51
|
Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
Collapse
Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
| |
Collapse
|
52
|
Nguyen VT, Lee BH, Kim SH, Gu MB. Aptamer-aptamer linkage based aptasensor for highly enhanced detection of small molecules. Biotechnol J 2016; 11:843-9. [PMID: 27221154 DOI: 10.1002/biot.201500433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/14/2016] [Accepted: 05/04/2016] [Indexed: 11/08/2022]
Abstract
The multi-target colorimetric aptasensors can be easily fabricated by using two different aptamer sequences. However, there have been no research reports about improvement or enhancing of colorimetric signals based on the aggregation properties of AuNPs. Herein, we report a simple and efficient method to control and enhance the function of the multi-target aptasensor using an aptamer-aptamer linkage method. The aptasensor was developed for highly sensitive multiple-target detection of small molecules. The extension of aptamer DNA sequences using this method resulted in the enhanced analytical sensitivity of this aptasensor in sensing applications for two small molecule targets. Furthermore, the mechanism of the interaction between DNA aptamer and AuNPs was studied by measuring the zeta potential to explain the enhancement of the sensitivity of this multi-target aptasensor. The limit of detection of this multi-target aptasensor was found to be 1 nM and 37 nM for kanamycin (KAN) and chlortetracycline (CHLOR), respectively. It is 25-fold lower than in the previous report using an AuNP-based sensor for defining the limit of detection (LOD) of KAN and five times lower than the LOD for CHLOR. This aptasensor has great potential in the simultaneous detection of a wide range of KAN and CHLOR concentrations.
Collapse
Affiliation(s)
- Van-Thuan Nguyen
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Bang Hyun Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Sang Hoon Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Man Bock Gu
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea.
| |
Collapse
|
53
|
Methods for Improving Aptamer Binding Affinity. Molecules 2016; 21:421. [PMID: 27043498 PMCID: PMC6273865 DOI: 10.3390/molecules21040421] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers.
Collapse
|
54
|
Development and characterization of an enzyme-linked DNA aptamer-magnetic bead-based assay for human IGF-I in serum. Microchem J 2016. [DOI: 10.1016/j.microc.2015.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
55
|
Trapaidze A, Hérault JP, Herbert JM, Bancaud A, Gué AM. Investigation of the selectivity of thrombin-binding aptamers for thrombin titration in murine plasma. Biosens Bioelectron 2015; 78:58-66. [PMID: 26594887 DOI: 10.1016/j.bios.2015.11.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 11/08/2015] [Indexed: 11/26/2022]
Abstract
Detection of thrombin in plasma raises timely challenges to enable therapeutic management of thrombosis in patients under vital threat. Thrombin binding aptamers represent promising candidates as sensing elements for the development of real-time thrombin biosensors; however implementation of such biosensor requires the clear understanding of thrombin-aptamer interaction properties in real-like environment. In this study, we used Surface Plasmon Resonance technique to answer the questions of specificity and sensitivity of thrombin detection by the thrombin-binding aptamers HD1, NU172 and HD22. We systematically characterized their properties in the presence of thrombin, as well as interfering molecular species such as the thrombin precursor prothrombin, thrombin in complex with some of its natural inhibitors, nonspecific serum proteins, and diluted plasma. Kinetic experiments show the multiple binding modes of HD1 and NU172, which both interact with multiple sites of thrombin with low nanomolar affinities and show little specificity of interaction for prothrombin vs. thrombin. HD22, on the other hand, binds specifically to thrombin exosite II and has no affinity to prothrombin at all. While thrombin in complex with some of its inhibitors could not be recognized by any aptamer, the binding of HD1 and NU172 properties is compromised by thrombin inhibitors alone, as well as with serum albumin. Finally, the complex nature of plasma was overwhelming for HD1, but we define conditions for the thrombin detection at 10nM range in 100-fold diluted plasma by HD22. Consequently HD22 showed key advantage over HD1 and NU172, and appears as the only alternative to design an aptasensor.
Collapse
Affiliation(s)
- Ana Trapaidze
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | | | | | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | - Anne-Marie Gué
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France
| |
Collapse
|
56
|
Gaddes ER, Lee D, Gydush G, Wang Y, Dong C. Regulation of fibrin-mediated tumor cell adhesion to the endothelium using anti-thrombin aptamer. Exp Cell Res 2015; 339:417-26. [PMID: 26481421 DOI: 10.1016/j.yexcr.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/29/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022]
Abstract
Molecular intervention during transient stages of various metastatic pathways may lead to development of promising therapeutic technologies. One of such involves soluble fibrin (sFn) that has been implicated as a cross-linker between circulating blood or tumor cells and endothelial cell receptors, promoting cell arrest on the endothelium during circulation. sFn generation is a result of thrombin-mediated fibrinogen (Fg) cleavage due to either vascular injuries or a tumor microenvironment. For cancer therapy, thrombin-mediated conversions of Fg to sFn thus serve as potential intervention points to decrease circulating tumor cell adhesion to the endothelium and subsequent metastatic events. The purpose of this work was to investigate the function of an anti-thrombin oligonucleotide aptamer in reducing tumor cell arrest. Both molecular and cellular interactions were examined to demonstrate the binding and inhibitory effects of anti-thrombin aptamer. The results show that the aptamer is capable of inhibiting thrombin-mediated Fg conversion, thereby reducing sFn-mediated tumor cell adhesion in a concentration-dependent manner. Notably, the aptamer is able to bind thrombin under dynamic flow conditions and reduce tumor cell adhesive events at various physiological shear rates. This study further indicates that oligonucleotide aptamers hold great promise as therapeutic regulators of tumor cell adhesion, and consequently, metastatic activity.
