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Wang X, Jing S, Wang W, Wang J. Direct and noninvasive fluorescence analysis of an RNA-protein interaction based on a CRISPR/Cas12a-powered assay. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122884. [PMID: 37210856 DOI: 10.1016/j.saa.2023.122884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
RNA-protein interactions (RPIs) play critical roles in gene transcription and protein expression, but current analytical methods for RPIs are mainly performed in an invasive manner, involving special RNA/protein labeling, hampering access to intact and precise information on RPIs. In this work, we present the first CRISPR/Cas12a-based fluorescence assay for the direct analysis of RPIs without RNA/protein labeling steps. Select vascular endothelial growth factor 165 (VEGF165)/its RNA aptamer interaction as a model, the RNA sequence simultaneously serves as both the aptamer of VEGF165 and crRNA of CRISPR/Cas12a system, and the presence of VEGF165 facilitates VEGF165/its RNA aptamer interaction, thus prohibiting the formation of Cas12a-crRNA-DNA ternary complex along with low fluorescence signal. The assay showed a detection limit of 0.23 pg mL-1, and good performance in serum-spiked samples with an RSD of 0.4 %-13.1 %. This simple and selective strategy opens the door for establishing CRISPR/Cas-based biosensors for gaining intact information on RPIs, and shows widespread potential for other RPIs analysis.
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Affiliation(s)
- Xueliang Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Shaozhen Jing
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China
| | - Wanhe Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
| | - Jing Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Collaborative Innovation Center of NPU, Shanghai 201100, P.R. China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China; Northwestern Polytechnical University Chongqing Technology Innovation Center, Chongqing 400000, PR China.
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Shraim AS, Abdel Majeed BA, Al-Binni M, Hunaiti A. Therapeutic Potential of Aptamer-Protein Interactions. ACS Pharmacol Transl Sci 2022; 5:1211-1227. [PMID: 36524009 PMCID: PMC9745894 DOI: 10.1021/acsptsci.2c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between 25 and 100 nucleotides which fold into three-dimensional structures capable of binding to target molecules. Specific aptamers can be isolated against a large variety of targets through efficient and relatively cheap methods, and they demonstrate target-binding affinities that sometimes surpass those of antibodies. Consequently, interest in aptamers has surged over the past three decades, and their application has shown promise in advancing knowledge in target analysis, designing therapeutic interventions, and bioengineering. With emphasis on their therapeutic applications, aptamers are emerging as a new innovative class of therapeutic agents with promising biochemical and biological properties. Aptamers have the potential of providing a feasible alternative to antibody- and small-molecule-based therapeutics given their binding specificity, stability, low toxicity, and apparent non-immunogenicity. This Review examines the general properties of aptamers and aptamer-protein interactions that help to understand their binding characteristics and make them important therapeutic candidates.
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Affiliation(s)
- Ala’a S. Shraim
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Bayan A. Abdel Majeed
- Department
of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328 Amman, Jordan
- Pharmacological
and Diagnostic Research Center (PDRC), Al-Ahliyya
Amman University, 19328 Amman, Jordan
| | - Maysaa’
Adnan Al-Binni
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
| | - Abdelrahim Hunaiti
- Department
of Clinical Laboratory Sciences, School of Science, The University of Jordan, 11942 Amman, Jordan
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3
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Uda MNA, Gopinath SCB, Hashim U, Halim NH, Parmin NA, Uda MNA, Adam T, Anbu P. Silica and graphene mediate arsenic detection in mature rice grain by a newly patterned current-volt aptasensor. Sci Rep 2021; 11:14688. [PMID: 34282233 PMCID: PMC8289824 DOI: 10.1038/s41598-021-94145-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Arsenic is a major global threat to the ecosystem. Here we describe a highly accurate sensing platform using silica nanoparticles/graphene at the surface of aluminum interdigitated electrodes (Al IDE), able to detect trace amounts of arsenic(III) in rice grain samples. The morphology and electrical properties of fabricated Al IDEs were characterized and standardized using AFM, and SEM with EDX analyses. Micrometer scale Al IDEs were fabricated with silicon, aluminum, and oxygen as primary elements. Validation of the bare Al IDE with electrolyte fouling was performed at different pH levels. The sensing surface was stable with no electrolyte fouling at pH 7. Each chemical modification step was monitored with current-volt measurement. The surface chemical bonds were characterized by fourier transform infrared spectroscopy (FTIR) and revealed different peaks when interacting with arsenic (1600-1000 cm-1). Both silica nanoparticles and graphene presented a sensitive limit of detection as measured by slope calibration curves at 0.0000001 pg/ml, respectively. Further, linear regression was established using ΔI (A) = 3.86 E-09 log (Arsenic concentration) [g/ml] + 8.67 E-08 [A] for silica nanoparticles, whereas for graphene Y = 3.73 E-09 (Arsenic concentration) [g/ml] + 8.52 E-08 on the linear range of 0.0000001 pg/ml to 0.01 pg/ml. The R2 for silica (0.96) and that of graphene (0.94) was close to the maximum (1). Modification with silica nanoparticles was highly stable. The potential use of silica nanoparticles in the detection of arsenic in rice grain extract can be attributed to their size and stability.
