aptamers based on genetic algorithms. ISM represents an intelligent exploitation of a random search within a defined sequence space to optimize aptamer sequences and improve their function of interest. Here we demonstrated a successful application of ISM of aptamers to simultaneously improve specificity and affinity for Streptococcus mutans with discovery of a core sequence, which was required to form a polymerized guanine quadruplex structure for target binding. We applied ISM to aptamers selected by whole-cell SELEX and identified an aptamer with up to 16-fold improvement in affinity compared to its parent aptamers, and specificity was increased to show 12-fold more binding to S. mutans than to Lactobacillus acidophilus. Furthermore, we demonstrated a specific flow-through detection of S. mutans at a concentration range of 1 × 10(5) -10(8) CFU/mL using the evolved aptamer immobilized on gold colloids.
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Affiliation(s)
- Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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154
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Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA. Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents. PLoS One 2013; 8:e71798. [PMID: 23967247 PMCID: PMC3742456 DOI: 10.1371/journal.pone.0071798] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022] Open
Abstract
Background DNA aptamers generated by cell-SELEX offer an attractive alternative to antibodies, but generating aptamers to specific, known membrane protein targets has proven challenging, and has severely limited the use of aptamers as affinity reagents for cell identification and purification. Methodology We modified the BJAB lymphoblastoma cell line to over-express the murine c-kit cell surface receptor. After six rounds of cell-SELEX, high-throughput sequencing and bioinformatics analysis, we identified aptamers that bound BJAB cells expressing c-kit but not wild-type BJAB controls. One of these aptamers also recognizes c-kit endogenously expressed by a mast cell line or hematopoietic progenitor cells, and specifically blocks binding of the c-kit ligand stem cell factor (SCF). This aptamer enables better separation by fluorescence-activated cell sorting (FACS) of c-kit+ hematopoietic progenitor cells from mixed bone marrow populations than a commercially available antibody, suggesting that this approach may be broadly useful for rapid isolation of affinity reagents suitable for purification of other specific cell types. Conclusions/Significance Here we describe a novel procedure for the efficient generation of DNA aptamers that bind to specific cell membrane proteins and can be used as high affinity reagents. We have named the procedure STACS (Specific TArget Cell-SELEX).
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Affiliation(s)
- Susanne Meyer
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - John P. Maufort
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Jeff Nie
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Brian E. McIntosh
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Lisa R. Conti
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Kareem M. Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - H. Tom Soh
- Department of Materials, University of California Santa Barbara, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - James A. Thomson
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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155
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Ozer A, White BS, Lis JT, Shalloway D. Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. Nucleic Acids Res 2013; 41:7167-75. [PMID: 23737446 PMCID: PMC3737557 DOI: 10.1093/nar/gkt477] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The non-specific binding of undesired ligands to a target is the primary factor limiting the enrichment of tight-binding ligands in affinity selection. Solution-phase non-specific affinity is determined by the free-energy of ligand binding to a single target. However, the solid-phase affinity might be higher if a ligand bound concurrently to multiple adjacent immobilized targets in a cooperative manner. Cooperativity could emerge in this case as a simple consequence of the relationship between the free energy of binding, localization entropy and the spatial distribution of the immobilized targets. We tested this hypothesis using a SELEX experimental design and found that non-specific RNA aptamer ligands can concurrently bind up to four bead-immobilized peptide targets, and that this can increase their effective binding affinity by two orders-of-magnitude. Binding curves were quantitatively explained by a new statistical mechanical model of density-dependent cooperative binding, which relates cooperative binding to both the target concentration and the target surface density on the immobilizing substrate. Target immobilization plays a key role in SELEX and other ligand enrichment methods, particularly in new multiplexed microfluidic purification devices, and these results have strong implications for optimizing their performance.
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Affiliation(s)
- Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology Building, Ithaca, NY 14853,USA
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156
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Latulippe DR, Szeto K, Ozer A, Duarte FM, Kelly CV, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG. Multiplexed microcolumn-based process for efficient selection of RNA aptamers. Anal Chem 2013; 85:3417-24. [PMID: 23398198 PMCID: PMC3753675 DOI: 10.1021/ac400105e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We describe a reusable microcolumn
and process for the efficient
discovery of nucleic acid aptamers for multiple target molecules.
The design of our device requires only microliter volumes of affinity
chromatography resin—a condition that maximizes the enrichment
of target-binding sequences over non-target-binding (i.e., background)
sequences. Furthermore, the modular design of the device accommodates
a multiplex aptamer selection protocol. We optimized the selection
process performance using microcolumns filled with green fluorescent
protein (GFP)-immobilized resin and monitoring, over a wide range
of experimental conditions, the enrichment of a known GFP-binding
RNA aptamer (GFPapt) against a random RNA aptamer library. We validated
the multiplex approach by monitoring the enrichment of GFPapt in de
novo selection experiments with GFP and other protein preparations.
After only three rounds of selection, the cumulative GFPapt enrichment
on the GFP-loaded resin was greater than 108 with no enrichment
for the other nonspecific targets. We used this optimized protocol
to perform a multiplex selection to two human heat shock factor (hHSF)
proteins, hHSF1 and hHSF2. High-throughput sequencing was used to
identify aptamers for each protein that were preferentially enriched
in just three selection rounds, which were confirmed and isolated
after five rounds. Gel-shift and fluorescence polarization assays
showed that each aptamer binds with high-affinity (KD < 20 nM) to the respective targets. 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.