Collapse
Affiliation(s)
- Erin R Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deborah Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Gregory Gydush
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheng Dong
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
57
|
Hsu CL, Lien CW, Wang CW, Harroun SG, Huang CC, Chang HT. Immobilization of aptamer-modified gold nanoparticles on BiOCl nanosheets: Tunable peroxidase-like activity by protein recognition. Biosens Bioelectron 2015; 75:181-7. [PMID: 26318787 DOI: 10.1016/j.bios.2015.08.049] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/11/2015] [Accepted: 08/21/2015] [Indexed: 11/28/2022]
Abstract
A self-assembled nanocomposite is prepared from an aqueous mixture of aptamer-modified gold nanoparticles (Apt-Au NPs), bismuth ions and chloride ions. The Apt-Au NPs are immobilized on bismuth oxychloride (BiOCl) nanosheets in situ to form Apt-Au NPs/BiOCl nanocomposites. The as-prepared nanocomposites exhibit high peroxidase-like activity for the catalytic conversion of Amplex Red (AR) to fluorescent resorufin in the presence of H2O2. The catalytic activity of Apt-Au NPs/BiOCl nanocomposites is at least 90-fold higher than that of Apt-Au NPs or BiOCl nanosheets, revealing synergistic effects on their activity. The catalytic activity of Apt-Au NPs/BiOCl nanocomposites is suppressed by vascular endothelial growth factor-A165 (VEGF-A165) molecules that specifically interact with the aptamer units (Del-5-1 and v7t-1) on the nanocomposite surface. The AR/H2O2-Apt-Au NPs/BiOCl nanocomposites probe shows high selectivity (>1000-fold over other proteins) and sensitivity (detection limit ~0.5nM) for the detection of VEGF-A165. Furthermore, the probe is employed for the detection of VEGF isoforms and for the study of interactions between VEGF and VEGF receptors. The practicality of this simple, rapid, cost-effective probe is validated by the analysis of VEGF-A165 in cell culture media, showing its great potential for the analysis of VEGF in biological samples.
Collapse
Affiliation(s)
- Chia-Lun Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Wen Lien
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Wei Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Scott G Harroun
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.
| |
Collapse
|
58
|
Fukaya T, Abe K, Savory N, Tsukakoshi K, Yoshida W, Ferri S, Sode K, Ikebukuro K. Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy. J Biotechnol 2015; 212:99-105. [PMID: 26302839 DOI: 10.1016/j.jbiotec.2015.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/25/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Abstract
Aptamers are mainly selected by in vitro selection using random nucleic acid libraries. These aptamers have often shown insufficient affinity for biomedical applications. We improved DNA aptamer binding affinity for vascular endothelial growth factor (VEGF) through in silico maturation (ISM) and aptamer multimerization. ISM is one of a number of evolutionary approaches and aptamer multimerization is one of several semi-rational strategies to improve function. We first reselected VEGF-binding aptamers using a partially randomized DNA library and identified two aptamers with higher binding ability than that of a known aptamer. We conducted ISM using the re-selected aptamers to optimize the key loop sequences created by a three-way junction structure. After five ISM rounds, we identified aptamer 2G19 [dissociation constant (Kd), 52 nM] as a local optimum of the defined search space. We characterized the aptamer and found that a specific stem-loop structure was involved in aptamer VEGF recognition. To further improve its affinity for VEGF, we multimerized 2G19 or its stem-loop structure. The designed SL5-trivalent aptamer (Kd, 0.37 nM) with three binding motifs significantly increased binding affinity, representing a 500-fold improvement from systematic evolution of ligands by exponential enrichment-selected aptamers.
Collapse
Affiliation(s)
- Takahiro Fukaya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koichi Abe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, Japan
| | - Stefano Ferri
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
| |
Collapse
|
59
|
Abstract
A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5’-end including the 5’-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer.
Collapse
|
60
|
Goda T, Higashi D, Matsumoto A, Hoshi T, Sawaguchi T, Miyahara Y. Dual aptamer-immobilized surfaces for improved affinity through multiple target binding in potentiometric thrombin biosensing. Biosens Bioelectron 2015; 73:174-180. [PMID: 26067329 DOI: 10.1016/j.bios.2015.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 11/26/2022]
Abstract
We developed a label-free and reagent-less potentiometric biosensor with improved affinity for thrombin. Two different oligomeric DNA aptamers that can recognize different epitopes in thrombin were introduced in parallel or serial manners on the sensing surface to capture the target via multiple contacts as found in many biological systems. The spacer and linker in the aptamer probes were optimized for exerting the best performance in molecular recognition. To gain the specificity of the sensor to the target, an antifouling molecule, sulfobeaine-3-undecanethiol (SB), was introduced on the sensor to form a self-assembled monolayer (SAM). Surface characterization revealed that the aptamer probe density was comparable to the distance of the two epitopes in thrombin, while the backfilling SB SAM was tightly aligned on the surface to resist nonspecific adsorption. The apparent binding parameters were obtained by thrombin sensing in potentiometry using the 1:1 Langmuir adsorption model, showing the improved dissociation constants (Kd) with the limit of detection of 5.5 nM on the dual aptamer-immobilized surfaces compared with single aptamer-immobilized ones. A fine control of spacer and linker length in the aptamer ligand was essential to realize the multivalent binding of thrombin on the sensor surface. The findings reported herein are effective for improving the sensitivity of potentiometric biosensor in an affordable way towards detection of tiny amount of biomolecules.
Collapse
Affiliation(s)
- Tatsuro Goda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan.
| | - Daiki Higashi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda, Tokyo 101-8308, Japan
| | - Akira Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Toru Hoshi
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda, Tokyo 101-8308, Japan
| | - Takashi Sawaguchi
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda, Tokyo 101-8308, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan.
| |
Collapse
|
61
|
Al-Kaidy H, Duwe A, Huster M, Muffler K, Schlegel C, Sieker T, Stadtmüller R, Tippkötter N, Ulber R. Biotechnology and Bioprocess Engineering - From the First Ullmann's Article to Recent Trends. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201500008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
62
|
Xie L, Cheng H, Qi H, Wang T, Zhao H, Huang G, Du Y. Nanostructural morphology master-regulated the cell capture efficiency of multivalent aptamers. RSC Adv 2015. [DOI: 10.1039/c5ra01919b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nanostructural features of stretched multivalent aptamers significantly improve the cell enrichment efficiency to about 16 fold higher than normal multivalent aptamers.
Collapse
Affiliation(s)
- Liping Xie
- College of Life and Health Science
- Northeastern University
- Shenyang 110819
- China
| | - Hao Cheng
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering
- Ministry of Education (Tianjin University)
- Tianjin
- China
- School of Chemical Engineering and Technology
| | - Tongzhou Wang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hui Zhao
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Guoliang Huang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Yanan Du
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| |
Collapse
|
63
|
Wang J, Ding K, Chen Y, Zhang L, Liu Z, Xue A, Gu W, Yang X, Li X, Huang J, Xing C, Cao Y, Chen M. Detection of thrombin with an aptamer-based macromolecule biosensor using bacterial ghost system. ACS Synth Biol 2014; 3:963-5. [PMID: 25524099 DOI: 10.1021/sb500018f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A rapid on-site detection of exogenous proteins without the need for equipped laboratories or skilled personnel would benefit many areas. We built a rapid protein detection platform based on aptamer-induced inner-membrane scaffolds dimerization by virtue of bacterial ghost system. When the detection platform was coincubated with two kinds of aptamers targeting two different sites of thrombin, green fluorescence or β-lactamase activity were yielded with two different designs. The latter was detected by commercially available testing strips.
