251
|
Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | | | | |
Collapse
|
252
|
Ali M, Li Y. Colorimetric Sensing by Using Allosteric-DNAzyme-Coupled Rolling Circle Amplification and a Peptide Nucleic Acid-Organic Dye Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805966] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
253
|
Xie S, Walton SP. Application and analysis of structure-switching aptamers for small molecule quantification. Anal Chim Acta 2009; 638:213-9. [PMID: 19327463 PMCID: PMC2746094 DOI: 10.1016/j.aca.2009.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 12/16/2008] [Accepted: 02/12/2009] [Indexed: 02/05/2023]
Abstract
Modern tools for the analysis of cellular function aim for the quantitative measurement of all members of a given class of biological molecules. Of the analyte classes, nucleic acid measurements are typically the most tractable, both on an individual analyte basis and in parallel. Thus, tools are being sought to enable measurement of other cellular molecules using nucleic acid biosensors. Of the variety of potential nucleic acid biosensor strategies, structure-switching aptamers (SSAs) present a unique opportunity to couple sensing and readout of the target molecule. However, little has been characterized about the parameters that determine the fidelity of the signal from SSA biosensors. In this study, a small molecule biosensor based on a SSA was engineered to detect the model small molecule, theophylline, in solution. Quantitative theophylline detection over nearly three orders-of-magnitude was achieved by scintillation counting and quantitative PCR. Further analysis showed that the biosensor fidelity is primarily controlled by the relative stability of the two conformations of the SSA.
Collapse
Affiliation(s)
- Shengnan Xie
- Applied Biomolecular Engineering Laboratory of the Cellular and Biomolecular Laboratory, Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI, 48824, USA
| | - S. Patrick Walton
- Applied Biomolecular Engineering Laboratory of the Cellular and Biomolecular Laboratory, Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
254
|
Nakamura I, Shi AC, Nutiu R, Yu JMY, Li Y. Kinetics of signaling-DNA-aptamer-ATP binding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:031906. [PMID: 19391970 DOI: 10.1103/physreve.79.031906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 01/16/2009] [Indexed: 05/27/2023]
Abstract
DNA aptamers are molecular biosensors consisting of single functionalized DNA molecules, which can bind to specific targets or complementary DNA sequences. The binding kinetics of DNA aptamers is studied by fluorescence quenching at 23 degrees C . A kinetic model for the binding reaction of DNA aptamer, antisense DNA, and ATP target is developed to describe experimental observations. The approach leads to a simple procedure to deduce relevant kinetic reactions and their rate constants. A comparison between theory and experiments indicates that the previously established bimolecular DNA-ATP binding does not provide a complete description of the experimental data. Side reactions such as trimolecular complexation are proposed. Rate constants of the model are determined by comparing the model predictions and experiments. Good agreements between the model and experiments have been obtained. Possible blocking reactions by the misfolded DNA aptamer are also discussed.
Collapse
Affiliation(s)
- Issei Nakamura
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8.
| | | | | | | | | |
Collapse
|
255
|
Deng C, Chen J, Nie Z, Wang M, Chu X, Chen X, Xiao X, Lei C, Yao S. Impedimetric aptasensor with femtomolar sensitivity based on the enlargement of surface-charged gold nanoparticles. Anal Chem 2009; 81:739-45. [PMID: 19072036 DOI: 10.1021/ac800958a] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple and ultrasensitive label-free electrochemical impedimetric aptasensor for thrombin based on the cascaded signal amplification was reported. The sandwich system of aptamer/thrombin/aptamer-functionalized Au nanoparticles (Apt-AuNPs) was fabricated as the sensing platform. The change of the interfacial feature of the electrode was characterized by electrochemical impedance analysis with the redox probe [Fe(CN)(6)](3-/4-). For improving detection sensitivity, the three-level cascaded impedimetric signal amplification was developed: (1) Apt-AuNPs as the first-level signal enhancer; (2) the steric-hindrance between the enlarged Apt-AuNPs as the second-level signal amplification; (3) the electrostatic-repulsion between sodium dodecylsulfate (SDS) stabilized Apt-AuNPs and the redox probe [Fe(CN)(6)](3-/4-) as the third-level signal amplification. Enlargement of Apt-AuNPs integrated with negatively charged surfactant (SDS) capping could not only improve the detection sensitivity of the impedimetric aptasensor for thrombin but also present a simple and general signal-amplification model for impedimetric sensor. The aptasensor based on the enlargement of negatively charged Apt-AuNPs showed an increased response of the electron-transfer resistance to the increase of thrombin concentration through a wide detection range from 100 fM to 100 nM. The linear detection range was 0.05-35 nM, and thrombin was easily detectable to a concentration of 100 fM. The aptasensor also has good selectivity and reproducibility.
