1
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High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics. Methods Mol Biol 2023; 2570:243-269. [PMID: 36156788 DOI: 10.1007/978-1-0716-2695-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Small-molecule sensing is a major issue as they can serve both in fundamental science and as makers of various diseases, contaminations, or even environment pollution. RNA aptamers are single-stranded nucleic acids that can adopt different conformations and specifically recognize a wide range of ligands, making them good candidates to develop biosensors of small molecules. Recently, light-up RNA aptamers have been introduced and used as starting building blocks of RNA-based fluorogenic biosensors. They are typically made of three domains: a reporter domain (a light-up aptamer), connected to a sensor domain (another aptamer) via a communication module. The latter is instrumental as being in charge of information transmission between the sensor and the reporting domains. Here we present an ultrahigh-throughput screening procedure to develop RNA-based fluorogenic biosensors by selecting optimized communication modules through an exhaustive functional exploration of every possible sequence permutation using droplet-based microfluidics and next-generation sequencing.
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2
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Wang Y, Hanrahan G, Azar FA, Mittermaier A. Binding interactions in a kinase active site modulate background ATP hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140720. [PMID: 34597835 DOI: 10.1016/j.bbapap.2021.140720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Kinases play central roles in many cellular processes, transferring the terminal phosphate groups of nucleoside triphosphates (NTPs) onto substrates. In the absence of substrates, kinases can also hydrolyse NTPs producing NDPs and inorganic phosphate. Hydrolysis is usually much less efficient than the native phosphoryl transfer reaction. This may be related to the fact that NTP hydrolysis is metabolically unfavorable as it unproductively consumes the cell's energy stores. It has been suggested that substrate interactions could drive changes in NTP binding pocket, activating catalysis only when substrates are present. Structural data show substrate-induced conformational rearrangements, however there is a lack of corresponding functional information. To better understand this phenomenon, we developed a suite of isothermal titration calorimetry (ITC) kinetics methods to characterize ATP hydrolysis by the antibiotic resistance enzyme aminoglycoside-3'-phosphotransferase-IIIa (APH(3')-IIIa). We measured Km, kcat, and product inhibition constants and single-turnover kinetics in the presence and absence of non-substrate aminoglycosides (nsAmgs) that are structurally similar to the native substrates. We found that the presence of an nsAmg increased the chemical step of cleaving the ATP γ-phosphate by at least 10- to 20-fold under single-turnover conditions, supporting the existence of interactions that link substrate binding to substantially enhanced catalytic rates. Our detailed kinetic data on the association and dissociation rates of nsAmgs and ADP shed light on the biophysical processes underlying the enzyme's Theorell-Chance reaction mechanism. Furthermore, they provide clues on how to design small-molecule effectors that could trigger efficient ATP hydrolysis and generate selective pressure against bacteria harboring the APH(3')-IIIa.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Grace Hanrahan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Frederic Abou Azar
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A 0B8, Canada.
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3
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López-Alled CM, Park SJ, Lee DJ, Murfin LC, Kociok-Köhn G, Hann JL, Wenk J, James TD, Kim HM, Lewis SE. Azulene-based fluorescent chemosensor for adenosine diphosphate. Chem Commun (Camb) 2021; 57:10608-10611. [PMID: 34570136 DOI: 10.1039/d1cc04122c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AzuFluor® 435-DPA-Zn, an azulene fluorophore bearing two zinc(II)-dipicolylamine receptor motifs, exhibits fluorescence enhancement in the presence of adenosine diphosphate. Selectivity for ADP over ATP, AMP and PPi results from appropriate positioning of the receptor motifs, since an isomeric sensor cannot discriminate between ADP and ATP.
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Affiliation(s)
- Carlos M López-Alled
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK. .,Centre for Sustainable Circular Technologies, University of Bath, Bath, BA2 7AY, UK.
| | - Sang Jun Park
- Department of Energy Systems Research, Ajou University, Suwon 443-749, South Korea.
| | - Dong Joon Lee
- Department of Energy Systems Research, Ajou University, Suwon 443-749, South Korea.
| | - Lloyd C Murfin
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Gabriele Kociok-Köhn
- Material and Chemical Characterisation Facility (MC2), University of Bath, Bath, BA2 7AY, UK
| | - Jodie L Hann
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Jannis Wenk
- Centre for Sustainable Circular Technologies, University of Bath, Bath, BA2 7AY, UK. .,Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, UK
| | - Tony D James
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK. .,Centre for Sustainable Circular Technologies, University of Bath, Bath, BA2 7AY, UK. .,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Hwan Myung Kim
- Department of Energy Systems Research, Ajou University, Suwon 443-749, South Korea.
| | - Simon E Lewis
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK. .,Centre for Sustainable Circular Technologies, University of Bath, Bath, BA2 7AY, UK.