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Affiliation(s)
- M. N. A. Uda
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia ,grid.430704.40000 0000 9363 8679Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
| | - Subash C. B. Gopinath
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia ,grid.430704.40000 0000 9363 8679Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
| | - Uda Hashim
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - N. H. Halim
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - N. A. Parmin
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - M. N. Afnan Uda
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia
| | - Tijjani Adam
- grid.430704.40000 0000 9363 8679Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis Malaysia ,grid.430704.40000 0000 9363 8679Faculty of Electronics Engineering Technology, Universiti Malaysia Perlis, 02600 Arau, Perlis Malaysia
| | - Periasamy Anbu
- grid.202119.90000 0001 2364 8385Department of Biological Engineering, College of Engineering, Inha University, Incheon, Republic of Korea
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Sun H, Bao X, Yao X, Gopinath SCB, Min Y. Aptasensing luteinizing hormone to determine gynecological endocrine complications on graphene oxide layered sensor. Biotechnol Appl Biochem 2021; 69:1509-1516. [PMID: 34278604 DOI: 10.1002/bab.2223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 11/09/2022]
Abstract
Luteinizing hormone (LH)/lutropin is an interstitial cell-stimulating hormone playing a predominant role in the reproductive system, and highly correlated with the infertility treatment in both men and women. This research was concentrated to quantify LH level by using interdigitated electrode sensor. To improve the electric current flow, sensing electrode was modified with graphene oxide (GO) and the aptamer probe was attached on GO through biotin-streptavidin linker. Current responses were measured with aptamer-LH interaction at the target concentrations between 7.5 nM and 1 μM and the detection limit of LH was calculated as 60 nM with the determination coefficient (R2 ) value, 0.9229 [y = 1.296x - 2.8435] on a linear range from 30 nM to 1 μM. Further, biofouling effect on sensing electrode surface was analyzed with complementary aptamer sequence, control proteins (albumin and globulin). The above GO-aptamer-modified interdigitated electrode sensor helps to quantify LH level and diagnose gynecological endocrinology-related complications.
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Affiliation(s)
- Huanhuan Sun
- Department of Obstetrics and Gynecology, Harbin Red Cross Central Hospital, Harbin, Heilongjiang, China
| | - Xiucui Bao
- Department of Obstetrics, Yihe Maternity District of Cangzhou People's Hospital, Cangzhou, Hebei, China
| | - Xiaoling Yao
- Department of Obstetrics and Gynecology, Yihe Maternity District of Cangzhou People's Hospital, Cangzhou, Hebei, China
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia.,Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - Yifei Min
- Department of Gynecology, Changzhou No. 2 People's Hospital, The Affiliated Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, China
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5
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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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6
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Wu C, Kurinomaru T. Development of the Bioluminescent Immunoassay for the Detection of 5-Hydroxymethylcytosine in Dinoflagellate. ANAL SCI 2018; 35:301-305. [PMID: 30416167 DOI: 10.2116/analsci.18p401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cypridina luciferase is a bioluminescent enzyme that has been used as a reporter either in gene expression reporter assays or in immunoassays accompanied by an antibody. To develop a novel bioluminescent assay for the detection of 5-hydroxymethylcytosine, we first conjugated Cypridina luciferase to the antibody against 5-hydroxymethylcytosine. Next, we performed modifications of guanine bases in the genome DNA samples with 4-azidophenylglyoxal and the biotinylation via the azide-Staudinger ligation, which allowed streptavidin to capture and immobilize the genome DNA samples under mild conditions. The detection of 5-hydroxymethylcytosine in the genome DNA samples was performed with the conjugates between Cypridina luciferase and the reduced antibody, which was also confirmed by a surface plasmon resonance assay with the antibody alone. The results obtained from the bioluminescent assay were in good agreement with that of the surface plasmon resonance assay. We succeeded in the detection of 5hmC in the genome DNA samples from the dinoflagellate Pyrocystis Lunula by using this method.
