101
|
Acousto-microfluidics for screening of ssDNA aptamer. Sci Rep 2016; 6:27121. [PMID: 27272884 PMCID: PMC4897735 DOI: 10.1038/srep27121] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022] Open
Abstract
We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (Kd) of 0.7 nM.
Collapse
|
102
|
|
103
|
Kim J, Olsen TR, Zhu J, Hilton JP, Yang KA, Pei R, Stojanovic MN, Lin Q. Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation. Sci Rep 2016; 6:26139. [PMID: 27217242 PMCID: PMC4877600 DOI: 10.1038/srep26139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/20/2016] [Indexed: 01/06/2023] Open
Abstract
We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the processes of affinity selection and amplification of target-binding oligonucleotides, and an electrophoretic DNA manipulation scheme for the coupling of these processes, which are required to occur in different buffers. This achieves the full microfluidic integration of SELEX, thereby enabling highly efficient isolation of aptamers in drastically reduced times and with minimized consumption of biological material. The approach as such also offers broad target applicability by allowing selection of aptamers with respect to targets that are either surface-immobilized or solution-borne, potentially allowing aptamers to be developed as readily available affinity reagents for a wide range of targets. We demonstrate the utility of this approach on two different procedures, respectively for isolating aptamers against a surface-immobilized protein (immunoglobulin E) and a solution-phase small molecule (bisboronic acid in the presence of glucose). In both cases aptamer candidates were isolated in three rounds of SELEX within a total process time of approximately 10 hours.
Collapse
Affiliation(s)
- Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Timothy R. Olsen
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - John P. Hilton
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| | - Kyung-Ae Yang
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Columbia University, New York, NY 10032, United States
| | - Renjun Pei
- Division of Nanobiomedicine, Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China
| | - Milan N. Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Columbia University, New York, NY 10032, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, New York 10027, United States
| |
Collapse
|
104
|
Gijs M, Penner G, Blackler GB, Impens NREN, Baatout S, Luxen A, Aerts AM. Improved Aptamers for the Diagnosis and Potential Treatment of HER2-Positive Cancer. Pharmaceuticals (Basel) 2016; 9:E29. [PMID: 27213406 PMCID: PMC4932547 DOI: 10.3390/ph9020029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 02/07/2023] Open
Abstract
Aptamers provide a potential source of alternative targeting molecules for existing antibody diagnostics and therapeutics. In this work, we selected novel DNA aptamers targeting the HER2 receptor by an adherent whole-cell SELEX approach. Individual aptamers were identified by next generation sequencing and bioinformatics analysis. Two aptamers, HeA2_1 and HeA2_3, were shown to bind the HER2 protein with affinities in the nanomolar range. In addition, both aptamers were able to bind with high specificity to HER2-overexpressing cells and HER2-positive tumor tissue samples. Furthermore, we demonstrated that aptamer HeA2_3 is being internalized into cancer cells and has an inhibitory effect on cancer cell growth and viability. In the end, we selected novel DNA aptamers with great potential for the diagnosis and possible treatment of HER2-positive cancer.
Collapse
Affiliation(s)
- Marlies Gijs
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
- Cyclotron Research Centre, University of Liège, 4000 Liège, Belgium.
| | - Gregory Penner
- NeoVentures Biotechnology Inc., London, N6A 1A1 ON, Canada.
| | | | | | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| | - André Luxen
- Cyclotron Research Centre, University of Liège, 4000 Liège, Belgium.
| | - An M Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium.
| |
Collapse
|
105
|
Rosch JC, Hollmann EK, Lippmann ES. In vitro selection technologies to enhance biomaterial functionality. Exp Biol Med (Maywood) 2016; 241:962-71. [PMID: 27188514 DOI: 10.1177/1535370216647182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cells make decisions and fate choices based in part on cues they receive from their external environment. Factors that affect the interpretation of these cues include the soluble proteins that are present at any given time, the cell surface receptors that are available to bind these proteins, and the relative affinities of the soluble proteins for their cognate receptors. Researchers have identified many of the biological motifs responsible for the high-affinity interactions between proteins and their receptors, and subsequently incorporated these motifs into biomaterials to elicit control over cell behavior. Common modes of control include localized sequestration of proteins to improve bioavailability and direct inhibition or activation of a receptor by an immobilized peptide or protein. However, naturally occurring biological motifs often possess promiscuous affinity for multiple proteins and receptors or lack programmable actuation in response to dynamic stimuli, thereby limiting the amount of control they can exert over cellular decisions. These natural motifs only represent a small fraction of the biological diversity that can be assayed by in vitro selection strategies, and the discovery of "artificial" motifs with varying affinity, specificity, and functionality could greatly expand the repertoire of engineered biomaterial properties. This minireview provides a brief summary of classical and emerging techniques in peptide phage display and nucleic acid aptamer selections and discusses prospective applications in the areas of cell adhesion, angiogenesis, neural regeneration, and immune modulation.
Collapse
Affiliation(s)
- Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Emma K Hollmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Ethan S Lippmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| |
Collapse
|
106
|
Ahirwar R, Vellarikkal SK, Sett A, Sivasubbu S, Scaria V, Bora U, Borthakur BB, Kataki AC, Sharma JD, Nahar P. Aptamer-Assisted Detection of the Altered Expression of Estrogen Receptor Alpha in Human Breast Cancer. PLoS One 2016; 11:e0153001. [PMID: 27043307 PMCID: PMC4820125 DOI: 10.1371/journal.pone.0153001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
An increase in the expression of estrogen receptors (ER) and the expanded population of ER-positive cells are two common phenotypes of breast cancer. Detection of the aberrantly expressed ERα in breast cancer is carried out using ERα-antibodies and radiolabelled ligands to make decisions about cancer treatment and targeted therapy. Capitalizing on the beneficial advantages of aptamer over the conventional antibody or radiolabelled ligand, we have identified a DNA aptamer that selectively binds and facilitates the detection of ERα in human breast cancer tissue sections. The aptamer is identified using the high throughput sequencing assisted SELEX screening. Biophysical characterization confirms the binding and formation of a thermodynamically stable complex between the identified DNA aptamer (ERaptD4) and ERα (Ka = 1.55±0.298×108 M-1; ΔH = 4.32×104±801.1 cal/mol; ΔS = -108 cal/mol/deg). Interestingly, the specificity measurements suggest that the ERaptD4 internalizes into ERα-positive breast cancer cells in a target-selective manner and localizes specifically in the nuclear region. To harness these characteristics of ERaptD4 for detection of ERα expression in breast cancer samples, we performed the aptamer-assisted histochemical analysis of ERα in tissue samples from breast cancer patients. The results were validated by performing the immunohistochemistry on same samples with an ERα-antibody. We found that the two methods agree strongly in assay output (kappa value = 0.930, p-value <0.05 for strong ERα positive and the ERα negative samples; kappa value = 0.823, p-value <0.05 for the weak/moderate ER+ve samples, n = 20). Further, the aptamer stain the ERα-positive cells in breast tissues without cross-reacting to ERα-deficient fibroblasts, adipocytes, or the inflammatory cells. Our results demonstrate a significant consistency in the aptamer-assisted detection of ERα in strong ERα positive, moderate ERα positive and ERα negative breast cancer tissues. We anticipate that the ERaptD4 aptamer targeting ERα may potentially be used for an efficient grading of ERα expression in cancer tissues.