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4
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Burton NR, Kim P, Backus KM. Photoaffinity labelling strategies for mapping the small molecule-protein interactome. Org Biomol Chem 2021; 19:7792-7809. [PMID: 34549230 PMCID: PMC8489259 DOI: 10.1039/d1ob01353j] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.
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Affiliation(s)
- Nikolas R Burton
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
| | - Phillip Kim
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
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5
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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6
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Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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7
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Wang Y, Guan J, Di Trani JM, Auclair K, Mittermaier AK. Inhibition and Activation of Kinases by Reaction Products: A Reporter-Free Assay. Anal Chem 2019; 91:11803-11811. [PMID: 31426630 DOI: 10.1021/acs.analchem.9b02456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Kinases are widely distributed in nature and are implicated in many human diseases. Thus, an understanding of their activity and regulation is of fundamental importance. Several kinases are known to be inhibited by ADP. However, thorough investigation of this phenomenon is hampered by the lack of a simple and effective assay for studying this inhibition. We now present a quick, general approach for measuring the effects of reaction products on kinase activity. The method, based on isothermal titration calorimetry, is the first universal, reporter-free, continuous assay for probing kinase inhibition or activation by ADP. In applications to an aminoglycoside phosphotransferase [APH(3')-IIIa] and pantothenate kinases from Escherichia coli (EcPanK) and Pseudomonas aeruginosa (PaPanK), we found ADP to be an efficient inhibitor of all three kinases, with inhibition constant (Ki) values similar to or lower than the Michaelis-Menten constant (Km) values of ATP. Interestingly, ADP was an activator at low concentrations and an inhibitor at high concentrations for EcPanK. This unusual effect was quantitatively modeled and attributed to cooperative interactions between the two subunits of the dimeric enzyme. Importantly, our results suggest that, at typical bacterial intracellular concentrations of ATP and ADP (approximately 1.5 mM and 180 μM, respectively), all three kinases are partially inhibited by ADP, allowing enzyme activity to rapidly respond to changes in the levels of both metabolites.
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Affiliation(s)
- Yun Wang
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Jinming Guan
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Justin M Di Trani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Anthony K Mittermaier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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8
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Karunanayake Mudiyanselage APKK, Wu R, Leon-Duque MA, Ren K, You M. "Second-generation" fluorogenic RNA-based sensors. Methods 2019; 161:24-34. [PMID: 30660865 PMCID: PMC6589113 DOI: 10.1016/j.ymeth.2019.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 02/07/2023] Open
Abstract
A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.
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Affiliation(s)
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mark A Leon-Duque
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA.
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9
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Nakano S, Shimizu M, Dinh H, Morii T. Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors. Chem Commun (Camb) 2019; 55:1611-1614. [PMID: 30657140 DOI: 10.1039/c8cc09934k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold. These sensors allow facile and quantitative detection of ATP and ADP simultaneously in a solution and enable monitoring of the time-course changes of ATP and ADP concentrations in an enzymatic reaction.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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10
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Liao AM, Pan W, Benson JC, Wong AD, Rose BJ, Caltagirone GT. A Simple Colorimetric System for Detecting Target Antigens by a Three-Stage Signal Transformation-Amplification Strategy. Biochemistry 2018; 57:5117-5126. [PMID: 30064210 DOI: 10.1021/acs.biochem.8b00523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inexpensive, straightforward, and rapid medical diagnostics are becoming increasingly important for disease identification in time- and resource-limited settings. Previous attempts to link oligonucleotide-based aptamers and hammerhead ribozymes to form ligand-induced ribozymes have been successful in identifying a variety of small molecule and protein targets. Isothermal exponential amplification reactions (EXPAR) amplify minute amounts of nucleic acid templates without requiring special instrumentation. We introduce a colorimetric assay that we engineered using an aptamer, hammerhead ribozyme, EXPAR, and peroxidase activity in conjunction with a 3,3',5,5'-tetramethylbenzidine (TMB) substrate. This is a modular signal enhancer system that can be easily modified to detect virtually any chosen analyte target within 5-10 min with minimal technical requirements. Ligand-aptamer binding causes the ribozyme to change conformation and self-cleave. The cleaved ribozyme triggers exponential amplification of a reporter sequence during EXPAR. The amplification products fold into single-stranded DNA guanine quadruplexes that exhibit peroxidase-like activity and can oxidize a colorless TMB substrate into a colored reaction product for visual detection. As a proof of concept, we examined the bronchodilator theophylline versus its chemical analogue, caffeine. We demonstrate linear changes in absorption readout across a wide range of target concentrations (0.5-1000 μM) and the ability to visually detect theophylline at 0.5 μM with an approximately 35-fold increased specificity versus that of caffeine. This three-stage detection system is a versatile platform that has the potential to improve the rapid identification of target analytes.