Collapse
Affiliation(s)
- Jiasheng Wang
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ke Ding
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Yujie Chen
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Lifeng Zhang
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Zukai Liu
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Angli Xue
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Wenjia Gu
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xiaoyue Yang
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xihan Li
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jin Huang
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Congcong Xing
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Yunlong Cao
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ming Chen
- Zhejiang
University Team (ZJU-China) for the International Genetically
Engineered Machine Competition (iGEM), ‡College of Life Sciences, §School of Medicine, ∥Department of Chemical
and Biological Engineering, ⊥College of Agriculture and Biotechnology, #Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- College of Computer Science and Technology, ○Department of Physics, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
64
|
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
|
65
|
Liao J, Liu B, Liu J, Zhang J, Chen K, Liu H. Cell-specific aptamers and their conjugation with nanomaterials for targeted drug delivery. Expert Opin Drug Deliv 2014; 12:493-506. [PMID: 25430795 DOI: 10.1517/17425247.2015.966681] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Aptamers are short, single-stranded DNA or RNA sequences that can fold into complex secondary and tertiary structures and bind to various target molecules with high affinity and specificity. These properties, as well as rapid tissue penetration and ease of chemical modification, make aptamers ideal recognition elements for in vivo targeted drug delivery and attractive molecules for use in disease diagnosis and therapy. AREAS COVERED The general properties of aptamers as well as advantages over their counterpart antibodies are briefly discussed. Next, aptamer selection by cell- systematic evolution of ligands by exponential enrichment is described in detail. Finally, the review summarizes recent progress in the field of targeted drug delivery based on aptamers and their conjugation to liposomes, micelles and other nanomaterials. EXPERT OPINION Advances in nanotechnology have led to new and improved nanomaterials for biomedical applications. Conjugation of nanoparticles (NPs) with aptamers exploits both technologies, making aptamer-NP conjugates ideal agents for drug delivery with proven therapeutic effects and the reduction of toxicity to normal tissue. The use of multivalent aptamer-conjugated nanomaterials represents one of the new directions for drug development in the future; as such, continuing studies of these multivalent aptamers and bioconjugates should result in important clinical applications in targeted drug delivery.
Collapse
Affiliation(s)
- Jie Liao
- Central South University, Xiang Ya Hospital , Changsha , China
| | | | | | | | | | | |
Collapse
|
66
|
Al-Kaidy H, Duwe A, Huster M, Muffler K, Schlegel C, Sieker T, Stadtmüller R, Tippkötter N, Ulber R. Biotechnologie und Bioverfahrenstechnik - Vom ersten Ullmanns Artikel bis hin zu aktuellen Forschungsthemen. CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201400083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
67
|
Hünniger T, Wessels H, Fischer C, Paschke-Kratzin A, Fischer M. Just in time-selection: A rapid semiautomated SELEX of DNA aptamers using magnetic separation and BEAMing. Anal Chem 2014; 86:10940-7. [PMID: 25286022 DOI: 10.1021/ac503261b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A semiautomated two-step method for in vitro selection of DNA aptamers using magnetic separation and solid-phase emulsion polymerase chain reaction has been developed. The application of a magnetic separator allows the simultaneous processing of up to 12 SELEXs (systematic evolution of ligands by exponential enrichment) with different targets or buffer conditions. Using a magnetic separator and covalent target immobilization on magnetic beads, the selection process was simplified and the substeps of aptamer/target incubation, washing, and elution of the aptamers were merged into one automated procedure called "FISHing". Without further processing the resulting FISHing eluates are suitable for BEAMing (beads, emulsion, amplification, and magnetics), which includes the amplification by emPCR (emulsion polymerase chain reaction) and strand separation by the implementation of covalently immobilized reverse primers on magnetic beads. The novel selection process has been proved and validated by selecting and characterization of aptamers to the wine fining agent lysozyme.
Collapse
Affiliation(s)
- Tim Hünniger
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | | | | | | | | |
Collapse
|
68
|
Kang S, Hah SS. Improved ligand binding by antibody-aptamer pincers. Bioconjug Chem 2014; 25:1421-7. [PMID: 25010569 DOI: 10.1021/bc500269y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To increase the affinities of antibodies or aptamers for their targets, we designed antibody-aptamer pincers (AAPs) or heterodimers for thrombin or human epidermal growth factor 2 (HER2) as a model system. For this purpose, we first conjugated a 15-mer or 29-mer anti-thrombin aptamer, which are well-known to bind to thrombin in two specific epitopes, with an anti-thrombin antibody to enable each binding part of the AAP to simultaneously recognize a different part of the thrombin molecule. The AAP comprising a 15-mer aptamer and an anti-thrombin antibody has an apparent dissociation constant (Kd(app)) value of 567 pM, and this value is approximately 1/100 of that of the antibody alone or 1/35 of that of the aptamer monomer alone. The AAP comprising a 29-mer aptamer and an anti-thrombin antibody has a much lower Kd(app) value than that of 15-mer aptamer-conjugated antibody. Furthermore, this concept of the AAP system was employed to HER2-targeted drug delivery system (DDS) based on both antibody and drug-loaded aptamer. Anti-HER2 aptamer was conjugated with anti-HER2 antibody and loaded with doxorubicin, and the resulting AAP-HER2-Dox was found to have approximately 3- and 6-fold higher cytotoxicity than drug alone and antibody alone, respectively. Therefore, this novel AAP system constructed by conjugation of the antibody with the aptamer can effectively improve the affinities of the resulting AAPs for their target molecules and the drug-loaded AAP system can possibly serve as a platform for targeted DDS against many malignancies.