Collapse
Affiliation(s)
- Chunyan Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | | | | | | | | | | | | | | | | |
Collapse
|
256
|
Higuchi A, Yang ST, Siao YD, Hsieh PV, Fukushima H, Chang Y, Chen WY. Preparation of fractioned DNA aptamer–Pt complex through ultrafiltration and the colorimetric sensing of thrombin. J Memb Sci 2009. [DOI: 10.1016/j.memsci.2008.11.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
257
|
Bai J, Wei H, Li B, Song L, Fang L, Lv Z, Zhou W, Wang E. [Ru(bpy)2(dcbpy)NHS] labeling/aptamer-based biosensor for the detection of lysozyme by increasing sensitivity with gold nanoparticle amplification. Chem Asian J 2009; 3:1935-41. [PMID: 18767101 DOI: 10.1002/asia.200800104] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel [Ru(bpy)(2)(dcbpy)NHS] labeling/aptamer-based biosensor combined with gold nanoparticle amplification for the determination of lysozyme with an electrochemiluminescence (ECL) method is presented. In this work, an aptamer, an ECL probe, gold nanoparticle amplification, and competition assay are the main protocols employed in ECL detection. With all the protocols used, an original biosensor coupled with an aptamer and [Ru(bpy)(2)(dcbpy)NHS] has been prepared. Its high selectivity and sensitivity are the main advantages over other traditional [Ru(bpy)(3)](2+) biosensors. The electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) characterization illustrate that this biosensor is fabricated successfully. Finally, the biosensor was applied to a displacement assay in different concentrations of lysozyme solution, and an ultrasensitive ECL signal was obtained. The ECL intensity decreased proportionally to the lysozyme concentration over the range 1.0x10(-13)-1.0x10(-8) mol L(-1) with a detection limit of 1.0x10(-13) mol L(-1). This strategy for the aptasensor opens a rapid, selective, and sensitive route for the detection of lysozyme and potentially other proteins.
Collapse
Affiliation(s)
- Jianguo Bai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | | | | | | | | | | | | | | |
Collapse
|
258
|
Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:241-64. [PMID: 20636061 DOI: 10.1146/annurev.anchem.1.031207.112851] [Citation(s) in RCA: 580] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.
Collapse
Affiliation(s)
- Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA.
| | | | | |
Collapse
|
259
|
Mutational analysis of a signaling aptamer suggests a mechanism for ligand-triggered structure-switching. Biochem Biophys Res Commun 2008; 378:51-6. [PMID: 19010303 DOI: 10.1016/j.bbrc.2008.10.180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 10/30/2008] [Indexed: 01/12/2023]
Abstract
Structure-switching signaling aptamers are nucleic acids that change shape upon binding to a specific ligand. Previously, we applied a new in vitro selection strategy to isolate structure-switching RNA aptamers responsive to the aminoglycoside antibiotic tobramycin. Here, we report the results of mutational analysis, secondary structure modeling, and ligand-specificity studies that suggest a mechanism for tobramycin-triggered structure switching.
Collapse
|
260
|
Lu Y, Liu J. Catalyst‐functionalized nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2008; 1:35-46. [DOI: 10.1002/wnan.21] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana, Champaign, IL, USA
| | - Juewen Liu
- Department of Chemistry, University of Illinois at Urbana, Champaign, IL, USA
| |
Collapse
|
261
|
Hasegawa T, Hagihara M, Fukuda M, Nakano S, Fujieda N, Morii T. Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide. J Am Chem Soc 2008; 130:8804-12. [PMID: 18597435 DOI: 10.1021/ja801734f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.
Collapse
Affiliation(s)
- Tetsuya Hasegawa
- Institute of Advanced Energy, Institute of Sustainability Science, and Pioneering Research Unit for Next Generation, Kyoto University, Uji, Kyoto 611-0011, Japan
| | | | | | | | | | | |
Collapse
|
262
|
Raddatz MSL, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed Engl 2008; 47:5190-3. [PMID: 18512861 DOI: 10.1002/anie.200800216] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marie-Sophie L Raddatz
- Life and Medical Science, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | | | | | | | | | | |
Collapse
|
263
|
Raddatz M, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of Cell‐Targeting and Population‐Specific Aptamers by Fluorescence‐Activated Cell Sorting. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800216] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
264
|
Du Y, Li B, Wei H, Wang Y, Wang E. Multifunctional label-free electrochemical biosensor based on an integrated aptamer. Anal Chem 2008; 80:5110-7. [PMID: 18522435 DOI: 10.1021/ac800303c] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aptamers, which are in vitro selected functional oligonucleotides, have been employed to design novel biosensors (i.e., aptasensors) due to their inherent selectivity, affinity, and their multifarious advantages over traditional recognition elements. In this work, we reported a multifunctional reusable label-free electrochemical biosensor based on an integrated aptamer for parallel detection of adenosine triphosphate (ATP) and alpha-thrombin, by using electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). A Au electrode as the sensing surface was modified with a part DNA duplex which contained a 5'-thiolated partly complementary strand (PCS) and a mixed aptamer (MBA). The unimolecular MBA contained small-molecule ATP binding aptamer (ABA) and also protein alpha-thrombin binding aptamer (TBA). Thus, the aptasensor could be used for detection of ATP and alpha-thrombin both. The detection limit of ATP was 1 x 10(-8) M, and its detection range could extend up to 10(-4) M, whereas the detection limit of alpha-thrombin was 1 x 10(-11) M, and its detection range was from 1 x 10(-11) to 1 x 10(-7) M. Meanwhile, after detecting alpha-thrombin, the sensing interface could be used for ATP recognition as well. The aptasensor regeneration could be realized by rehybridizing of the MBA strand with the partly complementary strand immobilized on the Au surface after ATP detection or by treating with a large amount of ATP and then rehybridizing the MBA strand with the partly complementary strand immobilized on the Au surface after alpha-thrombin detection. The aptasensor fabricated exhibited several advantages such as label-free detection, high sensitivity, regeneration, and multifunctional recognition. It also showed the detectability in biological fluid. Therein it held promising potential for integration of the sensing ability such as the simultaneous detection for multianalysis in the future.