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Affiliation(s)
- Albert M Liao
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
| | - Weihua Pan
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
| | - James C Benson
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
| | - Andrew D Wong
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
| | - Benjamin J Rose
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
| | - G Thomas Caltagirone
- Aptagen LLC , 250 North Main Street , Jacobus , Pennsylvania 17407 , United States
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11
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Singh G, Kaur M, Shiekh BA, Kang TS. Luminescent micellar nano-interfaces of surface active ionic liquid for the selective recognition of ADP in aqueous medium. Chem Commun (Camb) 2018; 54:7463-7466. [DOI: 10.1039/c8cc02985g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Selective recognition of ADP by the micellar nano-interfaces of SAIL is observed whereas monomers/bilayers are not sensitive towards ADP.
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Affiliation(s)
- G. Singh
- Department of Chemistry
- Department of Chemistry, University Grants Commission (UGC) Centre for Advanced Studies-II
- Guru Nanak Dev University
- Amritsar-143005
- India
| | - M. Kaur
- Department of Chemistry
- Department of Chemistry, University Grants Commission (UGC) Centre for Advanced Studies-II
- Guru Nanak Dev University
- Amritsar-143005
- India
| | - B. A. Shiekh
- Department of Chemistry
- Department of Chemistry, University Grants Commission (UGC) Centre for Advanced Studies-II
- Guru Nanak Dev University
- Amritsar-143005
- India
| | - T. S. Kang
- Department of Chemistry
- Department of Chemistry, University Grants Commission (UGC) Centre for Advanced Studies-II
- Guru Nanak Dev University
- Amritsar-143005
- India
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12
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Berni E, Le Henaff L, Jarrige L, Girard E, Jonusauskas G, Gosse I, Pinet S. Functionalized Ruthenium Complexes: Selective “Turn-on” Detection of Biologically Relevant Anionic Species. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Emanuela Berni
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
| | - Laurent Le Henaff
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
| | - Lucie Jarrige
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
| | - Emeline Girard
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
| | - Gediminas Jonusauskas
- LOMA; UMR 5798; CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
| | - Isabelle Gosse
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
| | - Sandra Pinet
- ISM; UMR 5255 CNRS; Univ. Bordeaux; 351 Cours de la libération 33400 Talence France
- ENSCBP; Bordeaux INP; 16 Avenue Pey Berland 33607 Pessac France
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13
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Menger M, Yarman A, Erdőssy J, Yildiz HB, Gyurcsányi RE, Scheller FW. MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing. BIOSENSORS 2016; 6:E35. [PMID: 27438862 PMCID: PMC5039654 DOI: 10.3390/bios6030035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/04/2016] [Accepted: 07/11/2016] [Indexed: 12/12/2022]
Abstract
Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application.
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Affiliation(s)
- Marcus Menger
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
- Turkish-German University, Faculty of Science, Molecular Biotechnology, Sahinkaya Cad. No. 86, Bekoz, Istanbul 34820, Turkey.
| | - Júlia Erdőssy
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Huseyin Bekir Yildiz
- Department of Materials Science and Nanotechnology Engineering, KTO Karatay University, Konya 42020, Turkey.
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Frieder W Scheller
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
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14
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Huang F, Hao G, Wu F, Feng G. Fluorescence sensing of ADP over ATP and PPi in 100% aqueous solution. Analyst 2016. [PMID: 26213259 DOI: 10.1039/c5an01291k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An anthracene-bridged dinuclear zinc(ii)-dipicolylamine complex was found to show high selectivity for ADP with a significant fluorescence enhancement over ATP, PPi and other common analytes in 100% aqueous solution. This complex can be used for fluorescence detection of ADP in living cells and for monitoring the activity of kinases.
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Affiliation(s)
- Feihu Huang
- Key laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China.