Collapse
Affiliation(s)
- Sungmuk Kang
- Department of Chemistry and Research Institute for Basic Sciences, Kyung Hee University , 1 Hoegi-dong Dongdaemun-gu, Seoul 131-701, South Korea
| | | |
Collapse
|
69
|
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
|
70
|
Billinge ER, Broom M, Platt M. Monitoring aptamer-protein interactions using tunable resistive pulse sensing. Anal Chem 2013; 86:1030-7. [PMID: 24380606 DOI: 10.1021/ac401764c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aptamers are short single-stranded pieces of DNA or RNA capable of binding to analytes with specificity and high affinity. Due to their comparable selectivity, stability, and cost, over the last two decades, aptamers have started to challenge antibodies in their use on many technology platforms. The binding event often leads to changes in the aptamer's secondary and tertiary structure; monitoring such changes has led to the creation of many new analytical sensors. Here, we demonstrate the use of a tunable resistive pulse sensing (TRPS) technology to monitor the interaction between several DNA aptamers and their target, thrombin. We immobilized the aptamers onto the surface of superparamagnetic beads, prior to their incubation with the thrombin protein. The protein binding to the aptamer caused a conformational change resulting in the shielding of the polyanion backbone; this was monitored by a change in the translocation time and pulse frequency of the particles traversing the pore. This signal was sensitive enough to allow the tagless detection of thrombin down to nanomolar levels. We further demonstrate the power of TRPS by performing real time detection and characterization of the aptamer-target interaction and measuring the association rates of the thrombin protein to the aptamer sequences.
Collapse
Affiliation(s)
- Emily R Billinge
- Department of Chemistry, Centre for Analytical Science, Loughborough University , Loughborough, Leicestershire LE11 3TU, United Kingdom
| | | | | |
Collapse
|
71
|
Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F. Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2403-11. [PMID: 24311581 DOI: 10.1107/s0907444913022269] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022]
Abstract
Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.
Collapse
Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, I-80126 Naples, Italy
| | | | | | | | | |
Collapse
|
72
|
Mairal T, Nadal P, Svobodova M, O'Sullivan CK. FRET-based dimeric aptamer probe for selective and sensitive Lup an 1 allergen detection. Biosens Bioelectron 2013; 54:207-10. [PMID: 24280051 DOI: 10.1016/j.bios.2013.10.070] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/14/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
Abstract
A sensitive method for the rapid and sensitive detection of the anaphylactic food allergen Lup an 1 (β-conglutin) exploiting fluorescence resonance energy transfer (FRET) has been developed. A high affinity dimeric form of a truncated 11-mer aptamer against β-conglutin was used, with each monomeric aptamer being flanked by donor/acceptor moieties. The dimeric form in the absence of target yields fluorescence emission due to the FRET from the excited fluorophore to the proximal second fluorophore. However, upon addition of β-conglutin, the specific interaction induces a change in the bi-aptameric structure resulting in an increase in fluorescence emission. The method is highly specific and sensitive, with a detection limit of 150 pM, providing an effective tool for the direct detection of the toxic β-conglutin subunit in foodstuffs in just 1 min at room temperature.
Collapse
Affiliation(s)
- T Mairal
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - P Nadal
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - M Svobodova
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain.
| | - C K O'Sullivan
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain; Institució Catalana de Recerca I Estudis Avancats, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| |
Collapse
|
73
|
Tan W, Donovan MJ, Jiang J. Aptamers from cell-based selection for bioanalytical applications. Chem Rev 2013; 113:2842-62. [PMID: 23509854 PMCID: PMC5519293 DOI: 10.1021/cr300468w] [Citation(s) in RCA: 469] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, People’s Republic of China
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Michael J. Donovan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, People’s Republic of China
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, People’s Republic of China
- Center For Research at Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
74
|
Bruno JG. A review of therapeutic aptamer conjugates with emphasis on new approaches. Pharmaceuticals (Basel) 2013; 6:340-57. [PMID: 24276022 PMCID: PMC3816688 DOI: 10.3390/ph6030340] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/09/2013] [Accepted: 03/11/2013] [Indexed: 12/14/2022] Open
Abstract
The potential to emulate or enhance antibodies with nucleic acid aptamers while lowering costs has prompted development of new aptamer-protein, siRNA, drug, and nanoparticle conjugates. Specific focal points of this review discuss DNA aptamers covalently bound at their 3' ends to various proteins for enhanced stability and greater pharmacokinetic lifetimes in vivo. The proteins can include Fc tails of IgG for opsonization, and the first component of complement (C1q) to trigger complement-mediated lysis of antibiotic-resistant Gram negative bacteria, cancer cells and possibly some parasites during vulnerable stages. In addition, the 3' protein adduct may be a biotoxin, enzyme, or may simply be human serum albumin (HSA) or a drug known to bind HSA, thereby retarding kidney and other organ clearance and inhibiting serum exonucleases. In this review, the author summarizes existing therapeutic aptamer conjugate categories and describes his patented concept for PCR-based amplification of double-stranded aptamers followed by covalent attachment of proteins or other agents to the chemically vulnerable overhanging 3' adenine added by Taq polymerase. PCR amplification of aptamers could dramatically lower the current $2,000/gram cost of parallel chemical oligonucleotide synthesis, thereby enabling mass production of aptamer-3'-protein or drug conjugates to better compete against expensive humanized monoclonal antibodies.
Collapse
Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 230, San Antonio, TX 78229, USA.
| |
Collapse
|
75
|
Kanakaraj I, Chen WH, Poongavanam M, Dhamane S, Stagg LJ, Ladbury JE, Kourentzi K, Strych U, Willson RC. Biophysical characterization of VEGF-aHt DNA aptamer interactions. Int J Biol Macromol 2013; 57:69-75. [PMID: 23470436 DOI: 10.1016/j.ijbiomac.2013.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 11/16/2022]
Abstract
The binding of the well-studied DNA aptamer aHt (5'-ATACCAGTCTATTCAATTGGGCCCGTCCGTAT GGTGGGTGTGCTGGCCAG-3'), which has been demonstrated to recognize human vascular endothelial growth factor (VEGF₁₆₅) to recombinant VEGF was characterized using fluorescence anisotropy, isothermal titration calorimetry and analytical ultracentrifugation. The negatively-charged DNA aptamer is selective for VEGF and does not recognize positively-charged hen egg lysozyme, or bovine serum albumin. In contrast to the VEGF association of the previously-described aV DNA aptamer, where the binding is enthalpically driven and sequence-specific, the binding of the aHt aptamer to VEGF is entropically-driven and not abolished by scrambling of the sequence.