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Affiliation(s)
- David R Latulippe
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
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157
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Whatley AS, Ditzler MA, Lange MJ, Biondi E, Sawyer AW, Chang JL, Franken JD, Burke DH. Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, "UCAA-motif" RNA Aptamers. MOLECULAR THERAPY-NUCLEIC ACIDS 2013; 2:e71. [PMID: 23385524 PMCID: PMC3586799 DOI: 10.1038/mtna.2012.62] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNA aptamers that bind the reverse transcriptase (RT) of human immunodeficiency virus (HIV) compete with nucleic acid primer/template for access to RT, inhibit RT enzymatic activity in vitro, and suppress viral replication when expressed in human cells. Numerous pseudoknot aptamers have been identified by sequence analysis, but relatively few have been confirmed experimentally. In this work, a screen of nearly 100 full-length and >60 truncated aptamer transcripts established the predictive value of the F1Pk and F2Pk pseudoknot signature motifs. The screen also identified a new, nonpseudoknot motif with a conserved unpaired UCAA element. High-throughput sequence (HTS) analysis identified 181 clusters capable of forming this novel element. Comparative sequence analysis, enzymatic probing and RT inhibition by aptamer variants established the essential requirements of the motif, which include two conserved base pairs (AC/GU) on the 5′ side of the unpaired UCAA. Aptamers in this family inhibit RT in primer extension assays with IC50 values in the low nmol/l range, and they suppress viral replication with a potency that is comparable with that of previously studied aptamers. All three known anti-RT aptamer families (pseudoknots, the UCAA element, and the recently described “(6/5)AL” motif) are therefore suitable for developing aptamer-based antiviral gene therapies.
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Affiliation(s)
- Angela S Whatley
- 1] Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA [2] Current addresses: Department of Veterans Affairs Office of Research and Development (10P9), Washington DC, USA
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158
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Janssen KPF, Knez K, Spasic D, Lammertyn J. Nucleic acids for ultra-sensitive protein detection. SENSORS (BASEL, SWITZERLAND) 2013; 13:1353-84. [PMID: 23337338 PMCID: PMC3574740 DOI: 10.3390/s130101353] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/26/2012] [Accepted: 12/28/2012] [Indexed: 12/13/2022]
Abstract
Major advancements in molecular biology and clinical diagnostics cannot be brought about strictly through the use of genomics based methods. Improved methods for protein detection and proteomic screening are an absolute necessity to complement to wealth of information offered by novel, high-throughput sequencing technologies. Only then will it be possible to advance insights into clinical processes and to characterize the importance of specific protein biomarkers for disease detection or the realization of "personalized medicine". Currently however, large-scale proteomic information is still not as easily obtained as its genomic counterpart, mainly because traditional antibody-based technologies struggle to meet the stringent sensitivity and throughput requirements that are required whereas mass-spectrometry based methods might be burdened by significant costs involved. However, recent years have seen the development of new biodetection strategies linking nucleic acids with existing antibody technology or replacing antibodies with oligonucleotide recognition elements altogether. These advancements have unlocked many new strategies to lower detection limits and dramatically increase throughput of protein detection assays. In this review, an overview of these new strategies will be given.
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Affiliation(s)
- Kris P. F. Janssen
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Karel Knez
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Dragana Spasic
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Jeroen Lammertyn
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
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159
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Uzawa T, Tada S, Wang W, Ito Y. Expansion of the aptamer library from a "natural soup" to an "unnatural soup". Chem Commun (Camb) 2013; 49:1786-95. [PMID: 23283144 DOI: 10.1039/c2cc36348h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of evolving a commonly existing biomolecule into a variety of functional biomolecules has now been realized in the form of aptamers through the development of in vitro selection. In addition to their high affinity and high specificity for the desired targets, aptamers are easily synthesized chemically and can be modified for downstream applications. Although aptamers were originally selected from a library containing only natural components, the past decade has seen a wealth of new aptamers selected from libraries containing unnatural components to provide new aptamer functions artificially. In this review, we highlight this transition (the shift between selection from natural components and selection from unnatural components) and the applications of selected aptamers.
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Affiliation(s)
- Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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160
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Ditzler MA, Lange MJ, Bose D, Bottoms CA, Virkler KF, Sawyer AW, Whatley AS, Spollen W, Givan SA, Burke DH. High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res 2012; 41:1873-84. [PMID: 23241386 PMCID: PMC3561961 DOI: 10.1093/nar/gks1190] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Systematic evolution of ligands through exponential enrichment (SELEX) is a well-established method for generating nucleic acid populations that are enriched for specified functions. High-throughput sequencing (HTS) enhances the power of comparative sequence analysis to reveal details of how RNAs within these populations recognize their targets. We used HTS analysis to evaluate RNA populations selected to bind type I human immunodeficiency virus reverse transcriptase (RT). The populations are enriched in RNAs of independent lineages that converge on shared motifs and in clusters of RNAs with nearly identical sequences that share common ancestry. Both of these features informed inferences of the secondary structures of enriched RNAs, their minimal structural requirements and their stabilities in RT-aptamer complexes. Monitoring population dynamics in response to increasing selection pressure revealed RNA inhibitors of RT that are more potent than the previously identified pseudoknots. Improved potency was observed for inhibition of both purified RT in enzymatic assays and viral replication in cell-based assays. Structural and functional details of converged motifs that are obscured by simple consensus descriptions are also revealed by the HTS analysis. The approach presented here can readily be generalized for the efficient and systematic post-SELEX development of aptamers for down-stream applications.