Collapse
Affiliation(s)
- Rajesh Ahirwar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Shamsudheen Karuthedath Vellarikkal
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Arghya Sett
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | - Sridhar Sivasubbu
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
| | - Utpal Bora
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | | | | | | | - Pradip Nahar
- Department of System and Chemical Biology, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative research, CSIR- Institute of Genomics and Integrative Biology, Delhi, India
- * E-mail:
| |
Collapse
|
107
|
Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
108
|
Thiel WH, Giangrande PH. Analyzing HT-SELEX data with the Galaxy Project tools--A web based bioinformatics platform for biomedical research. Methods 2016; 97:3-10. [PMID: 26481156 PMCID: PMC4792767 DOI: 10.1016/j.ymeth.2015.10.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 01/25/2023] Open
Abstract
The development of DNA and RNA aptamers for research as well as diagnostic and therapeutic applications is a rapidly growing field. In the past decade, the process of identifying aptamers has been revolutionized with the advent of high-throughput sequencing (HTS). However, bioinformatics tools that enable the average molecular biologist to analyze these large datasets and expedite the identification of candidate aptamer sequences have been lagging behind the HTS revolution. The Galaxy Project was developed in order to efficiently analyze genome, exome, and transcriptome HTS data, and we have now applied these tools to aptamer HTS data. The Galaxy Project's public webserver is an open source collection of bioinformatics tools that are powerful, flexible, dynamic, and user friendly. The online nature of the Galaxy webserver and its graphical interface allow users to analyze HTS data without compiling code or installing multiple programs. Herein we describe how tools within the Galaxy webserver can be adapted to pre-process, compile, filter and analyze aptamer HTS data from multiple rounds of selection.
Collapse
Affiliation(s)
- William H Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; The François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
| | - Paloma H Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; The François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA; The Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; The Molecular and Cell Biology Program, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
109
|
Ouellet E, Foley JH, Conway EM, Haynes C. Hi-Fi SELEX: A High-Fidelity Digital-PCR Based Therapeutic Aptamer Discovery Platform. Biotechnol Bioeng 2016; 112:1506-22. [PMID: 25727321 DOI: 10.1002/bit.25581] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/14/2015] [Indexed: 12/30/2022]
Abstract
Current technologies for aptamer discovery typically leverage the systematic evolution of ligands by exponential enrichment (SELEX) concept by recursively panning semi-combinatorial ssDNA or RNA libraries against a molecular target. The expectation is that this iterative selection process will be sufficiently stringent to identify a candidate pool of specific high-affinity aptamers. However, failure of this process to yield promising aptamers is common, due in part to (i) limitations in library designs, (ii) retention of non-specific aptamers during screening rounds, (iii) excessive accumulation of amplification artifacts, and (iv) the use of screening criteria (binding affinity) that does not reflect therapeutic activity. We report a new selection platform, High-Fidelity (Hi-Fi) SELEX, that introduces fixed-region blocking elements to safeguard the functional diversity of the library. The chemistry of the target-display surface and the composition of the equilibration solvent are engineered to strongly inhibit non-specific retention of aptamers. Partition efficiencies approaching 10(6) are thereby realized. Retained members are amplified in Hi-Fi SELEX by digital PCR in a manner that ensures both elimination of amplification artifacts and stoichiometric conversion of amplicons into the single-stranded library required for the next selection round. Improvements to aptamer selections are first demonstrated using human α-thrombin as the target. Three clinical targets (human factors IXa, X, and D) are then subjected to Hi-Fi SELEX. For each, rapid enrichment of ssDNA aptamers offering an order-nM mean equilibrium dissociation constant (Kd) is achieved within three selection rounds, as quantified by a new label-free qPCR assay reported here. Therapeutic candidates against factor D are identified.
Collapse
|
110
|
McKeague M, Wong RS, Smolke CD. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res 2016; 44:2987-99. [PMID: 26969733 PMCID: PMC4838379 DOI: 10.1093/nar/gkw151] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
The past decade of synthetic biology research has witnessed numerous advances in the development of tools and frameworks for the design and characterization of biological systems. Researchers have focused on the use of RNA for gene expression control due to its versatility in sensing molecular ligands and the relative ease by which RNA can be modeled and designed compared to proteins. We review the recent progress in the field with respect to RNA-based genetic devices that are controlled through small molecule and protein interactions. We discuss new approaches for generating and characterizing these devices and their underlying components. We also highlight immediate challenges, future directions and recent applications of synthetic RNA devices in engineered biological systems.
Collapse
Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Remus S Wong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
111
|
In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules. Sci Rep 2016; 6:21285. [PMID: 26899418 PMCID: PMC4761961 DOI: 10.1038/srep21285] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/21/2016] [Indexed: 11/17/2022] Open
Abstract
Aptamers, the chemical-antibody substitute to conventional antibodies, are primarily discovered through SELEX technology involving multi-round selections and enrichment. Circumventing conventional methodology, here we report an in silico selection of aptamers to estrogen receptor alpha (ERα) using RNA analogs of human estrogen response elements (EREs). The inverted repeat nature of ERE and the ability to form stable hairpins were used as criteria to obtain aptamer-alike sequences. Near-native RNA analogs of selected single stranded EREs were modelled and their likelihood to emerge as ERα aptamer was examined using AutoDock Vina, HADDOCK and PatchDock docking. These in silico predictions were validated by measuring the thermodynamic parameters of ERα -RNA interactions using isothermal titration calorimetry. Based on the in silico and in vitro results, we selected a candidate RNA (ERaptR4; 5′-GGGGUCAAGGUGACCCC-3′) having a binding constant (Ka) of 1.02 ± 0.1 × 108 M−1 as an ERα-aptamer. Target-specificity of the selected ERaptR4 aptamer was confirmed through cytochemistry and solid-phase immunoassays. Furthermore, stability analyses identified ERaptR4 resistant to serum and RNase A degradation in presence of ERα. Taken together, an efficient ERα-RNA aptamer is identified using a non-SELEX procedure of aptamer selection. The high-affinity and specificity can be utilized in detection of ERα in breast cancer and related diseases.