Collapse
Affiliation(s)
- Indhu Kanakaraj
- Department of Biology and Biochemistry, University of Houston, TX, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
76
|
Janssen KPF, Knez K, Spasic D, Lammertyn J. Nucleic acids for ultra-sensitive protein detection. SENSORS (BASEL, SWITZERLAND) 2013; 13:1353-84. [PMID: 23337338 PMCID: PMC3574740 DOI: 10.3390/s130101353] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/26/2012] [Accepted: 12/28/2012] [Indexed: 12/13/2022]
Abstract
Major advancements in molecular biology and clinical diagnostics cannot be brought about strictly through the use of genomics based methods. Improved methods for protein detection and proteomic screening are an absolute necessity to complement to wealth of information offered by novel, high-throughput sequencing technologies. Only then will it be possible to advance insights into clinical processes and to characterize the importance of specific protein biomarkers for disease detection or the realization of "personalized medicine". Currently however, large-scale proteomic information is still not as easily obtained as its genomic counterpart, mainly because traditional antibody-based technologies struggle to meet the stringent sensitivity and throughput requirements that are required whereas mass-spectrometry based methods might be burdened by significant costs involved. However, recent years have seen the development of new biodetection strategies linking nucleic acids with existing antibody technology or replacing antibodies with oligonucleotide recognition elements altogether. These advancements have unlocked many new strategies to lower detection limits and dramatically increase throughput of protein detection assays. In this review, an overview of these new strategies will be given.
Collapse
Affiliation(s)
- Kris P. F. Janssen
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Karel Knez
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Dragana Spasic
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| | - Jeroen Lammertyn
- MeBioS Biosensor Group, Faculteit Bio-Ingenieurswetenschappen, KU Leuven, Willem De Croylaan, Leuven, Belgium; E-Mails: (K.P.F.J.); (K.K.); (D.S.)
| |
Collapse
|
77
|
Nonaka Y, Yoshida W, Abe K, Ferri S, Schulze H, Bachmann TT, Ikebukuro K. Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system. Anal Chem 2012; 85:1132-7. [PMID: 23237717 DOI: 10.1021/ac303023d] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is an efficient method to identify aptamers; however, it sometimes fails to identify aptamers that bind to their target with high affinity. Thus, post-SELEX optimization of aptamers is required to improve aptamer binding affinity. We developed in silico maturation based on a genetic algorithm (1) as an efficient mutagenesis method to improve aptamer binding affinity. In silico maturation was performed to improve a VEGF-binding DNA aptamer (VEap121). The VEap121 aptamer is considered to fold into a G-quadruplex structure and this structure may be important for VEGF recognition. Using in silico maturation, VEap121 was mutated with the exception of the guanine tracts that are considered to form the G-quartet. As a result, four aptamers were obtained that showed higher affinity compared with VEap121. The dissociation constant (K(d)) of the most improved aptamer (3R02) was 300 pM. The affinity of 3R02 was 16-fold higher than that of VEap121. Moreover, a bivalent aptamer was constructed by connecting two identical 3R02s through a 10-mer thymine linker for further improvement of affinity. The bivalent aptamer (3R02 Bivalent) bound to VEGF with a K(d) value of 30 pM. Finally, by constructing a VEGF-detection system using a VEGF antibody as the capture molecule and monovalent 3R02 as the detection molecule, a more sensitive assay was developed compared with the system using VEap121. These results indicate that in silico maturation could be an efficient method to improve aptamer affinity for construction of sensitive detection systems.
Collapse
Affiliation(s)
- Yoshihiko Nonaka
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | | | | | | | | | | | | |
Collapse
|
78
|
Le TT, Scott S, Cass AEG. Streptavidin binding bifunctional aptamers and their interaction with low molecular weight ligands. Anal Chim Acta 2012; 761:143-8. [PMID: 23312325 DOI: 10.1016/j.aca.2012.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/04/2012] [Accepted: 11/09/2012] [Indexed: 02/07/2023]
Abstract
This paper describes the measurement of the binding affinities of two bifunctional RNA aptamers to their respective ligands. The aptamers comprise either a theophylline or malachite green binding sequence fused to a streptavidin binding sequence. These bifunctional aptamers are shown to bind simultaneously to both the small ligand and to streptavidin whether in free solution or on gold surfaces. Binding isotherms for both interactions were measured by different physiochemical techniques: surface plasmon resonance, fluorescence spectroscopy and dynamic light scattering. Both qualitatively and quantitatively there is little difference in binding affinities between the bifunctional aptamers and their monofunctional components. The respective K(d) values for streptavidin binding in the monofunctional aptamer and in the theophylline bifunctional aptamer were 12 nM and 65 nM, respectively whilst the K(d) values for theophylline binding in the monofunctional aptamer and the streptavidin bifunctional aptamer were 300 nM and 120 nM. These results are consistent with treating each aptamer sequence as a module that can be combined with others without significant loss of function. This allows for the use of streptavidin based immobilization strategies without either the cost of biotinylated dNTPs or the variable yields associated with the chemical biotinylation of RNA.
Collapse
Affiliation(s)
- Thao T Le
- Department of Chemistry, Imperial College London, SW7 2AZ, UK
| | | | | |
Collapse
|
79
|
Ahmad KM, Xiao Y, Soh HT. Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution. Nucleic Acids Res 2012; 40:11777-83. [PMID: 23042245 PMCID: PMC3526301 DOI: 10.1093/nar/gks899] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (Kd) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.
Collapse
Affiliation(s)
- Kareem M Ahmad
- Interdepartmental Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 91306, USA
| | | | | |
Collapse
|
80
|
Liao YJ, Shiang YC, Huang CC, Chang HT. Molecularly imprinted aptamers of gold nanoparticles for the enzymatic inhibition and detection of thrombin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8944-8951. [PMID: 22300379 DOI: 10.1021/la204651t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We prepared thrombin-binding aptamer-conjugated gold nanoparticles (TBA-Au NPs) through a molecularly imprinted (MP) approach, which provide highly efficient inhibition activity toward the polymerization of fibrinogen. Au NPs (diameter, 13 nm), 15-mer thrombin-binding aptamer (TBA(15)) with different thymidine linkers, and 29-mer thrombin-binding aptamer (TBA(29)) with different thymidine linkers (Tn) in the presence of thrombin (Thr) as a template were used to prepare MP-Thr-TBA(15)/TBA(29)-Tn-Au NPs. Thrombin molecules were then removed from Au NPs surfaces by treating with 100 mM Tris-NaOH (pH ca. 13.0) to form MP-TBA(15)/TBA(29)-Tn-Au NPs. The length of the thymidine linkers and TBA density on Au NPs surfaces have strong impact on the orientation, flexibility, and stability of MP-TBA(15)/TBA(29)-Tn-Au NPs, leading to their stronger binding strength with thrombin. MP-TBA(15)/TBA(29)-T(15)-Au NPs (ca. 42 TBA(15) and 42 TBA(29) molecules per Au NP; 15-mer thymidine on aptamer terminal) provided the highest binding affinity toward thrombin with a dissociation constant of 5.2 × 10(-11) M. As a result, they had 8 times higher anticoagulant (inhibitory) potency relative to TBA(15)/TBA(29)-T(15)-Au NPs (prepared in the absence of thrombin). We further conducted thrombin clotting time (TCT) measurements in plasma samples and found that MP-TBA(15)/TBA(29)-T(15)-Au NPs had greater anticoagulation activity relative to four commercial drugs (heparin, argatroban, hirudin, and warfarin). In addition, we demonstrated that thrombin induced the formation of aggregates from MP-TBA(15)-T(15)-Au NPs and MP-TBA(29)-T(15)-Au NPs, thereby allowing the colorimetric detection of thrombin at the nanomolar level in serum samples. Our result demonstrates that our simple molecularly imprinted approach can be applied for preparing various functional nanomaterials to control enzyme activity and targeting important proteins.