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Affiliation(s)
- Mark A Ditzler
- Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
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161
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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162
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163
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Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R. Single-Round, Multiplexed Antibody Mimetic Design through mRNA Display. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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164
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Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R. Single-round, multiplexed antibody mimetic design through mRNA display. Angew Chem Int Ed Engl 2012; 51:12449-53. [PMID: 23125174 DOI: 10.1002/anie.201207005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Indexed: 11/07/2022]
Abstract
In a single round: By combining the high-efficiency enrichment through the continuous-flow magnetic separation (CFMS) technique with the analytical power of next-generation sequencing, the generation of antibody mimetics with a single round of mRNA display is made possible. This approach eliminates iterative selection cycles and provides a path to fully automated ligand generation (see picture).
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Affiliation(s)
- C Anders Olson
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
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165
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Thiel WH, Bair T, Peek AS, Liu X, Dassie J, Stockdale KR, Behlke MA, Miller FJ, Giangrande PH. Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS One 2012; 7:e43836. [PMID: 22962591 PMCID: PMC3433472 DOI: 10.1371/journal.pone.0043836] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023] Open
Abstract
Background The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers. Methodology/Principal Findings We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs. Conclusions and Significance We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies.
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Affiliation(s)
- William H. Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Thomas Bair
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Andrew S. Peek
- Roche Molecular Systems, San Francisco, California, United States of America
| | - Xiuying Liu
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Justin Dassie
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Katie R. Stockdale
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Francis J. Miller
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Radiation Oncology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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166
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Janssen KPF, Knez K, Spasic D, Schrooten J, Lammertyn J. Multiplexed protein detection using an affinity aptamer amplification assay. Anal Bioanal Chem 2012; 404:2073-81. [PMID: 22825678 DOI: 10.1007/s00216-012-6252-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/29/2012] [Accepted: 07/06/2012] [Indexed: 12/01/2022]
Abstract
Affinity probe capillary electrophoresis (APCE) is potentially one of the most versatile technologies for protein diagnostics, offering an excellent balance between robustness, analysis speed and sensitivity. Combining the immunosensing and separating strength of capillary electrophoresis with the signal enhancement power of nucleic acid amplification, aptamers can further push the analytical limits of APCE to offer ultrasensitive, multiplexed detection of protein biomarkers, even when differences in electrophoretic mobility between the different aptamer-target complexes are limited. It is demonstrated how, through careful selection of experimental parameters, simultaneous detection of picomolar levels of three target proteins can be achieved even with aptamers that were initially selected under very different conditions and further taking into account that the aptamers need to be modified to allow successful PCR amplification. Aptamer-enhanced APCE offers limits of detection that are orders of magnitude lower than those that can be achieved through traditional capillary electrophoresis-based immunosensing. With recent developments in aptamer selection that for the first time realise the promise of aptamers as easily accessible, high affinity recognition molecules, it can therefore be envisioned that aptamer-enhanced APCE on parallel microfluidic platforms can be the basis for a truly high-throughput multiplexed proteomics platform, rivalling genetic screening for the first time.
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167
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Weng CH, Huang CJ, Lee GB. Screening of aptamers on microfluidic systems for clinical applications. SENSORS 2012; 12:9514-29. [PMID: 23012556 PMCID: PMC3444114 DOI: 10.3390/s120709514] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 12/20/2022]
Abstract
The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening by a microfluidic-based method has demonstrated remarkable advantages over competing traditional methods. In this paper, we first reviewed microfluidic systems which demonstrated efficient and rapid screening of a specific aptamer. Then, the clinical applications of screened aptamers, also performed by microfluidic systems, are further reviewed. These automated microfluidic systems can provide advantages over their conventional counterparts including more compactness, faster analysis, less sample/reagent consumption and automation. An aptamer-based compact microfluidic system for diagnosis may even lead to a point-of-care device. The use of microfluidic systems for aptamer screening and diagnosis is expected to continue growing in the near future and may make a substantial impact on biomedical applications.
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Affiliation(s)
- Chen-Hsun Weng
- Department of Microbiology and Immunology, National Cheng Kung University, Tainan 70101, Taiwan; E-Mail:
| | - Chao-Jyun Huang
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Author to whom correspondence should be addressed; ; Tel: +886-3-571-5131 (ext. 33765); Fax: +886-3-572-2840
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168
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Gong Q, Wang J, Ahmad KM, Csordas A, Zhou J, Nie J, Stewart R, Thomson JA, Rossi JJ, Soh HT. Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Anal Chem 2012; 84:5365-71. [PMID: 22624874 PMCID: PMC3382006 DOI: 10.1021/ac300873p] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many analytical techniques benefit greatly from the use of affinity reagent pairs, wherein each reagent recognizes a discrete binding site on a target. For example, antibody pairs have been widely used to dramatically increase the specificity of enzyme linked immunosorbent assays (ELISA). Nucleic acid-based aptamers offer many advantageous features relative to protein-based affinity reagents, including well-established chemical synthesis, thermostability, and low production cost. However, the generation of suitable aptamer pairs has posed a significant challenge, and few such pairs have been reported to date. To address this important challenge, we present multivalent aptamer isolation systematic evolution of ligands by exponential enrichment (MAI-SELEX), a technique designed for the efficient selection of aptamer pairs. In contrast to conventional selection methods, our method utilizes two selection modules to generate separate aptamer pools that recognize distinct binding sites on a single target. Using MAI-SELEX, we have isolated two groups of 2'-fluoro-modified RNA aptamers that specifically recognize the αV or β3 subunits of integrin αVβ3. These aptamers exhibit low nanomolar affinities for their targets, with minimal cross-reactivity to other closely related integrin homologues. 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.