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15
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Langton MJ, Serpell CJ, Beer PD. Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective. Angew Chem Int Ed Engl 2016; 55:1974-87. [PMID: 26612067 PMCID: PMC4755225 DOI: 10.1002/anie.201506589] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 12/22/2022]
Abstract
The recognition of anions in water remains a key challenge in modern supramolecular chemistry, and is essential if proposed applications in biological, medical, and environmental arenas that typically require aqueous conditions are to be achieved. However, synthetic anion receptors that operate in water have, in general, been the exception rather than the norm to date. Nevertheless, a significant step change towards routinely conducting anion recognition in water has been achieved in the past few years, and this Review highlights these approaches, with particular focus on controlling and using the hydrophobic effect, as well as more exotic interactions such as C-H hydrogen bonding and halogen bonding. We also look beyond the field of small-molecule recognition into the macromolecular domain, covering recent advances in anion recognition based on biomolecules, polymers, and nanoparticles.
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Affiliation(s)
- Matthew J Langton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Serpell
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
- School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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16
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Langton MJ, Serpell CJ, Beer PD. Anionenerkennung in Wasser: aktuelle Fortschritte aus supramolekularer und makromolarer Sicht. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506589] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Matthew J. Langton
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
| | - Christopher J. Serpell
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
- School of Physical Sciences, Ingram Building; University of Kent; Canterbury Kent CT2 7NH Vereinigtes Königreich
| | - Paul D. Beer
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
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17
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Breaker RR, Joyce GF. The expanding view of RNA and DNA function. CHEMISTRY & BIOLOGY 2014; 21:1059-65. [PMID: 25237854 PMCID: PMC4171699 DOI: 10.1016/j.chembiol.2014.07.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 07/16/2014] [Accepted: 07/21/2014] [Indexed: 11/28/2022]
Abstract
RNA and DNA are simple linear polymers consisting of only four major types of subunits, and yet these molecules carry out a remarkable diversity of functions in cells and in the laboratory. Each newly discovered function of natural or engineered nucleic acids enforces the view that prior assessments of nucleic acid function were far too narrow and that many more exciting findings are yet to come. This Perspective highlights just a few of the numerous discoveries over the past 20 years pertaining to nucleic acid function, focusing on those that have been of particular interest to chemical biologists. History suggests that there will continue to be many opportunities to engage chemical biologists in the discovery, creation, and manipulation of nucleic acid function in the years to come.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, and Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.
| | - Gerald F Joyce
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Inhibited aptazyme-based catalytic molecular beacon for amplified detection of adenosine. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Shi L, Hu P, Ren Y, Feng G. An unexpected highly selective mononuclear zinc complex for adenosine diphosphate (ADP). Chem Commun (Camb) 2014; 49:11704-6. [PMID: 24192643 DOI: 10.1039/c3cc47437b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A simple and readily available mononuclear zinc complex, which appends two anthracene groups, was unexpectedly found to show high selectivity for ADP with a unique increased fluorescence response in neutral aqueous solution.
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Affiliation(s)
- Lei Shi
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China.
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21
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Huang J, He Y, Yang X, Wang K, Quan K, Lin X. Split aptazyme-based catalytic molecular beacons for amplified detection of adenosine. Analyst 2014; 139:2994-7. [DOI: 10.1039/c4an00454j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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22
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Strack RL, Song W, Jaffrey SR. Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat Protoc 2013; 9:146-55. [PMID: 24356773 DOI: 10.1038/nprot.2014.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically encoded fluorescent sensors can be valuable tools for studying the abundance and flux of molecules in living cells. We recently developed a novel class of sensors composed of RNAs that can be used to detect diverse small molecules and untagged proteins. These sensors are based on Spinach, an RNA mimic of GFP, and they have successfully been used to image several metabolites and proteins in living bacteria. Here we discuss the generation and optimization of these Spinach-based sensors, which, unlike most currently available genetically encoded reporters, can be readily generated to any target of interest. We also provide a detailed protocol for imaging ADP dynamics in living Escherichia coli after a change from glucose-containing medium to other carbon sources. The entire procedure typically takes ∼4 d including bacteria transformation and image analysis. The majority of this protocol is applicable to sensing other metabolites and proteins in living bacteria.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
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23
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Nakao S, Oishi M. Rational Design of a Fluorescence-amplified Aptasensor Based on Enzyme-assisted Target Recycling Strategy. CHEM LETT 2013. [DOI: 10.1246/cl.130439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shingo Nakao
- Division of Materials Science, Graduate School of Pure and Applied Sciences, University of Tsukuba
| | - Motoi Oishi
- Division of Materials Science, Graduate School of Pure and Applied Sciences, University of Tsukuba
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24
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Strack RL, Jaffrey SR. New approaches for sensing metabolites and proteins in live cells using RNA. Curr Opin Chem Biol 2013; 17:651-5. [PMID: 23746618 DOI: 10.1016/j.cbpa.2013.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
Abstract
Tools to study the abundance, distribution, and flux of intracellular molecules are crucial for understanding cellular signaling and physiology. Although powerful, the current FRET-based technology for imaging cellular metabolites is not easily generalizable. Thus, new platforms for generating genetically encoded sensors are needed. We recently developed a new class of biosensors on the basis of Spinach, an RNA mimic of GFP. In this case, RNA aptamers against a target ligand are modularly fused to Spinach that substantially induce Spinach fluorescence in the presence of ligand. We have used this approach to detect metabolites and proteins both in vitro and in living bacteria, thus providing an alternative to FRET-based sensors and a generalizable approach for generating fluorescent sensors to any ligand of interest.