Collapse
Affiliation(s)
- Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | | | | | | | | |
Collapse
|
265
|
Xiao Z, Shangguan D, Cao Z, Fang X, Tan W. Cell-specific internalization study of an aptamer from whole cell selection. Chemistry 2008; 14:1769-75. [PMID: 18092308 DOI: 10.1002/chem.200701330] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nucleic acid aptamers have been shown many unique applications as excellent probes in molecular recognition. However, few examples are reported which show that aptamers can be internalized inside living cells for aptamer functional studies and for targeted intracellular delivery. This is mainly due to the limited number of aptamers available for cell-specific recognition, and the lack of research on their extra- and intracellular functions. One of the major difficulties in aptamers' in vivo application is that most of aptamers, unlike small molecules, cannot be directly taken up by cells without external assistance. In this work, we have studied a newly developed and cell-specific DNA aptamer, sgc8. This aptamer has been selected through a novel cell selection process (cell-SELEX), in which whole intact cells are used as targets while another related cell line is used as a negative control. The cell-SELEX enables generation of multiple aptamers for molecular recognition of the target cells and has significant advantages in discovering cell surface binding molecules for the selected aptamers. We have studied the cellular internalization of one of the selected aptamers. Our results show that sgc8 is internalized efficiently and specifically to the lymphoblastic leukemia cells. The internalized sgc8 aptamers are located inside the endosome. Comparison studies are done with the antibody for the binding protein of sgc8, PTK7 (Human protein tyrosine kinase-7) on cell surface. We also studied the internalization kinetics of both the aptamer and the antibody for the same protein on the living cell surface. We have further evaluated the effects of sgc8 on cell viability, and no cytotoxicity is observed. This study indicates that sgc8 is a promising agent for cell-type specific intracellular delivery.
Collapse
Affiliation(s)
- Zeyu Xiao
- Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center and UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | | | | | |
Collapse
|
266
|
Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
Collapse
Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
| | | |
Collapse
|
267
|
Danielsson B. Artificial receptors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:97-122. [PMID: 17985098 DOI: 10.1007/10_2007_088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Herein I will provide a brief overview of artificial receptors with emphasis on molecularly imprinted polymers (MIPs) and their applications. Alternative techniques to produce artificial receptors such as in silico designed and modelled polymers as well as different receptors designed using libraries of more or less natural composition will also be mentioned. Examples of these include aptamers and bio-nanocomposites. The physical presentation of the receptors is important and may depend on the application. Block polymerization of MIPs and grinding to particles of suitable size used to be the preferred technique, but today beaded materials can be produced in sizes down to nanobeads and also nanofibers can be used to increase available surface area and thereby capacity. For sensor applications it may be attractive to include the artificial receptors in surface coatings or in membrane structures. Different composite designs can be used to provide additional desirable properties. MIPs and other artificial receptors are gaining rapidly increasing attention in very shifting application areas and an attempt to provide a systematic account for current applications has been made with examples from separation, solid-phase extraction, analysis, carbohydrate specific experiments, and MIPs-directed synthesis.
Collapse
|
268
|
Su S, Ali MM, Filipe CDM, Li Y, Pelton R. Microgel-based inks for paper-supported biosensing applications. Biomacromolecules 2008; 9:935-41. [PMID: 18293902 DOI: 10.1021/bm7013608] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As a first step for the development of biosensing inks for inexpensive paper-based biodetection, we prepared paper strips printed with carboxylic poly( N-isopropylacrylamide) microgels that were modified either with an antibody or with a DNA aptamer. We found that the antibody and the DNA aptamer retained their recognition capabilities when coupled to microgel. The printed microgel remains stationary during chromatographic elution while the microgel-supported molecular recognition elements are accessible to their intended targets present in the elution solution. Our work indicates that microgels, large enough to isolate the biosensors from the paper surface, are sufficiently hydrophilic to be wetted during chromatographic elution, exposing the gel-supported affinity probes to their targets.
Collapse
Affiliation(s)
- Shunxing Su
- Department of Chemical Engineering and Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | | | | | | | | |
Collapse
|
269
|
Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal Bioanal Chem 2007; 390:1067-75. [PMID: 18049815 DOI: 10.1007/s00216-007-1735-8] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 10/25/2007] [Accepted: 11/05/2007] [Indexed: 10/22/2022]
Abstract
In order to generate nucleic acid biosensors that could undergo a reversible conformation change in the presence of the metal zinc, a random sequence pool of single-stranded DNA was immobilized on an oligonucleotide affinity column. In the presence of zinc, those species that underwent a conformational change were released from the column, collected, and amplified. A series of negative and positive selections refined the metal specificity of the selected aptamer beacons. Since the aptamer beacons contained a fluorophore, while the bound oligonucleotide contained a quencher, zinc binding also resulted in an increase in fluorescence. One of the selected beacons, Zn-6m2, bound zinc in the low micromolar range, gave a dose-dependent fluorescence signal, and showed an approximately sixfold increase in fluorescence on zinc binding. While some cross-reactivity with cadmium was observed, it should nonetheless prove possible to use the novel selection method to generate and tune the specificity of a variety of reversible metal biosensors. Such biosensors could potentially be used for continuous monitoring of metals in environmental samples.