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Affiliation(s)
- Qiang Gong
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106
| | - Jinpeng Wang
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Kareem M. Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106
| | - Andrew Csordas
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010
| | - Jeff Nie
- Morgridge Institute for Research, Madison, WI 53707
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53707
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706
| | - James A. Thomson
- Morgridge Institute for Research, Madison, WI 53707
- Genome Center of Wisconsin, University of Wisconsin, Madison, WI 53706
| | - John J. Rossi
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010
| | - H. Tom Soh
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Department of Materials, University of California, Santa Barbara, CA 93106
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169
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Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction? Pharmaceuticals (Basel) 2012; 5:493-513. [PMID: 24281560 PMCID: PMC3763653 DOI: 10.3390/ph5050493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/19/2012] [Accepted: 05/10/2012] [Indexed: 01/02/2023] Open
Abstract
The use of nucleic acid derived aptamers has rapidly expanded since the introduction of SELEX in 1990. Nucleic acid aptamers have demonstrated their ability to target a broad range of molecules in ways that rival antibodies, but advances have been very uneven for different biochemical classes of targets, and clinical applications have been slow to emerge. What sets different aptamers apart from each other and from rivaling molecular recognition platforms, specifically proteins? What advantages do aptamers as a reagent class offer, and how do the chemical properties and selection procedures of aptamers influence their function? Do the building blocks of nucleic acid aptamers dictate inherent limitations in the nature of molecular targets, and do existing aptamers give us insight in how these challenges might be overcome? This review is written as an introduction for potential endusers of aptamer technology who are evaluating the advantages of aptamers as a versatile, affordable, yet highly expandable platform to target a broad range of biological processes or interactions.
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170
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Hoon S, Zhou B, Janda KD, Brenner S, Scolnick J. Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques 2012; 51:413-6. [PMID: 22150332 DOI: 10.2144/000113786] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 11/03/2011] [Indexed: 11/23/2022] Open
Abstract
Traditional methods for selecting aptamers require multiple rounds of selection and optimization in order to identify aptamers that bind with high affinity to their targets. Here we describe an assay that requires only one round of positive selection followed by high-throughput DNA sequencing and informatic analysis in order to select high-affinity aptamers. The assay is flexible, requires less hands on time, and can be used by laboratories with minimal expertise in aptamer biology to quickly select high-affinity aptamers to a target of interest. This assay has been utilized to successfully identify aptamers that bind to thrombin with dissociation constants in the nanomolar range.
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Affiliation(s)
- Shawn Hoon
- Molecular Engineering Lab, Agency for Science Technology and Research, Singapore
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171
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Zhu Y, Chandra P, Ban C, Shim YB. Electrochemical Evaluation of Binding Affinity for Aptamer Selection Using the Microarray Chip. ELECTROANAL 2012. [DOI: 10.1002/elan.201100734] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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172
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Isolation and optimization of murine IL-10 receptor blocking oligonucleotide aptamers using high-throughput sequencing. Mol Ther 2012; 20:1242-50. [PMID: 22434135 DOI: 10.1038/mt.2012.18] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Interleukin-10 (IL-10) is a key suppressor of inflammation in chronic infections and in cancer. In mice, the inability of the immune system to clear viral infections or inhibit tumor growth can be reversed by antibody-mediated blockade of IL-10 action. We used a modified selection protocol to isolate RNA-based, nuclease-resistant, aptamers that bind to the murine IL-10 receptor. After 5 rounds of selection high-throughput sequencing (HTS) was used to analyze the library. Using distribution statistics on about 11 million sequences, aptamers were identified which bound to IL-10 receptor in solution with low K(d). After 12 rounds of selection the predominant IL-10 receptor-binding aptamer identified in the earlier rounds remained, whereas other high-affinity aptamers were not detected. Prevalence of certain nucleotide (nt) substitutions in the sequence of a high-affinity aptamer present in round 5 was used to deduce its secondary structure and guide the truncation of the aptamer resulting in a shortened 48-nt long aptamer with increased affinity. The aptamer also bound to IL-10 receptor on the cell surface and blocked IL-10 function in vitro. Systemic administration of the truncated aptamer was capable of inhibiting tumor growth in mice to an extent comparable to that of an anti- IL-10 receptor antibody.
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173
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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174
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Lee S, Song KM, Jeon W, Jo H, Shim YB, Ban C. A highly sensitive aptasensor towards Plasmodium lactate dehydrogenase for the diagnosis of malaria. Biosens Bioelectron 2012; 35:291-296. [PMID: 22459583 DOI: 10.1016/j.bios.2012.03.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/28/2012] [Accepted: 03/02/2012] [Indexed: 11/24/2022]
Abstract
Finding a highly sensitive diagnostic technique for malaria has challenged scientists for the last century. In the present study, we identified versatile single-strand DNA aptamers for Plasmodium lactate dehydrogenase (pLDH), a biomarker for malaria, via the Systematic Evolution of Ligands by EXponential enrichment (SELEX). The pLDH aptamers selectively bound to the target proteins with high sensitivity (K(d)=16.8-49.6 nM). The selected aptamers were characterized using an electrophoretic mobility shift assay, a quartz crystal microbalance, a fluorescence assay, and circular dichroism spectroscopy. We also designed a simple aptasensor using electrochemical impedance spectroscopy; both Plasmodium vivax LDH and Plasmodium falciparum LDH were selectively detected with a detection limit of 1 pM. Furthermore, the pLDH aptasensor clearly distinguished between malaria-positive blood samples of two major species (P. vivax and P. falciparum) and a negative control, indicating that it may be a useful tool for the diagnosis, monitoring, and surveillance of malaria.