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Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, 1300 York Avenue, LC 523, New York, NY 10065, USA
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25
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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26
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Shapiro AB, Livchak S, Gao N, Whiteaker J, Thresher J, Jahić H, Huang J, Gu RF. A homogeneous, high-throughput-compatible, fluorescence intensity-based assay for UDP-N-acetylenolpyruvylglucosamine reductase (MurB) with nanomolar product detection. ACTA ACUST UNITED AC 2011; 17:327-38. [PMID: 22068704 DOI: 10.1177/1087057111425188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A novel assay for the NADPH-dependent bacterial enzyme UDP-N-acetylenolpyruvylglucosamine reductase (MurB) is described that has nanomolar sensitivity for product formation and is suitable for high-throughput applications. MurB catalyzes an essential cytoplasmic step in the synthesis of peptidoglycan for the bacterial cell wall, reduction of UDP-N-acetylenolpyruvylglucosamine to UDP-N-acetylmuramic acid (UNAM). Interruption of this biosynthetic pathway leads to cell death, making MurB an attractive target for antibacterial drug discovery. In the new assay, the UNAM product of the MurB reaction is ligated to L-alanine by the next enzyme in the peptidoglycan biosynthesis pathway, MurC, resulting in hydrolysis of adenosine triphosphate (ATP) to adenosine diphosphate (ADP). The ADP is detected with nanomolar sensitivity by converting it to oligomeric RNA with polynucleotide phosphorylase and detecting the oligomeric RNA with a fluorescent dye. The product sensitivity of the new assay is 1000-fold greater than that of the standard assay that follows the absorbance decrease resulting from the conversion of NADPH to NADP(+). This sensitivity allows inhibitor screening to be performed at the low substrate concentrations needed to make the assay sensitive to competitive inhibition of MurB.
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Affiliation(s)
- Adam B Shapiro
- Bioscience Department, Infection Innovative Medicines, AstraZeneca R&D Boston, Waltham, MA 02451, USA.
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27
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Abstract
Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Jan L Vinkenborg
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit, Laboratory of Chemical Biology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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28
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Ozalp VC, Nielsen LJ, Olsen LF. An aptamer-based nanobiosensor for real-time measurements of ATP dynamics. Chembiochem 2011; 11:2538-41. [PMID: 21086483 DOI: 10.1002/cbic.201000500] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Veli C Ozalp
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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29
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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30
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Sando S. Design of Functional Nucleic Acid Systems for Biomolecular Analysis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Abstract
ATP-driven translocation of helicases along DNA can be assayed in several ways. Reagentless biosensors, based on fluorophore-protein adducts, provide convenient ways for real-time assays of both the separation of dsDNA and the hydrolysis of ATP. Single-stranded DNA can be assayed using a modified single-stranded DNA-binding protein (SSB), and phosphate production during ATP hydrolysis can be measured by a modified phosphate-binding protein. Advantages and limitations of these approaches are compared with those of other types of measurements.
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Affiliation(s)
- Martin R Webb
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK
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32
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Hackney DD. When is weaker better? Design of an ADP sensor with weak ADP affinity, but still selective against ATP. ACS Chem Biol 2010; 5:353-4. [PMID: 20394442 DOI: 10.1021/cb1000839] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A simple ADP biosensor would be of broad usefulness in monitoring the large number of metabolic processes that produce ADP. Several new systems have been recently described including one in the current issue of ACS Chemical Biology that provides a simple readout of the ADP concentration without significant interference by ATP.