Collapse
Affiliation(s)
- Yu-Ju Liao
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | | | | | | |
Collapse
|
81
|
DNA aptamer configuration affects the sensitivity and binding kinetics of thrombin. ACTA CHIMICA SLOVACA 2012. [DOI: 10.2478/v10188-012-0009-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA aptamer configuration affects the sensitivity and binding kinetics of thrombinThrombin is serine protease involved in the coagulation cascade, which converts soluble fibrinogen into insoluble strands of fibrin - a matrix of the blood clot formation. Development of the sensitive method of the thrombin detection in nanomolar level is important for clinical practice. In this work we applied acoustic thickness shear mode method (TSM) for study the binding of human thrombin depending on DNA aptamer configuration. We compared sensitivity of detection and binding kinetics of the thrombin to the conventional DNA aptamers and aptamer dimers immobilized at the surface of quartz crystal transducer. We have shown that aptasensors based on aptamer dimers more sensitively detect thrombin. The aptamer-thrombin complexes were also more stable as revealed from equilibrium dissociation constant,KD, that was 4 times lower for aptamer dimers in comparison with conventional aptamers. Determination of motional resistance,Rm, from acoustic impedance analysis allowed us to find important differences in physico-chemical properties of layers formed by conventional aptamers and aptamer dimers.
Collapse
|
82
|
Mayer G, Rohrbach F, Pötzsch B, Müller J. Aptamer-based modulation of blood coagulation. Hamostaseologie 2012; 31:258-63. [PMID: 22065102 DOI: 10.5482/ha-1156] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/06/2011] [Indexed: 11/05/2022] Open
Abstract
Nucleic acid based aptamers are single-stranded oligonucleotide ligands isolated from random libraries by an in-vitro selection procedure. Through the formation of unique three-dimensional structures, aptamers are able to selectively interact with a variety of target molecules and are therefore also promising candidates for the development of anticoagulant drugs. While thrombin represents the most prominent enzymatic target in this field, also aptamers directed against other coagulation proteins and proteases have been identified with some currently being tested in clinical trials. In this review, we summarize recent developments in the design and evaluation of aptamers for anticoagulant therapy and research.
Collapse
Affiliation(s)
- G Mayer
- University of Bonn, Life & Medical Sciences Institute, Bonn, Germany.
| | | | | | | |
Collapse
|
83
|
De Rache A, Kejnovská I, Vorlíčková M, Buess-Herman C. Elongated thrombin binding aptamer: a G-quadruplex cation-sensitive conformational switch. Chemistry 2012; 18:4392-400. [PMID: 22362492 DOI: 10.1002/chem.201103381] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 11/08/2022]
Abstract
Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5' end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba(2+), Ca(2+), K(+), Mg(2+), Na(+), NH(4)(+), Sr(2+) and the [Ru(NH(3))(6)](2+/3+) redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH(3))(6)](3+), which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K(+) reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.
Collapse
Affiliation(s)
- Aurore De Rache
- Université Libre de Bruxelles, Faculté des Sciences, Service de Chimie Analytique et Chimie des Interfaces, CP 255, Boulevard du Triomphe 2, 1050 Bruxelles, Belgium
| | | | | | | |
Collapse
|
84
|
Kaur H, Yung LYL. Probing high affinity sequences of DNA aptamer against VEGF165. PLoS One 2012; 7:e31196. [PMID: 22359573 PMCID: PMC3281051 DOI: 10.1371/journal.pone.0031196] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 01/03/2012] [Indexed: 11/19/2022] Open
Abstract
Vascular endothelial growth factor (VEGF165) is a potent angiogenic mitogen commonly overexpressed in cancerous cells. It contains two main binding domains, the receptor-binding domain (RBD) and the heparin-binding domain (HBD). This study attempted to identify the specific sequences of the VEa5 DNA aptamer that exhibit high binding affinity towards the VEGF165 protein by truncating the original VEa5 aptamer into different segments. Using surface plasmon resonance (SPR) spectroscopy for binding affinity analysis, one of the truncated aptamers showed a >200-fold increase in the binding affinity for HBD. This truncated aptamer also exhibited high specificity to HBD with negligible binding affinity for VEGF121, an isoform of VEGF lacking HBD. Exposing colorectal cancer cells to the truncated aptamer sequence further confirmed the binding affinity and specificity of the aptamer to the target VEGF165 protein. Hence, our approach of aptamer truncation can potentially be useful in identifying high affinity aptamer sequences for the biological molecules and targeting them as antagonist for cancer cell detection.
Collapse
Affiliation(s)
- Harleen Kaur
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
85
|
Rotem D, Jayasinghe L, Salichou M, Bayley H. Protein detection by nanopores equipped with aptamers. J Am Chem Soc 2012; 134:2781-7. [PMID: 22229655 PMCID: PMC3278221 DOI: 10.1021/ja2105653] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Protein nanopores have been used as stochastic sensors
for the
detection of analytes that range from small molecules to proteins.
In this approach, individual analyte molecules modulate the ionic
current flowing through a single nanopore. Here, a new type of stochastic
sensor based on an αHL pore modified with an aptamer is described.
The aptamer is bound to the pore by hybridization to an oligonucleotide
that is attached covalently through a disulfide bond to a single cysteine
residue near a mouth of the pore. We show that the binding of thrombin
to a 15-mer DNA aptamer, which forms a cation-stabilized quadruplex,
alters the ionic current through the pore. The approach allows the
quantification of nanomolar concentrations of thrombin, and provides
association and dissociation rate constants and equilibrium dissociation
constants for thrombin·aptamer interactions. Aptamer-based nanopores
have the potential to be integrated into arrays for the parallel detection
of multiple analytes.