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Affiliation(s)
- Seonghwan Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Weejeong Jeon
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea
| | - Yoon-Bo Shim
- Department of Chemistry, Pusan National University, Busan, 609-735, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, Republic of Korea.
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175
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A coordination polymer nanobelt (CPNB)-based aptasensor for sulfadimethoxine. Biosens Bioelectron 2012; 33:113-9. [DOI: 10.1016/j.bios.2011.12.034] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/09/2011] [Accepted: 12/16/2011] [Indexed: 12/17/2022]
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176
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Göringer HU. Parasite-specific aptamers as biosynthetic reagents and potential pharmaceuticals. Trends Parasitol 2012; 28:106-13. [PMID: 22300805 DOI: 10.1016/j.pt.2011.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 10/14/2022]
Abstract
Aptamers are short, synthetic nucleic acid molecules. They are generated by a Darwinian-type in vitro evolution method known as 'systematic evolution of ligands by exponential enrichment' (SELEX). SELEX represents an experimental platform to identify rare ligands with predetermined functionality from combinatorial nucleic acid libraries. Since its discovery about 20 years ago the method has been instrumental in identifying a large number of aptamers that recognize targets of very different chemistry and molecular complexity. Although aptamers have been converted into sophisticated biomolecular tools for a diverse set of technologies, only a limited number of aptamers have been selected as binding reagents for parasites or parasite-derived molecules. Here the published examples of aptamers that target Leishmania-, Trypanosoma- and Plasmodia-specific molecules are reviewed.
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Affiliation(s)
- H Ulrich Göringer
- Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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177
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Kovarik ML, Gach PC, Ornoff DM, Wang Y, Balowski J, Farrag L, Allbritton NL. Micro total analysis systems for cell biology and biochemical assays. Anal Chem 2012; 84:516-40. [PMID: 21967743 PMCID: PMC3264799 DOI: 10.1021/ac202611x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Phillip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joseph Balowski
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lila Farrag
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
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178
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Song KM, Jeong E, Jeon W, Cho M, Ban C. Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods. Anal Bioanal Chem 2012; 402:2153-61. [PMID: 22222912 DOI: 10.1007/s00216-011-5662-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 10/23/2011] [Accepted: 12/13/2011] [Indexed: 01/02/2023]
Abstract
A gold nanoparticle based dual fluorescence-colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. The selected aptamers, AMP4 (5'-CACGGCATGGTGGGCGTCGTG-3'), AMP17 (5'-GCGGGCGGTTGTATAGCGG-3'), and AMP18 (5'-TTAGTTGGGGTTCAGTTGG-3'), were confirmed to have high sensitivity and specificity to ampicillin (K(d), AMP7 = 9.4 nM, AMP17 = 13.4 nM, and AMP18 = 9.8 nM, respectively). The 5'-fluorescein amidite (FAM)-modified aptamer was used as a dual probe for observing fluorescence differences and color changes simultaneously. The lower limits of detection for this dual method were a 2 ng/mL by fluorescence and a 10 ng/mL by colorimetry for ampicillin in the milk as well as in distilled water. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues. In addition, this dual aptasensor will be a more accurate method for antibiotics in food products as it concurrently uses two detection methods: fluorescence and colorimetry.
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Affiliation(s)
- Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
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179
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Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M, Erdmann VA, Lehrach H, Konthur Z, Menger M, Arndt PF, Glökler J. Probing the SELEX process with next-generation sequencing. PLoS One 2011; 6:e29604. [PMID: 22242135 PMCID: PMC3248438 DOI: 10.1371/journal.pone.0029604] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/01/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. METHODOLOGY We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. CONCLUSIONS High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. 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.