Collapse
|
112
|
Dausse E, Barré A, Aimé A, Groppi A, Rico A, Ainali C, Salgado G, Palau W, Daguerre E, Nikolski M, Toulmé JJ, Di Primo C. Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation. Biosens Bioelectron 2016; 80:418-425. [PMID: 26874109 DOI: 10.1016/j.bios.2016.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 01/02/2023]
Abstract
A surface plasmon resonance (SPR)-based SELEX approach has been used to raise RNA aptamers against a structured RNA, derived from XBP1 pre-mRNA, that folds as two contiguous hairpins. Thanks to the design of the internal microfluidic cartridge of the instrument, the selection was performed during the dissociation phase of the SPR analysis by recovering the aptamer candidates directly from the target immobilized onto the sensor chip surface. The evaluation of the pools was performed by SPR, simultaneously, during the association phase, each time the amplified and transcribed candidates were injected over the immobilized target. SPR coupled with SELEX from the first to the last round allowed identifying RNA aptamers that formed highly stable loop-loop complexes (KD equal to 8nM) with the hairpin located on the 5' side of the target. High throughput sequencing of two key rounds confirmed the evolution observed by SPR and also revealed the selection of hairpins displaying a loop not fully complementary to the loop of its target. These candidates were selected mainly because they bound 79 times faster to the target than those having a complementary loop. SELEX coupled with SPR is expected to speed up the selection process because selection and evaluation are performed simultaneously.
Collapse
Affiliation(s)
- Eric Dausse
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Aurélien Barré
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Ahissan Aimé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Alexis Groppi
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Alain Rico
- Thermo Fisher Scientific, Saint Aubin F-91190, France
| | | | - Gilmar Salgado
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - William Palau
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | | | - Macha Nikolski
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Carmelo Di Primo
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
| |
Collapse
|
113
|
Elle IC, Karlsen KK, Terp MG, Larsen N, Nielsen R, Derbyshire N, Mandrup S, Ditzel HJ, Wengel J. Selection of LNA-containing DNA aptamers against recombinant human CD73. MOLECULAR BIOSYSTEMS 2016; 11:1260-70. [PMID: 25720604 DOI: 10.1039/c5mb00045a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
LNA-containing DNA aptamers against CD73 (human ecto-5'-nucleotidase), a protein frequently overexpressed in solid tumours, were isolated by SELEX. A pre-defined stem-loop library, containing LNA in the forward primer region, was enriched with CD73 binding sequences through six rounds of SELEX with recombinant his-tagged CD73 immobilised on anti-his plates. Enriched pools isolated from rounds one, three and six were subjected to next-generation sequencing and analysed for enrichment using custom bioinformatics software. The software identified aptamer sequences via the primers and then performed several steps including sequence unification, clustering and alignment to identify enriched sequences. Three enriched sequences were synthesised for further analysis, two of which showed sequence similarities. These sequences exhibited binding to the recombinant CD73 with KD values of 10 nM and 3.5 nM when tested by surface plasmon resonance. Truncated variants of these aptamers and variants where the LNA nucleotides were substituted for the DNA equivalent also exhibited affinity for the recombinant CD73 in the low nanomolar range. In enzyme inhibition assays with recombinant CD73 the aptamer sequences were able to decrease the activity of the protein. However, the aptamers exhibited no binding to cellular CD73 by flow cytometry analysis likely since the epitope recognised by the aptamer was not available for binding on the cellular protein.
Collapse
Affiliation(s)
- Ida C Elle
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
114
|
Abstract
Fuelled by massive whole genome sequencing projects such as the human genome project, enormous technological advancements and therefore tremendous price drops could be achieved, rendering next-generation sequencing very attractive for deep sequencing of SELEX libraries. Herein we describe the preparation of SELEX samples for Illumina sequencing, based on the already established whole genome sequencing workflow. We describe the addition of barcode sequences for multiplexing and the adapter ligation, avoiding associated pitfalls.
Collapse
Affiliation(s)
- Fabian Tolle
- Life & Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str. 1, Bonn, 53121, Germany
| | - Günter Mayer
- Life & Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str. 1, Bonn, 53121, Germany.
| |
Collapse
|
115
|
Thiel WH. Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e345. [PMID: 28131286 PMCID: PMC5023399 DOI: 10.1038/mtna.2016.54] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/10/2016] [Indexed: 01/29/2023]
Abstract
Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). High-throughput sequencing (HTS) revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs.
Collapse
Affiliation(s)
- William H Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA; François M. Abboud Cardiovascular Research Center, University of Iowa, Iowa City, Iowa, USA.
| |
Collapse
|
116
|
Rozenblum GT, Lopez VG, Vitullo AD, Radrizzani M. Aptamers: current challenges and future prospects. Expert Opin Drug Discov 2015; 11:127-35. [PMID: 26630462 DOI: 10.1517/17460441.2016.1126244] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Aptamers are oligonucleotide molecules raised in vitro from large combinatorial libraries of nucleic acids and developed to bind to targets with high affinity and specificity. Whereas novel target molecules are proposed for therapeutic intervention and diagnostic, aptamer technology has a great potential to become a source of lead compounds. AREAS COVERED In this review, the authors address the current status of the technology and highlight the recent progress in aptamer-based technologies. They also discuss the current major technical limitations of aptamer technology and propose original solutions based on existing technologies that could result in a solid aptamer-discovery platform. EXPERT OPINION Whereas aptamers have shown to bind to targets with similar affinities and specificities to those of antibodies, aptamers have several advantages that could outweigh antibody technology and open new opportunities for better medical and diagnostic solutions. However, the current status of the aptamer technology suffers from several technical limitations that slowdown the progression of novel aptamers into the clinic and makes the business around aptamers challenging.
Collapse
Affiliation(s)
- Guido Tomás Rozenblum
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Vanina Gisela Lopez
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Alfredo Daniel Vitullo
- a Departamento de Investigaciones Biomédicas y Biotecnológicas , Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD - Universidad Maimónides , Buenos Aires , Argentina
| | - Martín Radrizzani
- b Laboratorio de Neuro y Citogenética Molecular , Centro de Estudios de Salud y Medio Ambiente, Universidad de San Martín - CONICET , Buenos Aires , Argentina
| |
Collapse
|
117
|
Ranallo S, Rossetti M, Plaxco KW, Vallée-Bélisle A, Ricci F. A Modular, DNA-Based Beacon for Single-Step Fluorescence Detection of Antibodies and Other Proteins. Angew Chem Int Ed Engl 2015; 54:13214-8. [PMID: 26337144 PMCID: PMC4757636 DOI: 10.1002/anie.201505179] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/20/2015] [Indexed: 12/17/2022]
Abstract
A versatile platform for the one-step fluorescence detection of both monovalent and multivalent proteins has been developed. This system is based on a conformation-switching stem-loop DNA scaffold that presents a small-molecule, polypeptide, or nucleic-acid recognition element on each of its two stem strands. The steric strain associated with the binding of one (multivalent) or two (monovalent) target molecules to these elements opens the stem, enhancing the emission of an attached fluorophore/quencher pair. The sensors respond rapidly (<10 min) and selectively, enabling the facile detection of specific proteins even in complex samples, such as blood serum. The versatility of the platform was demonstrated by detecting five bivalent proteins (four antibodies and the chemokine platelet-derived growth factor) and two monovalent proteins (a Fab fragment and the transcription factor TBP) with low nanomolar detection limits and no detectable cross-reactivity.
Collapse
Affiliation(s)
- Simona Ranallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Marianna Rossetti
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Kevin W Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 (USA)
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7 (Canada).