Collapse
|
270
|
Li B, Wang Y, Wei H, Dong S. Amplified electrochemical aptasensor taking AuNPs based sandwich sensing platform as a model. Biosens Bioelectron 2007; 23:965-70. [PMID: 17997091 DOI: 10.1016/j.bios.2007.09.019] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 09/19/2007] [Accepted: 09/27/2007] [Indexed: 11/16/2022]
Abstract
Here, we report a sensitive amplified electrochemical impedimetric aptasensor for thrombin, a kind of serine protease that plays important role in thrombosis and haemostasis. For improving detection sensitivity, a sandwich sensing platform is fabricated, in which the thiolated aptamers are firstly immobilized on a gold substrate to capture the thrombin molecules, and then the aptamer functionalized Au nanoparticles (AuNPs) are used to amplify the impedimetric signals. Such designed aptamer/thrombin/AuNPs sensing system could not only improve the detection sensitivity compared to the reported impedimetric aptasensors but also provide a promising signal amplified model for aptamer-based protein detection. In this paper, we realize a sensitive detection limit of 0.02 nM, with a linear range of 0.05-18 nM. Meanwhile, the effect of 6-mercaptohexanol (MCH) and 2-mercaptoethanol (MCE) on the modification of the electrode is investigated.
Collapse
Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, PR China
| | | | | | | |
Collapse
|
271
|
Boese BJ, Breaker RR. In vitro selection and characterization of cellulose-binding DNA aptamers. Nucleic Acids Res 2007; 35:6378-88. [PMID: 17881365 PMCID: PMC2095800 DOI: 10.1093/nar/gkm708] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 08/24/2007] [Accepted: 08/24/2007] [Indexed: 01/09/2023] Open
Abstract
Many nucleic acid enzymes and aptamers have modular architectures that allow them to retain their functions when combined with other nucleotide sequences. This modular function facilitates the engineering of RNAs and DNAs that have more complex functions. We sought to create new DNA aptamers that bind cellulose to provide a module for immobilizing DNAs. Cellulose has been used in a variety of applications ranging from coatings and films to pharmaceutical preparations, and therefore DNA aptamers that bind cellulose might enable new applications. We used in vitro selection to isolate aptamers from a pool of random-sequence DNAs and subjected two distinct clones to additional rounds of mutagenesis and selection. One aptamer (CELAPT 14) was chosen for sequence minimization and more detailed biochemical analysis. CELAPT 14 aptamer variants exhibit robust binding both to cellulose powder and paper. Also, an allosteric aptamer construct was engineered that exhibits ATP-mediated cellulose binding during paper chromatography.
Collapse
Affiliation(s)
- Benjamin J. Boese
- Department of Chemical Engineering, Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R. Breaker
- Department of Chemical Engineering, Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| |
Collapse
|
272
|
Li B, Du Y, Wei H, Dong S. Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules. Chem Commun (Camb) 2007:3780-2. [PMID: 17851626 DOI: 10.1039/b707057h] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.
Collapse
Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | | | | | | |
Collapse
|
273
|
Rupcich N, Nutiu R, Li Y, Brennan JD. Solid-phase enzyme activity assay utilizing an entrapped fluorescence-signaling DNA aptamer. Angew Chem Int Ed Engl 2007; 45:3295-9. [PMID: 16619330 DOI: 10.1002/anie.200504576] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Nicholas Rupcich
- Department of Chemistry, McMaster University, 1280 Main St. W. Hamilton, ON L8S 4M1, Canada
| | | | | | | |
Collapse
|
274
|
Zhao W, Chiuman W, Brook MA, Li Y. Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. Chembiochem 2007; 8:727-31. [PMID: 17410623 DOI: 10.1002/cbic.200700014] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weian Zhao
- Department of Chemistry, McMaster University, 1280 Main St., W. Hamilton, ON, L8S 4M1, Canada
| | | | | | | |
Collapse
|
275
|
Urata H, Nomura K, Wada SI, Akagi M. Fluorescent-labeled single-strand ATP aptamer DNA: chemo- and enantio-selectivity in sensing adenosine. Biochem Biophys Res Commun 2007; 360:459-63. [PMID: 17599804 DOI: 10.1016/j.bbrc.2007.06.075] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 06/14/2007] [Indexed: 11/26/2022]
Abstract
One of the intriguing applications of aptamers is sensing molecules. In principle, an aptamer can specifically recognize and bind to a unique ligand, leading to a structural change of an aptamer. By acquiring information for the structural change, the detection of the ligand can be achieved. To design and explore an aptamer molecule to detect adenosine, we have synthesized some ATP aptamer variants labeled with donor and acceptor fluorophores. Although the fluorescent response of the aptamer variants was highly dependent on experimental temperature, we have found one of the variants showing suitable fluorescent response by titration with adenosine. The aptamer variant showed remarkable selectivity for adenosine over the other ribonucleosides. On the other hand, the enantio-specificity of the aptamer variant in the ligand recognition was not enough to selectively detect d-adenosine over l-adenosine.