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Affiliation(s)
- Tatjana Schütze
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Chemistry/Biochemistry, Free University Berlin, Berlin, Germany
| | - Barbara Wilhelm
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nicole Greiner
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Alacris Theranostics GmbH, Berlin, Germany
| | - Hannsjörg Braun
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Alacris Theranostics GmbH, Berlin, Germany
| | - Franziska Peter
- Institute of Biochemistry, Universität Leipzig, Leipzig, Germany
| | - Mario Mörl
- Institute of Biochemistry, Universität Leipzig, Leipzig, Germany
| | - Volker A. Erdmann
- Institute for Chemistry/Biochemistry, Free University Berlin, Berlin, Germany
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zoltán Konthur
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marcus Menger
- RiNA RNA-Netzwerk Technologien GmbH, Berlin, Germany
| | - Peter F. Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jörn Glökler
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Alacris Theranostics GmbH, Berlin, Germany
- * E-mail:
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180
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Aquino-Jarquin G, Toscano-Garibay JD. RNA aptamer evolution: two decades of SELEction. Int J Mol Sci 2011; 12:9155-71. [PMID: 22272125 PMCID: PMC3257122 DOI: 10.3390/ijms12129155] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/24/2011] [Accepted: 11/28/2011] [Indexed: 11/16/2022] Open
Abstract
Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First developed in 1990, the SELEX process has become a powerful tool to select structured oligonucleotides for the recognition of targets, starting with small molecules, going through protein complexes until whole cells. SELEX has also evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. This review is an historical follow-up of SELEX method over the two decades since its first appearance.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Unit of Research on Oncological Disease, Children’s Hospital of Mexico Federico Gomez, Mexico City 06720, Mexico; E-Mail:
| | - Julia D. Toscano-Garibay
- Regenerative Medicine Laboratory. Research Direction, Mexico’s Juarez Hospital, Mexico City 07760, Mexico
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +52-55-57477560 ext.7476
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181
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Advances in binder identification and characterisation: the case of oligonucleotide aptamers. N Biotechnol 2011; 29:550-4. [PMID: 22178698 DOI: 10.1016/j.nbt.2011.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 02/07/2023]
Abstract
Aptamers represent an important class of synthetic protein binders useful for proteome-wide applications. The identification and characterisation of such molecules have been greatly facilitated by the development of Systematic Evolution of Ligands by Exponential Amplification (SELEX). Since then numerous advances and alternatives to improve efficient aptamer discovery have been reported. In the present manuscript we discuss the recent advances performed around the SELEX approach that may help to expand the availability of new aptamers and the subsequent applications that may be developed.
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182
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Kogot JM, Zhang Y, Moore SJ, Pagano P, Stratis-Cullum DN, Chang-Yen D, Turewicz M, Pellegrino PM, de Fusco A, Soh HT, Stagliano NE. Screening of peptide libraries against protective antigen of Bacillus anthracis in a disposable microfluidic cartridge. PLoS One 2011; 6:e26925. [PMID: 22140433 PMCID: PMC3225367 DOI: 10.1371/journal.pone.0026925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/05/2011] [Indexed: 11/21/2022] Open
Abstract
Bacterial surface peptide display has gained popularity as a method of affinity reagent generation for a wide variety of applications ranging from drug discovery to pathogen detection. In order to isolate the bacterial clones that express peptides with high affinities to the target molecule, multiple rounds of manual magnetic activated cell sorting (MACS) followed by multiple rounds of fluorescence activated cell sorting (FACS) are conventionally used. Although such manual methods are effective, alternative means of library screening which improve the reproducibility, reduce the cost, reduce cross contamination, and minimize exposure to hazardous target materials are highly desired for practical application. Toward this end, we report the first semi-automated system demonstrating the potential for screening bacterially displayed peptides using disposable microfluidic cartridges. The Micro-Magnetic Separation platform (MMS) is capable of screening a bacterial library containing 3 × 10¹⁰ members in 15 minutes and requires minimal operator training. Using this system, we report the isolation of twenty-four distinct peptide ligands that bind to the protective antigen (PA) of Bacilus anthracis in three rounds of selection. A consensus motif WXCFTC was found using the MMS and was also found in one of the PA binders isolated by the conventional MACS/FACS approach. We compared MMS and MACS rare cell recovery over cell populations ranging from 0.1% to 0.0000001% and found that both magnetic sorting methods could recover cells down to 0.0000001% initial cell population, with the MMS having overall lower standard deviation of cell recovery. We believe the MMS system offers a compelling approach towards highly efficient, semi-automated screening of molecular libraries that is at least equal to manual magnetic sorting methods and produced, for the first time, 15-mer peptide binders to PA protein that exhibit better affinity and specificity than peptides isolated using conventional MACS/FACS.
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Affiliation(s)
- Joshua M. Kogot
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Yanting Zhang
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Stephen J. Moore
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
| | - Paul Pagano
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Dimitra N. Stratis-Cullum
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - David Chang-Yen
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Marek Turewicz
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Paul M. Pellegrino
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Andre de Fusco
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Nancy E. Stagliano
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
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183
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Ahmad KM, Oh SS, Kim S, McClellen FM, Xiao Y, Soh HT. Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS One 2011; 6:e27051. [PMID: 22110600 PMCID: PMC3215713 DOI: 10.1371/journal.pone.0027051] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/10/2011] [Indexed: 01/14/2023] Open
Abstract
Nucleic acid-based aptamers offer many potential advantages relative to antibodies and other protein-based affinity reagents, including facile chemical synthesis, reversible folding, improved thermal stability and lower cost. However, their selection requires significant time and resources and selections often fail to yield molecules with affinities sufficient for molecular diagnostics or therapeutics. Toward a selection technique that can efficiently and reproducibly generate high performance aptamers, we have developed a microfluidic selection process (M-SELEX) that can be used to obtain high affinity aptamers against diverse protein targets. Here, we isolated DNA aptamers against three protein targets with different isoelectric points (pI) using a common protocol. After only three rounds of selection, we discovered novel aptamer sequences that bind to platelet derived growth factor B (PDGF-BB; pI = 9.3) and thrombin (pI = 8.3) with respective dissociation constants (Kd) of 0.028 nM and 0.33 nM, which are both superior to previously reported aptamers against these targets. In parallel, we discovered a new aptamer that binds to apolipoprotein E3 (ApoE; pI = 5.3) with a Kd of 3.1 nM. Furthermore, we observe that the net protein charge may exert influence on the affinity of the selected aptamers. 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 Kd.