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy).
| |
Collapse
|
118
|
Ranallo S, Rossetti M, Plaxco KW, Vallée‐Bélisle A, Ricci F. A Modular, DNA‐Based Beacon for Single‐Step Fluorescence Detection of Antibodies and Other Proteins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505179] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Simona Ranallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Marianna Rossetti
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Kevin W. Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 (USA)
| | - Alexis Vallée‐Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre‐ville, Montréal, Québec H3C 3J7 (Canada)
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| |
Collapse
|
119
|
Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
Collapse
Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| |
Collapse
|
120
|
Zhao T, Liu R, Ding X, Zhao J, Yu H, Wang L, Xu Q, Wang X, Lou X, He M, Xiao Y. Nanoprobe-Enhanced, Split Aptamer-Based Electrochemical Sandwich Assay for Ultrasensitive Detection of Small Molecules. Anal Chem 2015; 87:7712-9. [PMID: 26171721 DOI: 10.1021/acs.analchem.5b01178] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is quite challenging to improve the binding affinity of antismall molecule aptamers. We report that the binding affinity of anticocaine split aptamer pairs improved by up to 66-fold by gold nanoparticles (AuNP)-attached aptamers due to the substantially increased local concentration of aptamers and multiple and simultaneous ligand interactions. The significantly improved binding affinity enables the detection of small molecule targets with unprecedented sensitivity, as demonstrated in nanoprobe-enhanced split aptamer-based electrochemical sandwich assays (NE-SAESA). NE-SAESA replaces the traditional molecular reporter probe with AuNPs conjugated to multiple reporter probes. The increased binding affinity allowed us to use 1,000-fold lower reporter probe concentrations relative to those employed in SAESA. We show that the near-elimination of background in NE-SAESA effectively improves assay sensitivity by ∼1,000-100,000-fold for ATP and cocaine detection, relative to equivalent SAESA. With the ongoing development of new strategies for the selection of aptamers, we anticipate that our sensor platform should offer a generalizable approach for the high-sensitivity detection of diverse targets. More importantly, we believe that NE-SAESA represents a novel strategy to improve the binding affinity between a small molecule and its aptamer and potentially can be extended to other detection platforms.
Collapse
Affiliation(s)
- Tao Zhao
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Ran Liu
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xiaofan Ding
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Juncai Zhao
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Haixiang Yu
- ‡Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Lei Wang
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Qing Xu
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xuan Wang
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xinhui Lou
- †Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Miao He
- §School of Environment, Tsinghua University, Beijing 100084, China
| | - Yi Xiao
- ‡Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
121
|
Guo PL, Tang M, Hong SL, Yu X, Pang DW, Zhang ZL. Combination of dynamic magnetophoretic separation and stationary magnetic trap for highly sensitive and selective detection of Salmonella typhimurium in complex matrix. Biosens Bioelectron 2015. [PMID: 26201979 DOI: 10.1016/j.bios.2015.07.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Foodborne illnesses have always been a serious problem that threats public health, so it is necessary to develop a method that can detect the pathogens rapidly and sensitively. In this study, we designed a magnetic controlled microfluidic device which integrated the dynamic magnetophoretic separation and stationary magnetic trap together for sensitive and selective detection of Salmonella typhimurium (S. typhimurium). Coupled with immunomagnetic nanospheres (IMNs), this device could separate and enrich the target pathogens and realize the sensitive detection of target pathogens on chip. Based on the principle of sandwich immunoassays, the trapped target pathogens identified by streptavidin modified QDs (SA-QDs) were detected under an inverted fluorescence microscopy. A linear range was exhibited at the concentration from 1.0×10(4) to 1.0×10(6) colony-forming units/mL (CFU/mL), the limit of detection (LOD) was as low as 5.4×10(3) CFU/mL in milk (considering the sample volume, the absolute detection limit corresponded to 540C FU). Compared with the device with stationary magnetic trap alone, the integrated device enhanced anti-interference ability and increased detection sensitivity through dynamic magnetophoretic separation, and made the detection in complex samples more accurate. In addition, it had excellent specificity and good reproducibility. The developed system provides a rapid, sensitive and accurate approach to detect pathogens in practice samples.
Collapse
Affiliation(s)
- Pei-Lin Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Man Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Shao-Li Hong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xu Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Dai-Wen Pang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China.
| |
Collapse
|
122
|
Dupont DM, Larsen N, Jensen JK, Andreasen PA, Kjems J. Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools. Nucleic Acids Res 2015; 43:e139. [PMID: 26163061 PMCID: PMC4666376 DOI: 10.1093/nar/gkv700] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/30/2015] [Indexed: 01/05/2023] Open
Abstract
Nucleic acid aptamer selection by systematic evolution of ligands by exponential enrichment (SELEX) has shown great promise for use in the development of research tools, therapeutics and diagnostics. Typically, aptamers are identified from libraries containing up to 1016 different RNA or DNA sequences by 5–10 rounds of affinity selection towards a target of interest. Such library screenings can result in complex pools of many target-binding aptamers. New high-throughput sequencing techniques may potentially revolutionise aptamer selection by allowing quantitative assessment of the dynamic changes in the pool composition during the SELEX process and by facilitating large-scale post-SELEX characterisation. In the present study, we demonstrate how high-throughput sequencing of SELEX pools, before and after a single round of branched selection for binding to different target variants, can provide detailed information about aptamer binding sites, preferences for specific target conformations, and functional effects of the aptamers. The procedure was applied on a diverse pool of 2′-fluoropyrimidine-modified RNA enriched for aptamers specific for the serpin plasminogen activator inhibitor-1 (PAI-1) through five rounds of standard selection. The results demonstrate that it is possible to perform large-scale detailed characterisation of aptamer sequences directly in the complex pools obtained from library selection methods, thus without the need to produce individual aptamers.
Collapse
Affiliation(s)
- Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Niels Larsen
- iNANO Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark Danish-Chinese Centre for Proteases and Cancer, Aarhus University, 8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark iNANO Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| |
Collapse
|
123
|
Sanmamed MF, Pastor F, Rodriguez A, Perez-Gracia JL, Rodriguez-Ruiz ME, Jure-Kunkel M, Melero I. Agonists of Co-stimulation in Cancer Immunotherapy Directed Against CD137, OX40, GITR, CD27, CD28, and ICOS. Semin Oncol 2015; 42:640-55. [PMID: 26320067 DOI: 10.1053/j.seminoncol.2015.05.014] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
T and natural killer (NK) lymphocytes are considered the main effector players in the immune response against tumors. Full activation of T and NK lymphocytes requires the coordinated participation of several surface receptors that meet their cognate ligands through structured transient cell-to-cell interactions known as immune synapses. In the case of T cells, the main route of stimulation is driven by antigens as recognized in the form of short polypeptides associated with major histocompatibility complex (MHC) antigen-presenting molecules. However, the functional outcome of T-cell stimulation towards clonal expansion and effector function acquisition is contingent on the contact of additional surface receptor-ligand pairs and on the actions of cytokines in the milieu. While some of those interactions are inhibitory, others are activating and are collectively termed co-stimulatory receptors. The best studied belong to either the immunoglobulin superfamily or the tumor necrosis factor-receptor (TNFR) family. Co-stimulatory receptors include surface moieties that are constitutively expressed on resting lymphocytes such as CD28 or CD27 and others whose expression is induced upon recent previous antigen priming, ie, CD137, GITR, OX40, and ICOS. Ligation of these glycoproteins with agonist antibodies actively conveys activating signals to the lymphocyte. Those signals, acting through a potentiation of the cellular immune response, give rise to anti-tumor effects in mouse models. Anti-CD137 antibodies are undergoing clinical trials with evidence of clinical activity and anti-OX40 monoclonal antibodies (mAbs) induce interesting immunomodulation effects in humans. Antibodies anti-CD27 and GITR have recently entered clinical trials. The inherent dangers of these immunomodulation strategies are the precipitation of excessive systemic inflammation or/and invigorating silent autoimmunity. Agonist antibodies, recombinant forms of the natural ligands, and polynucleotide-based aptamers constitute the pharmacologic tools to manipulate such receptors. Preclinical data suggest that the greatest potential of these agents is achieved in combined treatment strategies.