Collapse
Affiliation(s)
- Hidehito Urata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | | | | | | |
Collapse
|
276
|
Shangguan D, Tang Z, Mallikaratchy P, Xiao Z, Tan W. Optimization and modifications of aptamers selected from live cancer cell lines. Chembiochem 2007; 8:603-6. [PMID: 17373017 DOI: 10.1002/cbic.200600532] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dihua Shangguan
- Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, Center for Research at Bio/nano Interface, University of Florida, Gainesville, FL 32611, USA
| | | | | | | | | |
Collapse
|
277
|
Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 937] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
Collapse
Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | | | | |
Collapse
|
278
|
Lin C, Katilius E, Liu Y, Zhang J, Yan H. Self-assembled signaling aptamer DNA arrays for protein detection. Angew Chem Int Ed Engl 2007; 45:5296-301. [PMID: 16847867 DOI: 10.1002/anie.200600438] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chenxiang Lin
- Department of Chemistry and Biochemistry, and The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | | | | | | | | |
Collapse
|
279
|
Morse DP. Direct selection of RNA beacon aptamers. Biochem Biophys Res Commun 2007; 359:94-101. [PMID: 17533112 PMCID: PMC2030492 DOI: 10.1016/j.bbrc.2007.05.072] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
A method for the direct selection of RNA molecules that can be easily converted into beacon aptamers is presented. Beacon aptamers are fluorescently labeled nucleic acids that signal the presence of a specific ligand through changes in fluorescence intensity. Typically, ligand binding causes an increase in fluorescence intensity by inducing a conformational change that separates a fluorophore/quencher pair. The method presented here simultaneously selects for ligand binding and induction of an appropriate conformational change. The method was tested by selecting RNA molecules that can detect the aminoglycoside antibiotic tobramycin. After 14 rounds of selection, two sequence families emerged. Upon conversion into beacon aptamers, representatives of the two selected sequence families specifically detected tobramycin, while a negative control RNA that did not survive the selection protocol did not function as a tobramycin beacon aptamer.
Collapse
Affiliation(s)
- Daniel P Morse
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA.
| |
Collapse
|
280
|
Shangguan D, Cao ZC, Li Y, Tan W. Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples. Clin Chem 2007; 53:1153-5. [PMID: 17463173 DOI: 10.1373/clinchem.2006.083246] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Molecular-level differentiation of neoplastic cells is essential for accurate and early diagnosis, but effective molecular probes for molecular analysis and profiling of neoplastic cells are not yet available. We recently developed a cell-based SELEX (systematic evolution of ligands by exponential enrichment) strategy to generate aptamers (designer DNA/RNA probes) as molecular probes to recognize neoplastic cells. METHODS We tested 6 cell-SELEX-generated aptamers with equilibrium dissociation constants in the nanomolar to subnanomolar range: sgd5, selected from Toledo cells, a human diffuse large-cell lymphoma cell line (B-cell), and sgc8, sgc3, sgc4, sgd2, and sgd3 from CCRF-CEM cells, a human precursor T cell acute lymphoblastic leukemia (T-ALL) cell line. Aptamers were labeled with fluorescein isothiocyanate fluorophores and then used to recognize, by flow cytometric analysis, neoplastic cells in cultured hematopoietic cell lines and clinical samples. RESULTS Aptamer sgd5 recognized only its target cells. Aptamers sgc3, sgd2, sgd3, sgc4, and sgc8, selected from a T-cell leukemia cell line, identified all of the cultured T-cell leukemia cell lines with relatively high fluorescence intensity. Aptamers sgc8, sgc3, and sgd3 showed good selectivity toward T-ALL cells and almost no binding to normal hematopoietic cells or lymphoma and myeloma cells. Selected aptamers also detected targets on the cell membranes of neoplastic cells in patient samples. CONCLUSIONS Aptamers selected against cultured neoplastic cells can effectively be used as molecular probes for recognition of neoplastic cells in patient samples. Cell-based aptamer selection can be used to generate aptamer probes to obtain molecular signatures of neoplastic cells in patient samples.
Collapse
Affiliation(s)
- Dihua Shangguan
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | | | | |
Collapse
|
281
|
Mayer G, Raddatz MSL, Grunwald JD, Famulok M. RNA ligands that distinguish metabolite-induced conformations in the TPP riboswitch. Angew Chem Int Ed Engl 2007; 46:557-60. [PMID: 17146816 DOI: 10.1002/anie.200603166] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Günter Mayer
- Life and Medical Sciences (LIMES), Program Unit Chemical Biology and Medicinal Chemistry c/o Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | | | | | | |
Collapse
|
282
|
Xu Y, Hirao Y, Nishimura Y, Sugiyama H. I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes. Bioorg Med Chem 2007; 15:1275-9. [PMID: 17142047 DOI: 10.1016/j.bmc.2006.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 11/10/2006] [Accepted: 11/10/2006] [Indexed: 10/23/2022]
Abstract
To expand the function of DNA machines, we constructed a non-DNA-fuel machine based on the G-quadruplex and i-motif structures within the telomere DNA sequence. Depending on the binding or non-binding of the specified form, the DNA machine is able to bind or release the telomere-binding protein TRF 1, and to release small quadruplex-binding molecules to impede progress of the polymerase. This DNA machine, driven by pH change, does not accumulate duplex DNA waste products to poison the system. These new functions undertaken by structured nucleic acids open many opportunities to create and expand the further functions and use of DNA and RNA.
Collapse
Affiliation(s)
- Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | | | |
Collapse
|
283
|
Su S, Nutiu R, Filipe CDM, Li Y, Pelton R. Adsorption and covalent coupling of ATP-binding DNA aptamers onto cellulose. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:1300-2. [PMID: 17241049 DOI: 10.1021/la060961c] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
With the long-term goal of developing paper surfaces that will detect pathogens, we have investigated physical adsorption and covalent coupling as strategies for treating cellulose surfaces with a DNA aptamer that binds ATP. Physical adsorption was reversible and the isotherms fitted the Langmuir equation with an adsorption maximum of 0.105 mg/m2 at high ionic strength (300 mM NaCl, 25 mM Tris-HCl) and only 0.024 mg/m2 in lower ionic strength buffer (25 mM Tris-HCl). Covalent coupling of amine-terminated aptamer with oxidized cellulose film (Schiff base + reduction) gave 25% coupling efficiency while maintaining the aptamer activity which was illustrated by using a known fluorescent aptamer that is capable of ATP detection. Therefore, covalent coupling, without spacer molecules, is a promising approach for supporting biosensing aptamers on cellulose.