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Affiliation(s)
- Kareem M. Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Seung Soo Oh
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Seon Kim
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Forrest M. McClellen
- Chemistry and Biochemistry Department, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Yi Xiao
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (YX); (HTS)
| | - H. Tom Soh
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
- Materials Department, University of California Santa Barbara, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail: (YX); (HTS)
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184
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Talbot LJ, Mi Z, Bhattacharya SD, Kim V, Guo H, Kuo PC. Pharmacokinetic characterization of an RNA aptamer against osteopontin and demonstration of in vivo efficacy in reversing growth of human breast cancer cells. Surgery 2011; 150:224-30. [PMID: 21801960 DOI: 10.1016/j.surg.2011.05.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 05/16/2011] [Indexed: 11/30/2022]
Abstract
BACKGROUND We report pharmacokinetic (PK) data, evaluation of modifications for increased stability, evaluation for cellular uptake, and mediation of regression of breast cancer for the aptamer OPN-R3. METHODS The OPN-R3 aptamer was assessed for PK data in vivo with additional comparison of IV and subcutaneous dosing. Five aptamer variants were generated by differential 2'-O-methylation for comparison with parent. OPN-R3-Cy3 was incubated with MDA-MB231 cells and cellular uptake evaluated under confocal microscopy. Mice were treated with OPN-R3, mutant, or saline 3 weeks after inoculation with MDA-MB231 cells and tumor size was evaluated. RESULTS OPN-R3 PK data were: t(1/2) 7.76 hours, T(max) 3 hours, C(max) 13.2 mmol/L, mean residence time 9 hours, AUC (0-t) 161.9 mmol/hr/L, and K(d) 57.2 nmol/L. The half-life was higher when given intravenously versus subcutaneously (E(1/2) 7.93 vs 0.74 hours). The 2' methylation of all available bases increased unmodified aptamer stability and affinity (t(1/2) 6.2 hours; K(d) 520 nmol/L), but this did not improve on parent aptamer (t(1/2) 7.78 hours, K(d) 18 nmol/L). The aptamer remained extracellular. OPN-R3 caused regression of tumor to levels seen at 1 week after tumor inoculation. CONCLUSION We show the efficacy of OPN-R3 for reversing growth of breast cancer cells with adequate PK stability for clinical application.
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185
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Oh SS, Ahmad KM, Cho M, Kim S, Xiao Y, Soh HT. Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. Anal Chem 2011; 83:6883-9. [PMID: 21774453 PMCID: PMC3165111 DOI: 10.1021/ac201269f] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The generation of nucleic acid aptamers with high affinity typically entails a time-consuming, iterative process of binding, separation, and amplification. It would therefore be beneficial to develop an efficient selection strategy that can generate these high-quality aptamers rapidly, economically, and reproducibly. Toward this goal, we have developed a method that efficiently generates DNA aptamers with slow off-rates. This methodology, called VDC-MSELEX, pairs the volume dilution challenge process with microfluidic separation for magnetic bead-assisted aptamer selection. This method offers improved aptamer selection efficiencies through the application of highly stringent selection conditions: it retrieves a small number (<10(6)) of magnetic beads suspended in a large volume (>50 mL) and concentrates them into a microfluidic chamber (8 μL) with minimal loss for continuous washing. We performed three rounds of the VDC-MSELEX using streptavidin (SA) as the target and obtained new DNA aptamer sequences with low nanomolar affinity that specifically bind to the SA proteins.
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Affiliation(s)
- Seung Soo Oh
- Materials Department, University of California, Santa Barbara, CA 93106
| | - Kareem M. Ahmad
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
| | - Minseon Cho
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Seon Kim
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106
| | - Yi Xiao
- Materials Department, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - H. Tom Soh
- Materials Department, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
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186
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
| | - Lianghai Hu
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
| | - W. Andy Tao
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907
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187
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Kupakuwana GV, Crill JE, McPike MP, Borer PN. Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing. PLoS One 2011; 6:e19395. [PMID: 21625587 PMCID: PMC3098231 DOI: 10.1371/journal.pone.0019395] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 03/29/2011] [Indexed: 12/12/2022] Open
Abstract
Background Aptamers are oligonucleotides that bind proteins and other targets with high affinity and selectivity. Twenty years ago elements of natural selection were adapted to in vitro selection in order to distinguish aptamers among randomized sequence libraries. The primary bottleneck in traditional aptamer discovery is multiple cycles of in vitro evolution. Methodology/Principal Findings We show that over-representation of sequences in aptamer libraries and deep sequencing enables acyclic identification of aptamers. We demonstrated this by isolating a known family of aptamers for human α-thrombin. Aptamers were found within a library containing an average of 56,000 copies of each possible randomized 15mer segment. The high affinity sequences were counted many times above the background in 2–6 million reads. Clustering analysis of sequences with more than 10 counts distinguished two sequence motifs with candidates at high abundance. Motif I contained the previously observed consensus 15mer, Thb1 (46,000 counts), and related variants with mostly G/T substitutions; secondary analysis showed that affinity for thrombin correlated with abundance (Kd = 12 nM for Thb1). The signal-to-noise ratio for this experiment was roughly 10,000∶1 for Thb1. Motif II was unrelated to Thb1 with the leading candidate (29,000 counts) being a novel aptamer against hexose sugars in the storage and elution buffers for Concanavilin A (Kd = 0.5 µM for α-methyl-mannoside); ConA was used to immobilize α-thrombin. Conclusions/Significance Over-representation together with deep sequencing can dramatically shorten the discovery process, distinguish aptamers having a wide range of affinity for the target, allow an exhaustive search of the sequence space within a simplified library, reduce the quantity of the target required, eliminate cycling artifacts, and should allow multiplexing of sequencing experiments and targets.