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Affiliation(s)
- Chun Wu
- BioMedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takaaki Kurinomaru
- BioMedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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7
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Wu C. Biotinylation of Deoxyguanosine at the Abasic Site in Double-Stranded Oligodeoxynucleotides. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2016; 2016:4681421. [PMID: 27818833 PMCID: PMC5080518 DOI: 10.1155/2016/4681421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Biotinylation of deoxyguanosine at an abasic site in double-stranded oligodeoxynucleotides was studied. The biotinylation of deoxyguanosine is achieved by copper-catalyzed click reaction after the conjugation of the oligodeoxynucleotide with 2-oxohex-5-ynal. The biotinylation enables visualization of the biotinylated oligodeoxynucleotides by chemiluminescence on a nylon membrane. In order to investigate the biotinylated site, the biotinylated oligodeoxynucleotides were amplified by the DNA polymerase chain reaction. Replacement of guanine opposing the abasic site with adenine generated by the activity of the terminal deoxynucleotidyl transferase of DNA polymerase was detected by DNA sequencing analysis and restriction endonuclease digestion. This study suggests that 2-oxohex-5-ynal may be useful for the detection of the unpaired deoxyguanosine endogenously generated at abasic sites in genomic DNA.
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Affiliation(s)
- Chun Wu
- Biomedical Research Institute, AIST, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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8
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Cell-targeting aptamers act as intracellular delivery vehicles. Appl Microbiol Biotechnol 2016; 100:6955-69. [PMID: 27350620 DOI: 10.1007/s00253-016-7686-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/12/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded nucleic acids or peptides identified from a randomized combinatorial library through specific interaction with the target of interest. Targets can be of any size, from small molecules to whole cells, attesting to the versatility of aptamers for binding a wide range of targets. Aptamers show drug properties that are analogous to antibodies, with high specificity and affinity to their target molecules. Aptamers can penetrate disease-causing microbial and mammalian cells. Generated aptamers that target surface biomarkers act as cell-targeting agents and intracellular delivery vehicles. Within this context, the "cell-internalizing aptamers" are widely investigated via the process of cell uptake with selective binding during in vivo systematic evolution of ligands by exponential enrichment (SELEX) or by cell-internalization SELEX, which targets cell surface antigens to be receptors. These internalizing aptamers are highly preferable for the localization and functional analyses of multiple targets. In this overview, we discuss the ways by which internalizing aptamers are generated and their successful applications. Furthermore, theranostic approaches featuring cell-internalized aptamers are discussed with the purpose of analyzing and diagnosing disease-causing pathogens.
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9
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Fillebeen C, Wilkinson N, Pantopoulos K. Electrophoretic mobility shift assay (EMSA) for the study of RNA-protein interactions: the IRE/IRP example. J Vis Exp 2014:52230. [PMID: 25548934 PMCID: PMC4396942 DOI: 10.3791/52230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron regulatory proteins, IRP1 and IRP2. They bind to iron responsive elements (IREs) within the untranslated regions (UTRs) of several target mRNAs, thereby controlling the mRNAs translation or stability. IRE/IRP interactions have been widely studied by EMSA. Here, we describe the EMSA protocol for analyzing the IRE-binding activity of IRP1 and IRP2, which can be generalized to assess the activity of other RNA-binding proteins as well. A crude protein lysate containing an RNA-binding protein, or a purified preparation of this protein, is incubated with an excess of(32) P-labeled RNA probe, allowing for complex formation. Heparin is added to preclude non-specific protein to probe binding. Subsequently, the mixture is analyzed by non-denaturing electrophoresis on a polyacrylamide gel. The free probe migrates fast, while the RNA/protein complex exhibits retarded mobility; hence, the procedure is also called "gel retardation" or "bandshift" assay. After completion of the electrophoresis, the gel is dried and RNA/protein complexes, as well as free probe, are detected by autoradiography. The overall goal of the protocol is to detect and quantify IRE/IRP and other RNA/protein interactions. Moreover, EMSA can also be used to determine specificity, binding affinity, and stoichiometry of the RNA/protein interaction under investigation.