Collapse
Affiliation(s)
- Shunxing Su
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada
| | | | | | | | | |
Collapse
|
284
|
Mayer G, Raddatz MS, Grunwald J, Famulok M. RNA Ligands That Distinguish Metabolite-Induced Conformations in the TPP Riboswitch. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
285
|
Niu W, Jiang N, Hu Y. Detection of proteins based on amino acid sequences by multiple aptamers against tripeptides. Anal Biochem 2006; 362:126-35. [PMID: 17223063 DOI: 10.1016/j.ab.2006.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 11/30/2006] [Accepted: 12/05/2006] [Indexed: 12/26/2022]
Abstract
A number of different ligands have been tested in the course of the development of protein array technology. The most extensively studied example of protein ligands has been based on antibody-antigen interaction. Other examples include protein-protein, protein-nucleic acid, and protein-small molecule interactions. All these ligands can recognize and specifically bind to protein epitopes. In this study, we have developed a novel technology using DNA-based aptamers to detect proteins based on their amino acid sequences. Mouse cathepsin D was used for the proof of principle experiment. Four tripeptides, Leu-Ala-Ser, Asp-Gly-Ile, Gly-Glu-Leu, and Lys-Ala-Ile, were selected based on the published amino acid sequence of mouse cathepsin D. DNA aptamers against the tripeptides were isolated using the systematic evolution of ligands of exponential enrichment method. We have demonstrated that the aptamers specifically interacted with mouse cathepsin D using the structure-switch method. We further performed a proximity-dependent ligation assay to demonstrate that multiple aptamers could specifically detect the protein from cell extracts. In principle, one library containing 8000 aptamers should be enough to detect almost all proteins in the whole proteome in all organisms. This technology could be applied to generate a new generation of protein arrays.
Collapse
Affiliation(s)
- Wenze Niu
- Key Lab of Brain Functional Genomics, MOE and STCSM, Shanghai Institute of Brain Functional Genomics, East China Normal University, 3663 Zhongshan Road N., Shanghai 200062, China
| | | | | |
Collapse
|
286
|
Li B, Wei H, Dong S. Sensitive detection of protein by an aptamer-based label-free fluorescing molecular switch. Chem Commun (Camb) 2006:73-5. [PMID: 17279265 DOI: 10.1039/b612080f] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an aptamer-based method for the sensitive detection of proteins by a label-free fluorescing molecular switch (ethidium bromide), which shows promising potential in making protein assay simple and economical.
Collapse
Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P R China
| | | | | |
Collapse
|
287
|
Liu J, Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew Chem Int Ed Engl 2006; 45:90-4. [PMID: 16292781 DOI: 10.1002/anie.200502589] [Citation(s) in RCA: 651] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Juewen Liu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana--Champaign, Urbana, IL, 61801, USA
| | | |
Collapse
|
288
|
Shen Y, Chiuman W, Brennan JD, Li Y. Catalysis and rational engineering of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way junction structure. Chembiochem 2006; 7:1343-8. [PMID: 16888734 DOI: 10.1002/cbic.200600195] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yutu Shen
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
| | | | | | | |
Collapse
|
289
|
Nutiu R, Li Y. A DNA-protein nanoengine for "on-demand" release and precise delivery of molecules. Angew Chem Int Ed Engl 2006; 44:5464-7. [PMID: 16041813 DOI: 10.1002/anie.200501214] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Razvan Nutiu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | | |
Collapse
|
290
|
Hall B, Hesselberth JR, Ellington AD. Computational selection of nucleic acid biosensors via a slip structure model. Biosens Bioelectron 2006; 22:1939-47. [PMID: 16996258 DOI: 10.1016/j.bios.2006.08.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 08/08/2006] [Accepted: 08/14/2006] [Indexed: 10/24/2022]
Abstract
Aptamers have been shown to undergo ligand-dependent conformational changes, and can be joined to ribozymes to create allosteric ribozymes (aptazymes). An anti-flavin (FMN) aptamer joined to the hammerhead ribozyme yielded an aptazyme that underwent small, FMN-dependent displacements in the helix that joined the aptamer and ribozyme. This 'slip structure' model in which alternative sets of base-pairs are formed in the absence and presence of ligand proved amenable to energetic and computational modeling. Initial successes in modeling the activities of known aptazymes led to the in silico selection of new ligand-dependent aptazymes from virtual pools that contained millions of members. Those aptazymes that were predicted to best fit the slip structure model were synthesized and assayed, and the best-designed aptazyme was activated 60-fold by FMN. The slip structure model proved to be generalizable, and could be applied with equal facility to computationally generate aptazymes that proved to be experimentally activated by other ligands (theophylline) or that contained other catalytic cores (hairpin ribozyme). Moreover, the slip structure model could be applied to the prediction of a ligand-dependent aptamer beacon biosensor in which the addition of the protein vascular endothelial growth factor (VegF) led to a 10-fold increase in fluorescent signal.