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Affiliation(s)
- David D. Hackney
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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33
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Kunzelmann S, Webb MR. A fluorescent, reagentless biosensor for ADP based on tetramethylrhodamine-labeled ParM. ACS Chem Biol 2010; 5:415-25. [PMID: 20158267 PMCID: PMC2855616 DOI: 10.1021/cb9003173] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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Fluorescence assays for ADP detection are of considerable current interest, both in basic research and in drug discovery, as they provide a generic method for measuring the activity of ATPases and kinases. The development of a novel fluorescent biosensor is described that is based on a tetramethylrhodamine-labeled, bacterial actin homologue, ParM. The design of the biosensor takes advantage of the large conformational change of ParM on ADP binding and the strong quenching of the tetramethylrhodamine fluorescence by stacking of the dye. ParM was labeled with two tetramethylrhodamines in close proximity, whereby the fluorophores are able to interact with each other. ADP binding alters the distance and relative orientation of the tetramethylrhodamines, which leads to a change in this stacking interaction and so in the fluorescence intensity. The final ADP biosensor shows ∼15-fold fluorescence increase in response to ADP binding. It has relatively weak affinity for ADP (Kd = 30 μM), enabling it to be used at substoichiometric concentrations relative to ADP, while reporting ADP concentration changes in a wide range around the Kd value, namely, submicromolar to tens of micromolar. The biosensor strongly discriminates against ATP (>100-fold), allowing ADP detection against a background of millimolar ATP. At 20 °C, the labeled ParM binds ADP with a rate constant of 9.5 × 104 M−1 s−1 and the complex dissociates at 2.9 s−1. Thus, the biosensor is suitable for real-time measurements, and its performance in such assays is demonstrated using a sugar kinase and a mammalian protein kinase.
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Affiliation(s)
- Simone Kunzelmann
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Martin R. Webb
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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34
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Furutani C, Shinomiya K, Aoyama Y, Yamada K, Sando S. Modular blue fluorescent RNA sensors for label-free detection of target molecules. MOLECULAR BIOSYSTEMS 2010; 6:1569-71. [DOI: 10.1039/c001230k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Kunzelmann S, Webb MR. A biosensor for fluorescent determination of ADP with high time resolution. J Biol Chem 2009; 284:33130-8. [PMID: 19801632 PMCID: PMC2785155 DOI: 10.1074/jbc.m109.047118] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nearly every cellular process requires the presence of ATP. This is reflected in the vast number of enzymes like kinases or ATP hydrolases, both of which cleave the terminal phosphate from ATP, thereby releasing ADP. Despite the fact that ATP hydrolysis is one of the most fundamental reactions in biological systems, there are only a few methods available for direct measurements of enzymatic-driven ATP conversion. Here we describe the development of a reagentless biosensor for ADP, the common product of all ATPases and kinases, which allows the real-time detection of ADP, produced enzymatically. The biosensor is derived from a bacterial actin homologue, ParM, as protein framework. A single fluorophore (a diethylaminocoumarin), attached to ParM at the edge of the nucleotide binding site, couples ADP binding to a >3.5-fold increase in fluorescence intensity. The labeled ParM variant has high affinity for ADP (0.46 μm) and a fast signal response, controlled by the rate of ADP binding to the sensor (0.65 μm−1s−1). Amino acids in the active site were mutated to reduce ATP affinity and achieve a >400-fold discrimination against triphosphate binding. A further mutation ensured that the final sensor did not form filaments and, as a consequence, has extremely low ATPase activity. The broad applicability of N-[2-(1-maleimidyl)ethyl]-7-diethylaminocoumarin-3-carboxamide (MDCC)-ParM as a sensitive probe for ADP is demonstrated in real-time kinetic assays on two different ATPases and a protein kinase.
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Affiliation(s)
- Simone Kunzelmann
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
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36
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Khlyntseva SV, Bazel’ YR, Vishnikin AB, Andruch V. Methods for the determination of adenosine triphosphate and other adenine nucleotides. JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1134/s1061934809070028] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Abstract
Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.