Collapse
Affiliation(s)
- Miguel F Sanmamed
- Department of Immunobiology, Yale School of Medicine, New Haven, CT.
| | - Fernando Pastor
- Centro de investigación médica aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Alfonso Rodriguez
- Centro de investigación médica aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | | | | | | | - Ignacio Melero
- Centro de investigación médica aplicada (CIMA), Universidad de Navarra, Pamplona, Spain; Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.
| |
Collapse
|
124
|
Jung YK, Woo MA, Soh HT, Park HG. Aptamer-based cell imaging reagents capable of fluorescence switching. Chem Commun (Camb) 2015; 50:12329-32. [PMID: 25182171 DOI: 10.1039/c4cc03888f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe an aptamer-conjugated polydiacetylene imaging probe (ACP) that shows highly specific fluorescence switching upon binding to epithelial cancer cells that overexpress the tumor biomarker protein EpCAM (epithelial cell adhesion molecule) on their surface.
Collapse
Affiliation(s)
- Yun Kyung Jung
- Department of Chemical and Biomolecular Engineering (BK21 + Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | | | | | | |
Collapse
|
125
|
Levay A, Brenneman R, Hoinka J, Sant D, Cardone M, Trinchieri G, Przytycka TM, Berezhnoy A. Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment. Nucleic Acids Res 2015; 43:e82. [PMID: 26007661 PMCID: PMC4499151 DOI: 10.1093/nar/gkv534] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/09/2015] [Indexed: 01/10/2023] Open
Abstract
Oligonucleotide aptamers represent a novel platform for creating ligands with desired specificity, and they offer many potentially significant advantages over monoclonal antibodies in terms of feasibility, cost, and clinical applicability. However, the isolation of high-affinity aptamer ligands from random oligonucleotide pools has been challenging. Although high-throughput sequencing (HTS) promises to significantly facilitate systematic evolution of ligands by exponential enrichment (SELEX) analysis, the enormous datasets generated in the process pose new challenges for identifying those rare, high-affinity aptamers present in a given pool. We show that emulsion PCR preserves library diversity, preventing the loss of rare high-affinity aptamers that are difficult to amplify. We also demonstrate the importance of using reference targets to eliminate binding candidates with reduced specificity. Using a combination of bioinformatics and functional analyses, we show that the rate of amplification is more predictive than prevalence with respect to binding affinity and that the mutational landscape within a cluster of related aptamers can guide the identification of high-affinity aptamer ligands. Finally, we demonstrate the power of this selection process for identifying cross-species aptamers that can bind human receptors and cross-react with their murine orthologs.
Collapse
Affiliation(s)
- Agata Levay
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Randall Brenneman
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jan Hoinka
- National Center of Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - David Sant
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Marco Cardone
- Cancer Inflammation Program, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, USA
| | - Giorgio Trinchieri
- Cancer Inflammation Program, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD, USA
| | - Teresa M Przytycka
- National Center of Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD 20894, USA
| | - Alexey Berezhnoy
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| |
Collapse
|
126
|
Martin JA, Mirau PA, Chushak Y, Chávez JL, Naik RR, Hagen JA, Kelley-Loughnane N. Single-Round Patterned DNA Library Microarray Aptamer Lead Identification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:137489. [PMID: 26075138 PMCID: PMC4446497 DOI: 10.1155/2015/137489] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface.
Collapse
Affiliation(s)
- Jennifer A. Martin
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Peter A. Mirau
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Yaroslav Chushak
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
| | - Jorge L. Chávez
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
- UES Inc., 4401 Dayton-Xenia Road, Dayton, Dayton, OH 45433, USA
| | - Rajesh R. Naik
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Joshua A. Hagen
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Nancy Kelley-Loughnane
- Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| |
Collapse
|
127
|
Wu Y, Zhan S, Wang L, Zhou P. Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles. Analyst 2015; 139:1550-61. [PMID: 24496116 DOI: 10.1039/c3an02117c] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The demand for selection of aptamers against various small chemical molecules has substantially increased in recent years. To incubate and separate target-specific aptamers, the conventional SELEX procedures generally need to immobilize target molecules on a matrix, which may be impotent to screen aptamers toward small molecules without enough sites for immobilization. Herein we chose Cd(II) as a model of a small molecule with less sites, and proposed a novel SELEX strategy of immobilizing ssDNA libraries rather than target molecules on a matrix, for selection of aptamers with high affinity to Cd(II). After eleven rounds of positive and negative selection, twelve T and G-rich of nonrepeating ssDNA sequences were identified, of which the Cd-4 aptamer displayed the highest binding affinity to Cd(II). The secondary structures of these sequences revealed that a stem-loop structure folded by the domain of their 30-random sequence is critical for aptamers to bind targets. Then the interaction between the selected Cd-4 aptamer and Cd(II) was confirmed by CD analysis, and the binding specificity toward other competitive metal ions was also investigated. The dissociation constant (Kd) of Cd-4 aptamer was determined as 34.5 nM for Cd(II). Moreover, the Cd-4 aptamer was considered a recognition element for the colorimetric detection of Cd(II) based on the aggregation of AuNPs by cationic polymer. Through spectroscopic quantitative analysis, Cd(II) in aqueous solution can be detected as low as 4.6 nM. The selected Cd-4 aptamer will offer a new substitute for the detection of Cd(II) or other applications like recovery of cadmium from polluted samples.
Collapse
Affiliation(s)
- Yuangen Wu
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | | | | | | |
Collapse
|
128
|
Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM. Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res 2015; 43:5699-707. [PMID: 25870409 PMCID: PMC4499121 DOI: 10.1093/nar/gkv308] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel in-silico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut—a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the ‘parent’ sequence and AptaCluster—an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.