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Affiliation(s)
- Gillian V. Kupakuwana
- Graduate Program in Structural Biology, Biochemistry and Biophysics, Syracuse University, Syracuse, New York, United States of America
| | - James E. Crill
- AptaMatrix, Inc., Syracuse, New York, United States of America
| | - Mark P. McPike
- AptaMatrix, Inc., Syracuse, New York, United States of America
| | - Philip N. Borer
- Graduate Program in Structural Biology, Biochemistry and Biophysics, Syracuse University, Syracuse, New York, United States of America
- AptaMatrix, Inc., Syracuse, New York, United States of America
- Department of Chemistry, Syracuse University, Syracuse, New York, United States of America
- * E-mail:
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188
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Deep mutational scanning: assessing protein function on a massive scale. Trends Biotechnol 2011; 29:435-42. [PMID: 21561674 DOI: 10.1016/j.tibtech.2011.04.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/01/2011] [Accepted: 04/11/2011] [Indexed: 12/23/2022]
Abstract
Analysis of protein mutants is an effective means to understand their function. Protein display is an approach that allows large numbers of mutants of a protein to be selected based on their activity, but only a handful with maximal activity have been traditionally identified for subsequent functional analysis. However, the recent application of high-throughput sequencing (HTS) to protein display and selection has enabled simultaneous assessment of the function of hundreds of thousands of mutants that span the activity range from high to low. Such deep mutational scanning approaches are rapid and inexpensive with the potential for broad utility. In this review, we discuss the emergence of deep mutational scanning, the challenges associated with its use and some of its exciting applications.
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189
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Song KM, Cho M, Jo H, Min K, Jeon SH, Kim T, Han MS, Ku JK, Ban C. Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer. Anal Biochem 2011; 415:175-81. [PMID: 21530479 DOI: 10.1016/j.ab.2011.04.007] [Citation(s) in RCA: 282] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/30/2011] [Accepted: 04/04/2011] [Indexed: 02/07/2023]
Abstract
A selective kanamycin-binding single-strand DNA (ssDNA) aptamer (TGGGGGTTGAGGCTAAGCCGA) was discovered through in vitro selection using affinity chromatography with kanamycin-immobilized sepharose beads. The selected aptamer has a high affinity for kanamycin and also for kanamycin derivatives such as kanamycin B and tobramycin. The dissociation constants (K(d) [kanamycin]=78.8 nM, K(d) [kanamycin B]=84.5 nM, and K(d) [tobramycin]=103 nM) of the new aptamer were determined by fluorescence intensity analysis using 5'-fluorescein amidite (FAM) modification. Using this aptamer, kanamycin was detected down to 25 nM by the gold nanoparticle-based colorimetric method. Because the designed colorimetric method is simple, easy, and visible to the naked eye, it has advantages that make it useful for the detection of kanamycin. Furthermore, the selected new aptamer has many potential applications as a bioprobe for the detection of kanamycin, kanamycin B, and tobramycin in pharmaceutical preparations and food products.
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Affiliation(s)
- Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk 790-784, South Korea
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Ahmad KM, Oh SS, Kim S, McClellen FM, Xiao Y, Soh HT. Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS One 2011. [PMID: 22110600 DOI: 10.1371/journal.-pone.0027051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
Nucleic acid-based aptamers offer many potential advantages relative to antibodies and other protein-based affinity reagents, including facile chemical synthesis, reversible folding, improved thermal stability and lower cost. However, their selection requires significant time and resources and selections often fail to yield molecules with affinities sufficient for molecular diagnostics or therapeutics. Toward a selection technique that can efficiently and reproducibly generate high performance aptamers, we have developed a microfluidic selection process (M-SELEX) that can be used to obtain high affinity aptamers against diverse protein targets. Here, we isolated DNA aptamers against three protein targets with different isoelectric points (pI) using a common protocol. After only three rounds of selection, we discovered novel aptamer sequences that bind to platelet derived growth factor B (PDGF-BB; pI = 9.3) and thrombin (pI = 8.3) with respective dissociation constants (K(d)) of 0.028 nM and 0.33 nM, which are both superior to previously reported aptamers against these targets. In parallel, we discovered a new aptamer that binds to apolipoprotein E3 (ApoE; pI = 5.3) with a K(d) of 3.1 nM. Furthermore, we observe that the net protein charge may exert influence on the affinity of the selected aptamers. 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).
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Affiliation(s)
- Kareem M Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
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Turner DJ, Tuytten R, Janssen KP, Lammertyn J, Wuyts J, Pollet J, Eyckerman S, Brown C, Kas K. Toward Clinical Proteomics on a Next-Generation Sequencing Platform. Anal Chem 2010; 83:666-70. [DOI: 10.1021/ac102666n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel J. Turner
- Sequencing Technology Development, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Robin Tuytten
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Kris P.F. Janssen
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Jeroen Lammertyn
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Jan Wuyts
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Jeroen Pollet
- BIOSYST−MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Sven Eyckerman
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Clive Brown
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
| | - Koen Kas
- Pronota nv, Technologiepark 4, B-9052 Zwijnaarde/Ghent, Belgium
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