1
|
Wang J, Zhu L, Li T, Li X, Huang K, Xu W. Multiple functionalities of functional nucleic acids for developing high-performance lateral flow assays. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
2
|
Jiang S, Liu M, Tantai W, Xu Q, Zou X, Ma F, Zhang CY. Aptamer-mediated rolling circle amplification for label-free and sensitive detection of histone acetyltransferase activity. Chem Commun (Camb) 2021; 57:2041-2044. [PMID: 33507183 DOI: 10.1039/d0cc07763a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We develop for the first time an aptamer-mediated rolling circle amplification approach for label-free and sensitive detection of histone-modifying enzyme (HME) activity. This method can achieve femtomolar sensitivity for histone acetyltransferase Tip60 assay, which is the most sensitive HME assay reported so far. It can be further applied for inhibitor screening, enzyme kinetic analysis, and endogenous Tip60 measurement in cancer cells.
Collapse
Affiliation(s)
- Su Jiang
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | | | | | | | | | | | | |
Collapse
|
3
|
Current trends in affinity-based monoliths in microextraction approaches: A review. Anal Chim Acta 2019; 1084:1-20. [DOI: 10.1016/j.aca.2019.07.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/15/2022]
|
4
|
Chen Y, Jiang B, Hu Y, Deng N, Zhao B, Li X, Liang Z, Zhang L, Zhang Y. Aptamer functionalized magnetic graphene oxide nanocomposites for highly selective capture of histones. Electrophoresis 2019; 40:2135-2141. [PMID: 30977149 DOI: 10.1002/elps.201900061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 11/11/2022]
Abstract
The binding coverage of aptamer was an important restricted factor for aptamer-based affinity enrichment strategy for capturing target molecules. Herein, we designed and prepared aptamer functionalized graphene oxide based nanocomposites (GO/NH2 -NTA/Fe3 O4 /PEI/Au), and the coverage density of aptamer was high to 33.1 nmol/mg. The high aptamer coverage density was contributed to the large surface area of graphene oxide. The successive modification of Nα,Nα-Bis(carboxymethyl)-L-lysine, magnetic nanoparticles, polyethylenimine, and Au nanoparticles ensured the histone purification with fast speed and high purity. Histones could be captured rapidly and specifically from nucleoproteins by our aptamer based purification strategy, while traditional acid-extraction could not specifically enrich histones. Compared with traditional acid-extraction method, rapid and efficient discovery of histones and their post-translational modifications, such as several kinds of methylation at H3.1K9 and H3.1K27, were achieved confidently. It demonstrated that our aptamer functionalized magnetic graphene oxide nanocomposites have a great potential for histone analysis.
Collapse
Affiliation(s)
- Yuanbo Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Bo Jiang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yechen Hu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Nan Deng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.,Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, P. R. China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Xiao Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Zhen Liang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China
| |
Collapse
|
5
|
Ma F, Jiang S, Zhang CY. Recent advances in histone modification and histone modifying enzyme assays. Expert Rev Mol Diagn 2018; 19:27-36. [DOI: 10.1080/14737159.2019.1559053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| |
Collapse
|
6
|
Catuogno S, Esposito CL, Ungaro P, de Franciscis V. Nucleic Acid Aptamers Targeting Epigenetic Regulators: An Innovative Therapeutic Option. Pharmaceuticals (Basel) 2018; 11:ph11030079. [PMID: 30149585 PMCID: PMC6161095 DOI: 10.3390/ph11030079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms include DNA methylation, posttranslational modifications of histones, chromatin remodeling factors, and post transcriptional gene regulation by noncoding RNAs. All together, these processes regulate gene expression by changing chromatin organization and DNA accessibility. Targeting enzymatic regulators responsible for DNA and chromatin modifications hold promise for modulating the transcriptional regulation of genes that are involved in cancer, as well as in chronic noncommunicable metabolic diseases like obesity, diabetes, and cardiovascular diseases. Increasingly studies are emerging, leading to the identification of specific and effective molecules targeting epigenetic pathways involved in disease onset. In this regard, RNA interference, which uses small RNAs to reduce gene expression and nucleic acid aptamers are arising as very promising candidates in therapeutic approach. Common to all these strategies is the imperative challenge of specificity. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules due to their ability to bind with high affinity to specific ligands, their high chemical flexibility as well as tissue penetration capability. In this review, we will focus on the recent progress in the field of aptamers used as targeting moieties able to recognize and revert epigenetics marks involved in diseases onset.