Collapse
Affiliation(s)
- Jan Hoinka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Alexey Berezhnoy
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Phuong Dao
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Zuben E Sauna
- Laboratory of Hemostasis, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Eli Gilboa
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| |
Collapse
|
129
|
Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing. Anal Bioanal Chem 2015; 407:6965-73. [PMID: 25863801 PMCID: PMC4551533 DOI: 10.1007/s00216-015-8665-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 12/22/2022]
Abstract
The development of novel affinity probes for cancer biomarkers may enable powerful improvements in analytical methods for detecting and treating cancer. In this report, we describe our use of capillary electrophoresis (CE) as the separation mechanism in the process of selecting DNA aptamers with affinity for the ovarian cancer biomarker HE4. Rather than the conventional use of cloning and sequencing as the last step in the aptamer selection process, we used high-throughput sequencing on an Illumina platform. This data-rich approach, combined with a bioinformatics pipeline based on freely available computational tools, enabled the entirety of the selection process-and not only its endpoint-to be characterized. Affinity probe CE and fluorescence anisotropy assays demonstrate the binding affinity of a set of aptamer candidates identified through this bioinformatics approach. Graphical Abstract A population of candidate aptamers is sequenced on an Illumina platform, enabling the process by which aptamers are selected over multiple SELEX rounds to be characterized. Bioinformatics tools are used to identify enrichment of selected aptamers and groupings into clusters based on sequence and structural similarity. A subset of sequenced aptamers may be intelligently chosen for in vitro testing.
Collapse
|
130
|
Lee S, Jo H, Her J, Lee HY, Ban C. Ultrasensitive electrochemical detection of engrailed-2 based on homeodomain-specific DNA probe recognition for the diagnosis of prostate cancer. Biosens Bioelectron 2015; 66:32-8. [DOI: 10.1016/j.bios.2014.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 12/13/2022]
|
131
|
Alam KK, Chang JL, Burke DH. FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e230. [PMID: 25734917 PMCID: PMC4354339 DOI: 10.1038/mtna.2015.4] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/08/2015] [Indexed: 12/22/2022]
Abstract
High-throughput sequence (HTS) analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.). FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html.
Collapse
Affiliation(s)
- Khalid K Alam
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jonathan L Chang
- 1] Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA [2] Current Address: School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Donald H Burke
- 1] Department of Biochemistry, University of Missouri, Columbia, Missouri, USA [2] Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, USA
| |
Collapse
|
132
|
Martin JA, Smith JE, Warren M, Chávez JL, Hagen JA, Kelley-Loughnane N. A method for selecting structure-switching aptamers applied to a colorimetric gold nanoparticle assay. J Vis Exp 2015:e52545. [PMID: 25870978 PMCID: PMC4401151 DOI: 10.3791/52545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.
Collapse
Affiliation(s)
- Jennifer A Martin
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base; The Henry M. Jackson Foundation
| | - Joshua E Smith
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base; The Henry M. Jackson Foundation
| | - Mercedes Warren
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base
| | - Jorge L Chávez
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base; UES, Inc
| | - Joshua A Hagen
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base
| | - Nancy Kelley-Loughnane
- 711th Human Performance Wing, Human Effectiveness Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base;
| |
Collapse
|
133
|
Darmostuk M, Rimpelova S, Gbelcova H, Ruml T. Current approaches in SELEX: An update to aptamer selection technology. Biotechnol Adv 2015; 33:1141-61. [PMID: 25708387 DOI: 10.1016/j.biotechadv.2015.02.008] [Citation(s) in RCA: 406] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 01/26/2015] [Accepted: 02/13/2015] [Indexed: 12/21/2022]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a well-established and efficient technology for the generation of oligonucleotides with a high target affinity. These SELEX-derived single stranded DNA and RNA molecules, called aptamers, were selected against various targets, such as proteins, cells, microorganisms, chemical compounds etc. They have a great potential in the use as novel antibodies, in cancer theragnostics and in biomedical research. Vast interest in aptamers stimulated continuous development of SELEX, which underwent numerous modifications since its first application in 1990. Novel modifications made the selection process more efficient, cost-effective and significantly less time-consuming. This article brings a comprehensive and up-to-date review of recent advances in SELEX methods and pinpoints advantages, main obstacles and limitations. The post-SELEX strategies and examples of application are also briefly outlined in this review.
Collapse
Affiliation(s)
- Mariia Darmostuk
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Silvie Rimpelova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| | - Helena Gbelcova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, Bratislava 811 08, Slovak Republic.
| | - Tomas Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, Prague 6 166 28, Czech Republic.
| |
Collapse
|
134
|
Identification and Characterization of an eIF4e DNA Aptamer That Inhibits Proliferation With High Throughput Sequencing. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e217. [PMID: 25514650 PMCID: PMC4272410 DOI: 10.1038/mtna.2014.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/06/2014] [Indexed: 12/19/2022]
Abstract
Development of DNA aptamer screens that are both simple and informative can increase the success rate of DNA aptamer selection and induce greater adoption. High eIF4e levels contribute to malignancies, thus eIF4e presents itself as a valuable target for DNA aptamer-based inhibition screen. Here, we demonstrate a method for the rapid selection of looped DNA aptamers against eIF4e by combining negative selection and purification in a single step, followed by characterization with high throughput sequencing. The resulting aptamers show functional binding to eIF4e and inhibit translation initiation in biochemical assays. When transfected into cells, eIF4e aptamers cause a dramatic loss of cell proliferation in tumor cells as seen with eIF4e knockdown with antisense oligonucleotides, shRNAs, and siRNAs, hinting at therapeutic possibilities. With the large data set provided by high throughput sequencing, we demonstrate that selection happens in waves and that sequencing data can be used to infer aptamer structure. Lastly, we show that ligation of looped aptamers can enhance their functional effects. These results demonstrate a rapid protocol to screen and optimize aptamers against macromolecules of interest.
Collapse
|
135
|
Cho M, Oh SS, Nie J, Stewart R, Radeke MJ, Eisenstein M, Coffey PJ, Thomson JA, Soh HT. Array-based discovery of aptamer pairs. Anal Chem 2014; 87:821-8. [PMID: 25495696 PMCID: PMC4287840 DOI: 10.1021/ac504076k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Affinity
reagent pairs that recognize distinct epitopes on a target
protein can greatly improve the sensitivity and specificity of molecular
detection. Importantly, such pairs can be conjugated to generate reagents
that achieve two-site “bidentate” target recognition,
with affinities greatly exceeding either monovalent component. DNA
aptamers are especially well-suited for such constructs, because they
can be linked via standard synthesis techniques without requiring
chemical conjugation. Unfortunately, aptamer pairs are difficult to
generate, primarily because conventional selection methods preferentially
yield aptamers that recognize a dominant “hot spot”
epitope. Our array-based discovery platform for multivalent aptamers
(AD-MAP) overcomes this problem to achieve efficient discovery of
aptamer pairs. We use microfluidic selection and high-throughput sequencing
to obtain an enriched pool of aptamer sequences. Next, we synthesize
a custom array based on these sequences, and perform parallel affinity
measurements to identify the highest-affinity aptamer for the target
protein. We use this aptamer to form complexes that block the primary
binding site on the target, and then screen the same array with these
complexes to identify aptamers that bind secondary epitopes. We used
AD-MAP to discover DNA aptamer pairs that bind distinct sites on human
angiopoietin-2 with high affinities, even in undiluted serum. To the
best of our knowledge, this is the first work to discover new aptamer
pairs using arrays. We subsequently conjugated these aptamers with
a flexible linker to construct ultra-high-affinity bidentate reagents,
with equilibrium dissociation constants as low as 97 pM: >200-fold
better than either component aptamer. Functional studies confirm that
both aptamers critically contribute to this ultrahigh affinity, highlighting
the promise of such reagents for research and clinical use.