Collapse
Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | |
Collapse
|
291
|
Lin C, Katilius E, Liu Y, Zhang J, Yan H. Self-Assembled Signaling Aptamer DNA Arrays for Protein Detection. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600438] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
292
|
Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, Mallikaratchy P, Sefah K, Yang CJ, Tan W. Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci U S A 2006; 103:11838-43. [PMID: 16873550 PMCID: PMC1567664 DOI: 10.1073/pnas.0602615103] [Citation(s) in RCA: 1128] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Indexed: 12/26/2022] Open
Abstract
Using cell-based aptamer selection, we have developed a strategy to use the differences at the molecular level between any two types of cells for the identification of molecular signatures on the surface of targeted cells. A group of aptamers have been generated for the specific recognition of leukemia cells. The selected aptamers can bind to target cells with an equilibrium dissociation constant (K(d)) in the nanomolar-to-picomolar range. The cell-based selection process is simple, fast, straightforward, and reproducible, and, most importantly, can be done without prior knowledge of target molecules. The selected aptamers can specifically recognize target leukemia cells mixed with normal human bone marrow aspirates and can also identify cancer cells closely related to the target cell line in real clinical specimens. The cell-based aptamer selection holds a great promise in developing specific molecular probes for cancer diagnosis and cancer biomarker discovery.
Collapse
Affiliation(s)
- Dihua Shangguan
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Ying Li
- Department of Pathology, Shands Cancer Center, Shands Hospital, College of Medicine, University of Florida, Gainesville, FL 32611-7200
| | - Zhiwen Tang
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Zehui Charles Cao
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Hui William Chen
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Prabodhika Mallikaratchy
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Kwame Sefah
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Chaoyong James Yang
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| | - Weihong Tan
- *Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, and
| |
Collapse
|
293
|
Baker BR, Lai RY, Wood MS, Doctor EH, Heeger AJ, Plaxco KW. An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids. J Am Chem Soc 2006; 128:3138-9. [PMID: 16522082 DOI: 10.1021/ja056957p] [Citation(s) in RCA: 597] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Whereas spectroscopic and chromatographic techniques for the detection of small organic molecules have achieved impressive results, these methods are generally slow and cumbersome, and thus the development of a general means for the real-time, electronic detection of such targets remains a compelling goal. Here we demonstrate a potentially general, label-free electronic method for the detection of small-molecule targets by building a rapid, reagentless biosensor for the detection of cocaine. The sensor, based on the electrochemical interrogation of a structure-switching aptamer, specifically detects micromolar cocaine in seconds. Because signal generation is based on binding-induced folding, the sensor is highly selective and works directly in blood serum and in the presence of commonly employed interferents and cutting agents, and because all of the sensor components are covalently attached to the electrode surface, the sensor is also reusable: we achieve >99% signal regeneration upon a brief, room temperature aqueous wash. Given recent advances in the generation of highly specific aptamers, this detection platform may be readily adapted for the detection of other small molecules of a wide range of clinically and environmentally relevant small molecules.
Collapse
Affiliation(s)
- Brian R Baker
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | | | | | | | | | | |
Collapse
|
294
|
Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H. Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett 2006; 16:4381-4. [PMID: 16757168 DOI: 10.1016/j.bmcl.2006.05.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2006] [Revised: 05/12/2006] [Accepted: 05/16/2006] [Indexed: 11/24/2022]
Abstract
Fluorescent DNA probes for L-argininamide were developed by a combination of DNA aptamers and fluorophore-quencher pairs. These molecules were synthesized by a combination of pre- and post-synthetic modification methods. The fluorescence-labeled aptamer could detect L-argininamide specifically. The binding affinities were defined by the binding affinity of the original aptamer to indicate that the end labeling of the aptamer did not influence the affinities.
Collapse
Affiliation(s)
- Hiroaki Ozaki
- Department of Chemistry, Faculty of Engineering, Gunma University, Kiryu, Japan.
| | | | | | | | | |
Collapse
|
295
|
Rupcich N, Nutiu R, Li Y, Brennan JD. Solid-Phase Enzyme Activity Assay Utilizing an Entrapped Fluorescence-Signaling DNA Aptamer. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504576] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
296
|
Schlosser K, Lam JC, Li Y. Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection. Nucleic Acids Res 2006; 34:2445-54. [PMID: 16682452 PMCID: PMC1458524 DOI: 10.1093/nar/gkl276] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We previously conducted an in vitro selection experiment for RNA-cleaving deoxyribozymes, using a combinatorial DNA library containing 80 random nucleotides. Ultimately, 110 different sequence classes were isolated, but the vast majority contained a short14-15 nt catalytic DNA motif commonly known as 8-17. Herein, we report extensive truncation experiments conducted on multiple sequence classes to confirm the suspected catalytic role played by 8-17 and to determine the effect of excess sequence elements on the activity of this motif and the outcome of selection. Although we observed beneficial, detrimental and neutral consequences for activity, the magnitude of the effect rarely exceeded 2-fold. These deoxyribozymes appear to have survived increasing selection pressure despite the presence of additional sequence elements, rather than because of them. A new deoxyribozyme with comparable activity, called G15-30, was approximately 2.5-fold larger and experienced a approximately 4-fold greater inhibitory effect from excess sequence elements than the average 8-17 motif. Our results suggest that 8-17 may be less susceptible to the potential inhibitory effects of excess arbitrary sequence than larger motifs, which represents a previously unappreciated selective advantage that may contribute to its widespread recurrence.