Collapse
Affiliation(s)
- Dvir Rotem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | | | | | | |
Collapse
|
86
|
Kwon MJ, Lee J, Wark AW, Lee HJ. Nanoparticle-Enhanced Surface Plasmon Resonance Detection of Proteins at Attomolar Concentrations: Comparing Different Nanoparticle Shapes and Sizes. Anal Chem 2012; 84:1702-7. [DOI: 10.1021/ac202957h] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Min Jeong Kwon
- Department
of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu,
Daegu-city, 702-701, Republic of Korea
| | - Jaeyoung Lee
- Ertl Center for Electrochemistry and Catalysis/RISE & School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Alastair W. Wark
- Centre
for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow,
U.K. G1 1XL
| | - Hye Jin Lee
- Department
of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu,
Daegu-city, 702-701, Republic of Korea
| |
Collapse
|
87
|
Neundlinger I, Poturnayova A, Karpisova I, Rankl C, Hinterdorfer P, Snejdarkova M, Hianik T, Ebner A. Characterization of enhanced monovalent and bivalent thrombin DNA aptamer binding using single molecule force spectroscopy. Biophys J 2012; 101:1781-7. [PMID: 21961605 DOI: 10.1016/j.bpj.2011.07.054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/27/2011] [Accepted: 07/28/2011] [Indexed: 11/15/2022] Open
Abstract
Thrombin aptamer binding strength and stability is dependent on sterical parameters when used for atomic force microscopy sensing applications. Sterical improvements on the linker chemistry were developed for high-affinity binding. For this we applied single molecule force spectroscopy using two enhanced biotinylated thrombin aptamers, BFF and BFA immobilized on the atomic force microscopy tip via streptavidin. BFF is a dimer composed of two single-stranded aptamers (aptabody) connected to each other by a complementary sequence close to the biotinylated end. In contrast, BFA consists of a single DNA strand and a complementary strand in the supporting biotinylated part. By varying the pulling velocity in force-distance cycles the formed thrombin-aptamer complexes were ruptured at different force loadings allowing determination of the energy landscape. As a result, BFA aptamer showed a higher binding force at the investigated loading rates and a significantly lower dissociation rate constant, k(off), compared to BFF. Moreover, the potential of the aptabody BFF to form a bivalent complex could clearly be demonstrated.
Collapse
|
88
|
NONAKA Y, ABE K, IKEBUKURO K. Electrochemical Detection of Vascular Endothelial Growth Factor with Aptamer Sandwich. ELECTROCHEMISTRY 2012. [DOI: 10.5796/electrochemistry.80.363] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
89
|
Hsu CL, Wei SC, Jian JW, Chang HT, Chen WH, Huang CC. Highly flexible and stable aptamer-caged nanoparticles for control of thrombin activity. RSC Adv 2012. [DOI: 10.1039/c1ra00344e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
90
|
ABE K, HASEGAWA H, IKEBUKURO K. Electrochemical Detection of Vascular Endothelial Growth Factor by an Aptamer-Based Bound/Free Separation System. ELECTROCHEMISTRY 2012. [DOI: 10.5796/electrochemistry.80.348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
91
|
Srinivas RL, Chapin SC, Doyle PS. Aptamer-functionalized microgel particles for protein detection. Anal Chem 2011; 83:9138-45. [PMID: 22017663 DOI: 10.1021/ac202335u] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly sensitive and multiplexed detection of clinically relevant proteins in biologically complex samples is crucial for the advancement of clinical proteomics. In recent years, aptamers have emerged as useful tools for protein analysis due to their specificity and affinity for protein targets as well as their compatibility with particle-based detection systems. In this study, we demonstrate the highly sensitive detection of human α-thrombin on encoded hydrogel microparticles functionalized with an aptamer capture sequence. We use static imaging and microfluidic flow-through analysis techniques to evaluate the detection capabilities of the microgels in sandwich-assay formats that utilize both aptamers and antibodies for the reporting of target-binding events. Buffers and reagent concentrations were optimized to provide maximum reaction efficiency while still maintaining an assay with a simple workflow that can be easily adapted to the multiplexed detection of other clinically relevant proteins. The three-dimensional, nonfouling hydrogel immobilization scaffold used in this work provides three logs of dynamic range, with a limit of detection of 4 pM using a single aptamer capture species and without the need for spacers or signal amplification.
Collapse
Affiliation(s)
- Rathi L Srinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | |
Collapse
|
92
|
Goji S, Matsui J. Direct detection of thrombin binding to 8-bromodeoxyguanosine-modified aptamer: effects of modification on affinity and kinetics. J Nucleic Acids 2011; 2011:316079. [PMID: 21941628 PMCID: PMC3175402 DOI: 10.4061/2011/316079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 07/15/2011] [Accepted: 07/21/2011] [Indexed: 11/20/2022] Open
Abstract
The affinity of an 8-bromodeoxyguanosine- (8-BrdG-) substituted thrombin-binding aptamer (TBA-Br), which has the 1st and 10th guanosine residues replaced with 8-BrdG, was estimated using reflectometric interference spectroscopy (RIfS). When comparing TBA-Br with unmodified TBA (TBA-H), it was demonstrated that the modification effectively improved the affinity of TBA; dissociation constants (KD) of TBA-H and TBA-Br were 45.4 nM and 1.99 nM, respectively. These values, which were obtained by direct observation of thrombin binding using RIfS, have the same order of magnitude as those obtained in our previous study utilizing conformational changes in TBA to detect thrombin binding, thus confirming the validity of the obtained KD values. RIfS measurements also revealed that the 8-BrdG modification resulted in a lower dissociation rate constant (kd), which suggests that the enhancement of affinity can be attributed to the stabilization of the G-quadruplex structure on introduction of 8-BrdG.