Collapse
Affiliation(s)
- Minseon Cho
- Department of Mechanical Engineering, University of California-Santa Barbara , Santa Barbara, California 93106, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
136
|
Zhang Y, Li X, Zou R, Xue Y, Lou X, He M. Bovine thrombin enhances the efficiency and specificity of polymerase chain reaction. Biotechniques 2014; 57:289-94. [PMID: 25495728 DOI: 10.2144/000114237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/25/2014] [Indexed: 11/23/2022] Open
Abstract
The polymerase chain reaction (PCR) has become one of the central techniques in molecular biology since its invention. However, PCR can be fraught with difficulties in various situations, and it is desirable to find novel PCR enhancers suitable for universal applications. Here we show that bovine thrombin (BT), a well-known coagulation protein, is exceptionally effective at preventing the formation of primer dimers and enhancing the formation of the desired PCR products. The PCR enhancement effects of BT were demonstrated by testing various types of samples, including low-copy synthetic single-stranded DNAs (ssDNAs), synthetic ssDNA pools, human genomic DNA, and hepatitis B virus genomic DNA. In addition, BT was also able to effectively relieve PCR inhibition by nanomaterial inhibitors such as gold nanoparticles (AuNPs) and graphene oxide (GO). Compared with BSA, one of the most popular PCR enhancers, BT was more effective and required concentrations 18-178 times less than that of BSA to achieve a similar level of PCR enhancement.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Xiaoning Li
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ruxing Zou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ying Xue
- Beijing Municipal Center for Disease Prevention and Control, Beijing, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Miao He
- School of Environment, Tsinghua University, Beijing, China
| |
Collapse
|
137
|
Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
|
138
|
Li F, Zhang H, Wang Z, Newbigging AM, Reid MS, Li XF, Le XC. Aptamers facilitating amplified detection of biomolecules. Anal Chem 2014; 87:274-92. [PMID: 25313902 DOI: 10.1021/ac5037236] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Feng Li
- Department of Laboratory Medicine and Pathology, ‡Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G3
| | | | | | | | | | | | | |
Collapse
|
139
|
New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
Collapse
|
140
|
Lin H, Zhang W, Jia S, Guan Z, Yang CJ, Zhu Z. Microfluidic approaches to rapid and efficient aptamer selection. BIOMICROFLUIDICS 2014; 8:041501. [PMID: 25379085 PMCID: PMC4189129 DOI: 10.1063/1.4890542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/07/2014] [Indexed: 05/04/2023]
Abstract
With their advantages as molecular recognition elements, aptamers have been extensively studied and used for bioanalytical and biomedical applications. However, the process of enrichment and screening of aptamers remains a bottleneck for aptamer development. Recently, microfluidic methods have been increasingly used for rapid and efficient aptamer selection, showing their remarkable advantages over conventional methods. This review briefly introduces aptamers and their advantages. The conventional process of generating aptamers is discussed, followed by the analysis of the key obstacles to efficient aptamer selection. Microfluidic methods for highly efficient enrichment and screening of aptamers are reviewed in detail.
Collapse
Affiliation(s)
- Hui Lin
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Weiting Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Shasha Jia
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| |
Collapse
|
141
|
Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J, Cossins A. Single-step selection of bivalent aptamers validated by comparison with SELEX using high-throughput sequencing. PLoS One 2014; 9:e100572. [PMID: 24963654 PMCID: PMC4070925 DOI: 10.1371/journal.pone.0100572] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/26/2014] [Indexed: 01/23/2023] Open
Abstract
The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is significant because it shows that next generation sequencing and motif finding informatics have the potential to simplify the selection of aptamers by avoiding multiple rounds of enzymatic transcription and amplification.
Collapse
Affiliation(s)
- Robert Wilson
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Christian Bourne
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Roy R. Chaudhuri
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Andrew Cossins
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
142
|
Zhu Z, Song Y, Li C, Zou Y, Zhu L, An Y, Yang CJ. Monoclonal surface display SELEX for simple, rapid, efficient, and cost-effective aptamer enrichment and identification. Anal Chem 2014; 86:5881-8. [PMID: 24863283 DOI: 10.1021/ac501423g] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel method, monoclonal surface display SELEX (MSD-SELEX), has been designed for simple, rapid, efficient, and cost-effective enrichment and identification of aptamers from a library of monoclonal DNA-displaying beads produced via highly parallel single-molecule emulsion PCR. The approach was successfully applied for the identification of high-affinity aptamers that bind specifically to different types of targets, including cancer biomarker protein EpCAM and small toxin molecule aflatoxin B1. Compared to the conventional sequencing-chemical synthesis-screening work flow, MSD-SELEX avoids large-scale DNA sequencing, expensive and time-consuming DNA synthesis, and labor-intensive screening of large populations of candidates, thus offering a new approach for simple, rapid, efficient, and cost-effective aptamer identification for a wide variety of applications.
Collapse
Affiliation(s)
- Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, P. R. China
| | | | | | | | | | | | | |
Collapse
|
143
|
Jiang P, Meyer S, Hou Z, Propson NE, Soh HT, Thomson JA, Stewart R. MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. ACTA ACUST UNITED AC 2014; 30:2665-7. [PMID: 24872422 DOI: 10.1093/bioinformatics/btu348] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Aptamers are 'synthetic antibodies' that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict the BIND: ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis. AVAILABILITY AND IMPLEMENTATION MPBind software and documents are available at http://www.morgridge.net/MPBind.html. The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/.
Collapse
Affiliation(s)
- Peng Jiang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Susanne Meyer
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Zhonggang Hou
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Nicholas E Propson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - H Tom Soh
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| |
Collapse
|
144
|
Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
Collapse
Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
| | | | | | | |
Collapse
|
145
|
Park SM, Sabour AF, Son JH, Lee SH, Lee LP. Toward integrated molecular diagnostic system (i MDx): principles and applications. IEEE Trans Biomed Eng 2014; 61:1506-21. [PMID: 24759281 PMCID: PMC4141683 DOI: 10.1109/tbme.2014.2309119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Integrated molecular diagnostic systems ( iMDx), which are automated, sensitive, specific, user-friendly, robust, rapid, easy-to-use, and portable, can revolutionize future medicine. This review will first focus on the components of sample extraction, preservation, and filtration necessary for all point-of-care devices to include for practical use. Subsequently, we will look for low-powered and precise methods for both sample amplification and signal transduction, going in-depth to the details behind their principles. The final field of total device integration and its application to the clinical field will also be addressed to discuss the practicality for future patient care. We envision that microfluidic systems hold the potential to breakthrough the number of problems brought into the field of medical diagnosis today.