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Affiliation(s)
- Günter Mayer
- Life and Medical Sciences, Prog. Unit Chemical Biology and Medicinal Chemistry, University of Bonn c/o Kekulé-Institute for Organic Chemistry and Biochemistry, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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38
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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39
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40
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Furchak JRW, Yang P, Jennings C, Walter NG, Kennedy RT. Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection. Anal Chem 2008; 80:8195-201. [PMID: 18842060 DOI: 10.1021/ac801410k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A naturally occurring aptazyme, the glmS ribozyme, is adapted to an assay for glucosamine 6-phosphate, an effector molecule for the aptazyme. In the assay, binding of analyte allosterically activates aptazyme to cleave a fluorescently labeled oligonucleotide substrate. The extent of reaction, and hence analyte concentration, is detected by either fluorescence resonance energy transfer (FRET) or capillary electrophoresis with laser-induced fluorescence (CE-LIF). With FRET, assay signal is the rate of increase in FRET in presence of analyte. With CE-LIF, the assay signal is the peak height of cleavage product formed after a fixed incubation time. The assay has a linear response up to 100 (CE-LIF) or 500 microM (FRET) and detection limit of approximately 500 nM for glucosamine 6-phosphate under single-turnover conditions. When substrate is present in excess of the aptazyme, it is possible to amplify the signal by multiple turnovers to achieve a 13-fold improvement in sensitivity and detection limit of 50 nM. Successful signal amplification requires a temperature cycle to alternately dissociate cleaved substrate and allow fresh substrate to bind aptazyme. The results show that aptazymes have potential utility as analytical reagents for quantification of effector molecules.
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Affiliation(s)
- Jennifer R W Furchak
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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41
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Ogasawara D, Hachiya NS, Kaneko K, Sode K, Ikebukuro K. Detection system based on the conformational change in an aptamer and its application to simple bound/free separation. Biosens Bioelectron 2008; 24:1372-6. [PMID: 18809306 DOI: 10.1016/j.bios.2008.07.082] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 07/15/2008] [Accepted: 07/31/2008] [Indexed: 11/25/2022]
Abstract
Aptamers are good molecular recognition elements for biosensors. Especially, their conformational change, which is induced by the binding to the target molecule, enables the development of several types of useful detection systems. We applied this property to bound/free separation, which is a crucial process for highly sensitive detection. We designed aptamers which change their conformation upon binding to the target molecule and thereby expose a single-strand bearing the complementary sequence to the capture probe immobilized onto the support. We named the designed aptamers "capturable aptamers" and the capture probe "capture DNA". Three capturable aptamers were designed based on the PrP aptamer, which binds to prion protein. One of these capturable aptamers was demonstrated to recognize prion protein and change its conformation upon binding to it. A detection system using this designed capturable aptamer for prion protein was developed. Capturable aptamers and capture DNA allow us to perform simple bound/free separation with only one target ligand.
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Affiliation(s)
- Daisuke Ogasawara
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
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42
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Allali-Hassani A, Pereira MP, Navani NK, Brown ED, Li Y. Isolation of DNA aptamers for CDP-ribitol synthase, and characterization of their inhibitory and structural properties. Chembiochem 2008; 8:2052-7. [PMID: 17929340 DOI: 10.1002/cbic.200700257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Abdellah Allali-Hassani
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
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43
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44
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Abstract
Aptamers are non-naturally occurring structured oligonucleotides that may bind to small molecules, peptides, and proteins. Typically, aptamers are generated by an in vitro selection process referred to as SELEX (systematic evolution of ligands by exponential enrichment). Aptamers that bind with high affinity and specificity to proteins that reside on the cell surface have potential utility as therapeutic antagonists, agonists, and diagnostic agents. When the target protein requires the presence of the cell membrane (e.g., G-protein-coupled receptors, ion channels) or a co-receptor to fold properly, it is difficult or impossible to program the SELEX experiment with purified, soluble protein target. Recent advances in which the useful range of SELEX has been extended from comparatively simple purified forms of soluble proteins to complex mixtures of proteins in membrane preparations or in situ on the surfaces of living cells offer the potential to discover aptamers against previously intractable targets. Additionally, in cases in which a cell-type specific diagnostic is sought, the most desirable target on the cell surface may not be known. Successful application of aptamer selection techniques to complex protein mixtures can be performed even in the absence of detailed target knowledge and characterization. This Account presents a review of recent work in which membrane preparations or whole cells have been utilized to generate aptamers to cell surface targets. SELEX experiments utilizing a range of target "scaffolds" are described, including cell fragments, parasites and bacteria, viruses, and a variety of human cell types including adult mesenchymal stem cells and tumor lines. Complex target SELEX can enable isolation of potent and selective aptamers directed against a variety of cell-surface proteins, including receptors and markers of cellular differentiation, as well as determinants of disease in pathogenic organisms, and as such should have wide therapeutic and diagnostic utility.