Collapse
Affiliation(s)
| | | | - Yingfu Li
- To whom correspondence should be addressed. Tel: 1 905 5259140; Fax: 1 905 522 9033;
| |
Collapse
|
297
|
Kell DB. Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest. FEBS J 2006; 273:873-94. [PMID: 16478464 DOI: 10.1111/j.1742-4658.2006.05136.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The newly emerging field of systems biology involves a judicious interplay between high-throughput 'wet' experimentation, computational modelling and technology development, coupled to the world of ideas and theory. This interplay involves iterative cycles, such that systems biology is not at all confined to hypothesis-dependent studies, with intelligent, principled, hypothesis-generating studies being of high importance and consequently very far from aimless fishing expeditions. I seek to illustrate each of these facets. Novel technology development in metabolomics can increase substantially the dynamic range and number of metabolites that one can detect, and these can be exploited as disease markers and in the consequent and principled generation of hypotheses that are consistent with the data and achieve this in a value-free manner. Much of classical biochemistry and signalling pathway analysis has concentrated on the analyses of changes in the concentrations of intermediates, with 'local' equations - such as that of Michaelis and Menten v=(Vmax x S)/(S+K m) - that describe individual steps being based solely on the instantaneous values of these concentrations. Recent work using single cells (that are not subject to the intellectually unsupportable averaging of the variable displayed by heterogeneous cells possessing nonlinear kinetics) has led to the recognition that some protein signalling pathways may encode their signals not (just) as concentrations (AM or amplitude-modulated in a radio analogy) but via changes in the dynamics of those concentrations (the signals are FM or frequency-modulated). This contributes in principle to a straightforward solution of the crosstalk problem, leads to a profound reassessment of how to understand the downstream effects of dynamic changes in the concentrations of elements in these pathways, and stresses the role of signal processing (and not merely the intermediates) in biological signalling. It is this signal processing that lies at the heart of understanding the languages of cells. The resolution of many of the modern and postgenomic problems of biochemistry requires the development of a myriad of new technologies (and maybe a new culture), and thus regular input from the physical sciences, engineering, mathematics and computer science. One solution, that we are adopting in the Manchester Interdisciplinary Biocentre (http://www.mib.ac.uk/) and the Manchester Centre for Integrative Systems Biology (http://www.mcisb.org/), is thus to colocate individuals with the necessary combinations of skills. Novel disciplines that require such an integrative approach continue to emerge. These include fields such as chemical genomics, synthetic biology, distributed computational environments for biological data and modelling, single cell diagnostics/bionanotechnology, and computational linguistics/text mining.
Collapse
Affiliation(s)
- Douglas B Kell
- School of Chemistry, Faraday Building, The University of Manchester, UK.
| |
Collapse
|
298
|
Liu J, Lu Y. Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502589] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
299
|
Yang CJ, Jockusch S, Vicens M, Turro NJ, Tan W. Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc Natl Acad Sci U S A 2005; 102:17278-83. [PMID: 16301535 PMCID: PMC1297691 DOI: 10.1073/pnas.0508821102] [Citation(s) in RCA: 298] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantitative protein bioanalysis in complex biological fluids presents considerable challenges in biological studies and disease diagnosis. The major obstacles are the background signals from both the probe and the biological fluids where the proteins reside. We have molecularly engineered light-switching excimer aptamer probes for rapid and sensitive detection of a biomarker protein, platelet-derived growth factor (PDGF). Labeled with one pyrene at each end, the aptamer switches its fluorescence emission from approximately 400 nm (pyrene monomer) to 485 nm (pyrene excimer) upon PDGF binding. This fluorescence wavelength change from monomer to excimer emission is a result of aptamer conformation rearrangement induced by target binding. The excimer probe is able to effectively detect picomolar PDGF in homogeneous solutions. Because the excimer has a much longer fluorescence lifetime (approximately 40 ns) than that of the background (approximately 5 ns), time-resolved measurements were used to eliminate the biological background. We thus were able to detect PDGF in a cell sample quantitatively without any sample pretreatment. This molecular engineering strategy can be used to develop other aptamer probes for protein monitoring. Combined with lifetime-based measurements and molecular engineering, light-switching excimer aptamer probes hold great potential in protein analysis for biomedical studies.
Collapse
Affiliation(s)
- Chaoyong James Yang
- Center for Research at Bio/Nano Interface, Department of Chemistry, University of Florida Genetics Institute, Gainesville, FL 32611, USA
| | | | | | | | | |
Collapse
|
300
|
Legiewicz M, Lozupone C, Knight R, Yarus M. Size, constant sequences, and optimal selection. RNA (NEW YORK, N.Y.) 2005; 11:1701-9. [PMID: 16177137 PMCID: PMC1370856 DOI: 10.1261/rna.2161305] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Because the abundance of functional molecules in RNA sequence space has many unexplored aspects, we compared the outcome of 11 independent selections, performed using the same affinity selection protocol and contiguous randomized regions of 16, 22, 26, 50, 70, and 90 nucleotides. All affinity selections targeted the simplest isoleucine aptamer, an asymmetric internal loop. This loop should be abundant in all selections, so that it can be compared across all experiments. In some cases, two primer sets intended to favor selection of different structures have also been compared. The simplest isoleucine aptamer dominates all selections except with the shortest tract, 16 contiguous randomized nucleotides. Here the isoleucine aptamer cannot be accommodated and no other motif can be selected. Our results suggest an optimum length for selection; surprisingly, both the shortest and the longest randomized tracts make it more difficult to recover the motif. Estimated apparent initial abundances suggest that the simplest isoleucine motif was 20- to 40-fold more frequent in selection with 50- or 70-nucleotide randomized regions than with any other length. Considering primer sets, a pre-formed stable stem within fixed flanking sequences had a five-to 10-fold negative effect on apparent motif abundance at all lengths. Differing random tract lengths also determined the probable motif permutation and the most abundant helix lengths. These data support a significant but lesser role for primer sequences in the outcome of selections.
Collapse
Affiliation(s)
- Michal Legiewicz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, 80309-0347, USA
| | | | | | | |
Collapse
|