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Affiliation(s)
- Carine Fillebeen
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University
| | - Nicole Wilkinson
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University;
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Gopinath SCB, Lakshmipriya T, Awazu K. Colorimetric detection of controlled assembly and disassembly of aptamers on unmodified gold nanoparticles. Biosens Bioelectron 2014; 51:115-23. [PMID: 23948242 PMCID: PMC7125824 DOI: 10.1016/j.bios.2013.07.037] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/24/2013] [Accepted: 07/21/2013] [Indexed: 10/27/2022]
Abstract
Aptamers are nucleic acid ligands that are generated artificially by in vitro selection and behave similar to antibodies. The development of aptamer-based sensing systems or strategies has been in vogue for the past few decades, because aptamers are smaller in size, stable, cheaper and undergo easier modifications. Owing to these advantages, several facile aptamer-based colorimetric strategies have been created by controlling the assembly and disassembly of aptamers on unmodified gold nanoparticle probes. As these kinds of assay systems are rapid and can be visualized unaided by instruments, they have recently become an attractive method of choice. The formation of purple-colored aggregates (attraction) from the red dispersed (repulsion) state of GNPs in the presence of mono- or divalent ions is the key principle behind this assay. Due to its simplicity and versatility, this assay can be an alternative to existing diagnostic assays. Here, we have investigated the critical elements involved in colorimetric assays, and have screened different proteins and small ligands to evaluate biofouling on GNPs.
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Affiliation(s)
- Subash C B Gopinath
- Electronics and Photonics Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
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11
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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12
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Lévesque D, Reymond C, Perreault JP. Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme. PLoS One 2012; 7:e40309. [PMID: 22768274 PMCID: PMC3386971 DOI: 10.1371/journal.pone.0040309] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/04/2012] [Indexed: 01/09/2023] Open
Abstract
The HDV ribozyme’s folding pathway is, by far, the most complex folding
pathway elucidated to date for a small ribozyme. It includes 6 different steps
that have been shown to occur before the chemical cleavage. It is likely that
other steps remain to be discovered. One of the most critical of these unknown
steps is the formation of the trans Watson-Crick GU base
pair within loop III. The U23 and G28 nucleotides that
form this base pair are perfectly conserved in all natural variants of the
HDV ribozyme, and therefore are considered as being part of the signature
of HDV-like ribozymes. Both the formation and the transformation of this base
pair have been studied mainly by crystal structure and by molecular dynamic
simulations. In order to obtain physical support for the formation of this
base pair in solution, a set of experiments, including direct mutagenesis,
the site-specific substitution of chemical groups, kinetic studies, chemical
probing and magnesium-induced cleavage, were performed with the specific goal
of characterizing this trans Watson-Crick GU base pair in
an antigenomic HDV ribozyme. Both U23 and G28 can be
substituted for nucleotides that likely preserve some of the H-bond interactions
present before and after the cleavage step. The formation of the more stable trans
Watson-Crick base pair is shown to be a post-cleavage event, while a possibly
weaker trans Watson-Crick/Hoogsteen interaction seems to
form before the cleavage step. The formation of this unusually stable post-cleavage
base pair may act as a driving force on the chemical cleavage by favouring
the formation of a more stable ground state of the product-ribozyme complex.
To our knowledge, this represents the first demonstration of a potential stabilising
role of a post-cleavage conformational switch event in a ribozyme-catalyzed
reaction.
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Affiliation(s)
- Dominique Lévesque
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
| | - Cédric Reymond
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Département de Biochimie, Faculté
de Médecine et des Sciences de la Santé, Université de
Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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13
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A rapid and cost effective method in purifying small RNA. World J Microbiol Biotechnol 2011; 28:105-11. [DOI: 10.1007/s11274-011-0797-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022]
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Jing M, Bowser MT. Methods for measuring aptamer-protein equilibria: a review. Anal Chim Acta 2011; 686:9-18. [PMID: 21237304 PMCID: PMC3026478 DOI: 10.1016/j.aca.2010.10.032] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 12/11/2022]
Abstract
Aptamers are single stranded DNA or RNA molecules that have been selected using in vitro techniques to bind target molecules with high affinity and selectivity, rivaling antibodies in many ways. In order to use aptamers in research and clinical applications, a thorough understanding of aptamer-target binding is necessary. In this article, we review methods for assessing aptamer-protein binding using separation based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis, and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry. For each method the principle, range of application and important features, such as sample consumption, experimental time and complexity, are summarized and compared.
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Affiliation(s)
- Meng Jing
- University of Minnesota, Department of Chemistry, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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