Collapse
Affiliation(s)
- Seung-min Park
- Department of Bioengineering, and the Berkeley Sensor and Actuator Center, UC Berkeley, University of California, Berkeley, Berkeley, CA 94720 USA, and also with the Department of Radiology, School of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Andrew F. Sabour
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Jun Ho Son
- Department of Bioengineering, and the Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Sang Hun Lee
- Department of Bioengineering, and the Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Luke P. Lee
- Department of Bioengineering, and the Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720 USA
| |
Collapse
|
146
|
He S, Yu X, Wang X, Tan J, Yan S, Wang P, Huang BH, Zhang ZL, Li L. Fast magnetic isolation of simple sequence repeat markers in microfluidic channels. LAB ON A CHIP 2014; 14:1410-1414. [PMID: 24615343 DOI: 10.1039/c3lc51371h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Simple sequence repeat (SSR) markers are widely used for genome mapping, genetic diversity characterization and medical diagnosis. The fast isolation by AFLP of sequence containing repeats (FIASCO) is a powerful method for SSR marker isolation, but it is laborious, costly, and time consuming and requires multiple rounds of washing. Here, we report a superparamagnetic bead (SPMB)-based FIASCO method in a magnetic field controllable microfluidic chip (MFCM-Chip). This method dramatically reduces the assay time by 4.25-fold and reduces the quantity of magnetic beads and probes by 10-fold through the magnetic capture of (AG)n-containing fragments from Herba Leonuri, followed by washing and eluting on a microchip. The feasibility of this method was further evaluated by PCR and sequencing, and the results showed that the proportion of fragments containing SSRs was 89%, confirming that this platform is a fast and efficient method for SSR marker isolation. This cost-effective platform will make the powerful FIASCO technique more accessible for routine use with a wide variety of materials.
Collapse
Affiliation(s)
- Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan 430072, PR China.
| | | | | | | | | | | | | | | | | |
Collapse
|
147
|
Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface. PLoS One 2014; 9:e93052. [PMID: 24675636 PMCID: PMC3968096 DOI: 10.1371/journal.pone.0093052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/28/2014] [Indexed: 02/07/2023] Open
Abstract
SELEX, the process of selecting aptamers, is often hampered by the difficulty of preparing target molecules in their native forms and by a lack of a simple yet quantitative assay for monitoring enrichment and affinity of reactive aptamers. In this study, we sought to discover DNA aptamers against human serum markers for potential therapeutic and diagnostic applications. To circumvent soluble expression and immobilization for performing SELEX, we ectopically expressed soluble growth factors on the surface of yeast cells to enable cell-SELEX and devised a flow cytometry-based method to quantitatively monitor progressive enrichment of specific aptamers. High-throughput sequencing of selected pools revealed that the emergence of highly enriched sequences concurred with the increase in the percentage of reactive aptamers shown by flow cytometry. Particularly, selected DNA aptamers against VEGF were specific and of high affinity (K(D) = ∼ 1 nM) and demonstrated a potent inhibition of capillary tube formation of endothelial cells, comparable to the effect of a clinically approved anti-VEGF antibody drug, bevacizumab. Considering the fact that many mammalian secretory proteins have been functionally expressed in yeast, the strategy of implementing cell-SELEX and quantitative binding assay can be extended to discover aptamers against a broad array of soluble antigens.
Collapse
|
148
|
Bawazer LA, Newman AM, Gu Q, Ibish A, Arcila M, Cooper JB, Meldrum FC, Morse DE. Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering. ACS NANO 2014; 8:387-395. [PMID: 24341560 DOI: 10.1021/nn404448s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA-based information systems drive the combinatorial optimization processes of natural evolution, including the evolution of biominerals. Advances in high-throughput DNA sequencing expand the power of DNA as a potential information platform for combinatorial engineering, but many applications remain to be developed due in part to the challenge of handling large amounts of sequence data. Here we employ high-throughput sequencing and a recently developed clustering method (AutoSOME) to identify single-stranded DNA sequence families that bind specifically to ZnO semiconductor mineral surfaces. These sequences were enriched from a diverse DNA library after a single round of screening, whereas previous screening approaches typically require 5-15 rounds of enrichment for effective sequence identification. The consensus sequence of the largest cluster was poly d(T)30. This consensus sequence exhibited clear aptamer behavior and was shown to promote the synthesis of crystalline ZnO from aqueous solution at near-neutral pH. This activity is significant, as the crystalline form of this wide-bandgap semiconductor is not typically amenable to solution synthesis in this pH range. High-resolution TEM revealed that this DNA synthesis route yields ZnO nanoparticles with an amorphous-crystalline core-shell structure, suggesting that the mechanism of mineralization involves nanoscale coacervation around the DNA template. We thus demonstrate that our new method, termed Single round Enrichment of Ligands by deep Sequencing (SEL-Seq), can facilitate biomimetic synthesis of technological nanomaterials by accelerating combinatorial selection of biomolecular-mineral interactions. Moreover, by enabling direct characterization of sequence family demographics, we anticipate that SEL-Seq will enhance aptamer discovery in applications employing additional rounds of screening.
Collapse
Affiliation(s)
- Lukmaan A Bawazer
- Department of Molecular, Cellular and Developmental Biology, Institute for Collaborative Biotechnologies, and Biomolecular Science and Engineering Program, University of California , Santa Barbara, California 93106 , United States
| | | | | | | | | | | | | | | |
Collapse
|
149
|
Yoshida W, Abe K, Ikebukuro K. Emerging techniques employed in aptamer-based diagnostic tests. Expert Rev Mol Diagn 2014; 14:143-51. [PMID: 24400930 DOI: 10.1586/14737159.2014.868307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since aptamers were reported in 1990, research into the applications of aptamers, particularly diagnostic applications, has been growing. Aptamers can act as recognition elements instead of antibodies. In this regard, aptamers have unique characteristics because they are composed of nucleic acids. Intra- and intermolecular interactions of nucleic acids can be easily tailored following straightforward hybridization rules. Nucleic acids can be enzymatically replicated and their sequences can be determined using high-throughput methods. Using these properties, ligand-induced structural change-based aptamer sensors for homogeneous assays, polymerase- and/or nuclease-combined aptamer sensors for ultrasensitive assays, and microarray/next-generation sequencing-based aptamer sensors for multiplexed assays have been developed. This article reviews these unique aptamer sensors, demonstrating their great potential for diagnostic applications.
Collapse
Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | | |
Collapse
|
150
|
Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG. RAPID-SELEX for RNA aptamers. PLoS One 2013; 8:e82667. [PMID: 24376564 PMCID: PMC3869713 DOI: 10.1371/journal.pone.0082667] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 01/11/2023] Open
Abstract
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX approach. High-throughput sequencing of the enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5×1015 sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance.
Collapse
Affiliation(s)
- Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David R Latulippe
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|