Collapse
Affiliation(s)
- Shou Goji
- Department of Nanobiochemistry, FIRST, Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | | |
Collapse
|
93
|
Hsu CL, Chang HT, Chen CT, Wei SC, Shiang YC, Huang CC. Highly efficient control of thrombin activity by multivalent nanoparticles. Chemistry 2011; 17:10994-1000. [PMID: 21850727 DOI: 10.1002/chem.201101081] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Indexed: 11/08/2022]
Abstract
We have demonstrated that the incorporation of sulfated galactose acid (sulf-Gal) into thrombin-binding-aptamer (TBA)-conjugated gold nanoparticles (TBA-AuNPs) enables highly effective inhibition of thrombin activity toward fibrinogen. AuNP bioconjugates (TBA(15)/TBA(29)/sulf-Gal-AuNPs) were prepared from 13 nm AuNPs, 15-mer thrombin-binding aptamer (TBA(15)), 29-mer thrombin-binding aptamer (TBA(29)), and sulf-Gal. The numbers of TBA and sulf-Gal molecules per AuNP proved to have a strong impact on inhibitory potency. The best results were observed for 15-TBA(15)/TBA(29)/sulf-Gal-AuNPs (with 15 TBA(15) and 15 TBA(29) molecules per AuNP), which, because of their particularly flexible conformation and multivalency, exhibited ultrahigh binding affinity toward thrombin (K(d)=3.4×10(-12) M) and thus extremely high anticoagulant (inhibitory) potency. Compared to the case without inhibitors (the "normal" value), their measured thrombin clotting time (TCT) was 91 times longer, whereas for TBA(15) alone it was only 7.2 times longer. Their anticoagulant activity was suppressed by TBA-complementary-sequence (cTBA)-modified AuNPs (cTBA(15)/cTBA(29)-AuNPs) at a rate that was 20 times faster than that of free cTBA(15)/cTBA(29). Thus, easily prepared, low-cost, multivalent AuNPs show great potential for biomedical control of blood clotting.
Collapse
Affiliation(s)
- Chia-Lun Hsu
- Institute of Bioscience and Biotechnology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, 2, Beining Road, Keelung, 20224, Taiwan
| | | | | | | | | | | |
Collapse
|
94
|
Shiang YC, Hsu CL, Huang CC, Chang HT. Gold Nanoparticles Presenting Hybridized Self-Assembled Aptamers That Exhibit Enhanced Inhibition of Thrombin. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101718] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
95
|
Shiang YC, Hsu CL, Huang CC, Chang HT. Gold nanoparticles presenting hybridized self-assembled aptamers that exhibit enhanced inhibition of thrombin. Angew Chem Int Ed Engl 2011; 50:7660-5. [PMID: 21717538 DOI: 10.1002/anie.201101718] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Yen-Chun Shiang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | | | | | | |
Collapse
|
96
|
Diculescu VC, Chiorcea-Paquim AM, Eritja R, Oliveira-Brett AM. Evaluation of the structure–activity relationship of thrombin with thrombin binding aptamers by voltammetry and atomic force microscopy. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2010.11.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
97
|
Rakhmetova SY, Radko SP, Gnedenko OV, Bodoev NV, Ivanov AS, Archakov AI. Comparative thermodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2011. [DOI: 10.1134/s1990750811020144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
98
|
Poniková S, Tlučková K, Antalík M, Víglaský V, Hianik T. The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers. Biophys Chem 2011; 155:29-35. [PMID: 21396765 DOI: 10.1016/j.bpc.2011.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/04/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
Abstract
We have applied circular dichroism (CD), temperature-gradient gel electrophoresis (TGGE) and differential scanning calorimetry (DSC) to study the properties of novel bioengineered DNA aptamer dimers sensitive to fibrinogen (F) and heparin (H) binding sites of thrombin and compared them with canonical single stranded aptamer sensitive to fibrinogen binding site of thrombin (Fibri). The homodimer (FF) and heterodimer (FH) aptamers were constructed based on hybridization of their supported parts. CD results showed that both FF and FH dimers form stable guanine quadruplexes in the presence of potassium ions like those in Fibri. The thermal stability of aptamer dimers was slightly lower compared to those of canonical aptamers, but sufficient for practical applications. Both FF and FH aptamer dimers exhibited a potassium-dependent inhibitory effect on thrombin-mediated fibrin gel formation, which was on average two-fold higher than those of canonical single stranded Fibri aptamers.
Collapse
Affiliation(s)
- Slavomíra Poniková
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, 84248 Bratislava, Slovakia
| | | | | | | | | |
Collapse
|
99
|
Chen CK, Shiang YC, Huang CC, Chang HT. Using self-assembled aptamers and fibrinogen-conjugated gold nanoparticles to detect DNA based on controlled thrombin activity. Biosens Bioelectron 2011; 26:3464-8. [PMID: 21324664 DOI: 10.1016/j.bios.2011.01.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/11/2011] [Accepted: 01/18/2011] [Indexed: 02/03/2023]
Abstract
We have developed a colorimetric probe, based on the aggregation of gold nanoparticles (Au NPs), for the detection of DNA and for the analysis of single-nucleotide polymorphism (SNP); this probe functions through the modulation of the activity of thrombin (Thr) in the presence of bivalent thrombin-binding aptamers (TBAs). The bivalent TBAs were formed from TBA(27') (comprising a 27-base sequence providing TBA(27) functionality, a T(5) linker, and an 11-base sequence for hybridization) and TBA(15') (comprising a 15-base sequence providing TBA(15) functionality, a T(5) linker, and a 12-base sequence for hybridization) through their hybridization with perfectly matched DNA (DNA(pm)). The bivalent TBAs interacted specifically with thrombin, suppressing its activity toward fibrinogen-modified Au NPs (Fib-Au NPs). The potency of the inhibitory effect of TBA(15')-TBA(27')/DNA(pm) toward thrombin - and, thus, the degree of aggregation of the Fib-Au NPs - was highly dependent on the concentration of DNA(pm). Under the optimal conditions (50 pM thrombin, 2 nM TBA(15'), 2 nM TBA(27'), and 38 pM Fib-Au NPs), the linear relationship of the response of the probe toward DNA(pm) extended from 0.1 to 2 nM, with a correlation coefficient of 0.97. The limit of detection (LOD) for DNA(pm) was 20 pM, based on a signal-to-noise ratio of 3. We also applied a corresponding TBA(15″)-TBA(27″)/Thr/Fib-Au NP probe to the detection of the SNP of the Arg249Ser unit in the TP53 gene, with an LOD of 32 pM. Relative to conventional molecular beacon-based and crosslinking aggregation-based Au NP probes, our new approach offers higher sensitivity and higher selectivity toward DNA.
Collapse
Affiliation(s)
- Chuan-Kuo Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | | | | |
Collapse
|
100
|
Lee RJ, Wu JS, Juang RH, Wu YJ, Lin CY, Wu SY, Huang PR, Chu CH, Chin LT, Chen HM. Increasing hybridoma viability and antibody repertoire after the cell fusion by the use of human plasma as an alternative supplement. J Immunol Methods 2010; 361:89-97. [DOI: 10.1016/j.jim.2010.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 08/06/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
|