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Affiliation(s)
- Steven M. Shamah
- Archemix Corporation, 300 Third Street, Cambridge, Massachusetts 02142
| | - Judith M. Healy
- Archemix Corporation, 300 Third Street, Cambridge, Massachusetts 02142
| | - Sharon T. Cload
- Archemix Corporation, 300 Third Street, Cambridge, Massachusetts 02142
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45
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Spangler C, Schaeferling M, Wolfbeis OS. Fluorescent probes for microdetermination of inorganic phosphates and biophosphates. Mikrochim Acta 2007. [DOI: 10.1007/s00604-007-0897-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Abstract
Recently, aptamers began to emerge as therapeutics. In this issue of Chemistry & Biology, Famulok and colleagues [1] present a twist on this concept, using an enzyme-inhibiting aptamer as a tool to screen for small molecules that block HIV replication.
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Affiliation(s)
- Casey C Fowler
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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47
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Chiuman W, Li Y. Simple fluorescent sensors engineered with catalytic DNA 'MgZ' based on a non-classic allosteric design. PLoS One 2007; 2:e1224. [PMID: 18030352 PMCID: PMC2077808 DOI: 10.1371/journal.pone.0001224] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2007] [Accepted: 10/30/2007] [Indexed: 11/20/2022] Open
Abstract
Most NAE (nucleic acid enzyme) sensors are composed of an RNA-cleaving catalytic motif and an aptameric receptor. They operate by activating or repressing the catalytic activity of a relevant NAE through the conformational change in the aptamer upon target binding. To transduce a molecular recognition event to a fluorescence signal, a fluorophore-quencher pair is attached to opposite ends of the RNA substrate such that when the NAE cleaves the substrate, an increased level of fluorescence can be generated. However, almost all NAE sensors to date harbor either NAEs that cannot accommodate a fluorophore-quencher pair near the cleavage site or those that can accept such a modification but require divalent transition metal ions for catalysis. Therefore, the signaling magnitude and the versatility of current NAE sensors might not suffice for analytical and biological applications. Here we report an RNA-cleaving DNA enzyme, termed ‘MgZ’, which depends on Mg2+ for its activity and can accommodate bulky dye moieties next to the cleavage site. MgZ was created by in vitro selection. The selection scheme entailed acidic buffering and ethanol-based reaction stoppage to remove selfish DNAs. Characterization of MgZ revealed a three-way junction structure, a cleavage rate of 1 min−1, and 26-fold fluorescence enhancement. Two ligand-responsive NAE sensors were rationally designed by linking an aptamer sequence to the substrate of MgZ. In the absence of the target, the aptamer-linked substrate is locked into a conformation that prohibits MgZ from accessing the substrate. In the presence of the target, the aptamer releases the substrate, which induces MgZ-mediated RNA cleavage. The discovery of MgZ and the introduction of the above NAE sensor design strategy should facilitate future efforts in sensor engineering.
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Affiliation(s)
- William Chiuman
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * To whom correspondence should be addressed. E-mail:
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48
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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49
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Elowe NH, Nutiu R, Allali-Hassani A, Cechetto JD, Hughes DW, Li Y, Brown ED. Small-molecule screening made simple for a difficult target with a signaling nucleic acid aptamer that reports on deaminase activity. Angew Chem Int Ed Engl 2007; 45:5648-52. [PMID: 16856187 DOI: 10.1002/anie.200601695] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nadine H Elowe
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
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50
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Sun H, Low KE, Woo S, Noble RL, Graham RJ, Connaughton SS, Gee MA, Lee LG. Real-time protein kinase assay. Anal Chem 2007; 77:2043-9. [PMID: 15801736 DOI: 10.1021/ac048280e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a novel, real-time fluorogenic kinase assay. The peptide substrates are synthesized with a fluorescent dye and a hydrocarbon tail. The substrate self-assembles into micelles, increasing the local concentration of the dye and quenching its fluorescence. Upon phosphorylation, the fluorescence intensity increases 4-6-fold due to micelle reorganization. Both dynamic light scattering data and cryoelectron microscope images show that the size and the shape of the phosphopeptide micelles are significantly different from micelles of substrate peptide. The system provides a robust fluorescence increase in a real-time protein kinase assay. Unlike other fluorogenic systems, the fluorophore may be distant from the serine, threonine, or tyrosine that is phosphorylated. Assays for several kinases, including PKA, PKC, p38, MAPKAP K2, akt, Erk1, and src-family kinases, have been developed. IC(50) values of inhibitors for PKC betaII determined with this technology are consistent with published values. The utility of this assay to high-throughput screening was demonstrated with Sigma's LOPAC library, a collection of 640 compounds with known biological activities, and satisfactory results were obtained.
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Affiliation(s)
- Hongye Sun
- Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA
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