Collapse
Affiliation(s)
- Silvia Catuogno
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Carla Lucia Esposito
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Paola Ungaro
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| | - Vittorio de Franciscis
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR "G. Salvatore", Via S. Pansini 5, 80131 Naples, Italy.
| |
Collapse
|
7
|
Lu C, Tian S, Zhai G, Yuan Z, Li Y, He X, Zhang Y, Zhang K. Probing the Binding Interfaces of Histone-Aptamer by Photo Cross-Linking Mass Spectrometry. ACS Chem Biol 2017; 12:57-62. [PMID: 27936569 DOI: 10.1021/acschembio.6b00797] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Histone proteins, which could interact with DNA, play important roles in the regulation of chromatin structures, transcription, and other DNA-based biological processes. Here, we developed a novel aptamer-based probe for the analysis of histone H4-aptamer interfaces. This probe contains a DNA sequence for specific recognition of histone H4, a biotin tag for affinity enrichment, an aryl azide photoactive group for cross-linking and a cleavable disulfide group to dissociate aptamer from labeled histones. We successfully achieved specific enrichment of histone H4 and further developed a new analysis strategy for histone-aptamer interaction by photo cross-linking mass spectrometry. The binding area of histone H4 to aptamer was investigated and discussed for the first time. This strategy exhibits great potential and might further contribute to the understanding of histone-DNA interaction patterns.
Collapse
Affiliation(s)
- Congcong Lu
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Shanshan Tian
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Guijin Zhai
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| | - Zuofei Yuan
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yijun Li
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Xiwen He
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
| | - Yukui Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Kai Zhang
- Department
of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
- Tianjin
Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment
and Disease (Ministry of Education), Department of Biochemistry and
Molecular Biology, Tianjin Medical University, Tianjin 300070, People’s Republic of China
| |
Collapse
|
8
|
Selective tools for the solid-phase extraction of Ochratoxin A from various complex samples: immunosorbents, oligosorbents, and molecularly imprinted polymers. Anal Bioanal Chem 2016; 408:6983-99. [PMID: 27585915 DOI: 10.1007/s00216-016-9886-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/21/2016] [Accepted: 08/16/2016] [Indexed: 12/27/2022]
Abstract
The evolution of instrumentation in terms of separation and detection has allowed a real improvement of the sensitivity and the analysis time. However, the analysis of ultra-traces of toxins such as ochratoxin A (OTA) from complex samples (foodstuffs, biological fluids…) still requires a step of purification and of preconcentration before chromatographic determination. In this context, extraction sorbents leading to a molecular recognition mechanism appear as powerful tools for the selective extraction of OTA and of its structural analogs in order to obtain more reliable and sensitive quantitative analyses of these compounds in complex media. Indeed, immunosorbents and oligosorbents that are based on the use of immobilized antibodies and of aptamers, respectively, and that are specific to OTA allow its selective clean-up from complex samples with high enrichment factors. Similar molecular recognition mechanisms can also be obtained by developing molecularly imprinted polymers, the synthesis of which leads to the formation of cavities that are specific to OTA, thus mimicking the recognition site of the biomolecules. Therefore, the principle, the advantages, the limits of these different types of extraction tools, and their complementary behaviors will be presented. The introduction of these selective tools in miniaturized devices will also be discussed.
Collapse
|
9
|
Du F, Guo L, Qin Q, Zheng X, Ruan G, Li J, Li G. Recent advances in aptamer-functionalized materials in sample preparation. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
10
|
Qiao L, Lv B, Feng X, Li C. A new application of aptamer: One-step purification and immobilization of enzyme from cell lysates for biocatalysis. J Biotechnol 2015; 203:68-76. [PMID: 25835950 DOI: 10.1016/j.jbiotec.2015.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 12/24/2022]
Abstract
Aptamers are nucleic acid-based high affinity ligands that are able to capture their corresponding target through molecular recognition. In this study, several DNA aptamers with high affinity and specificity for β-glucuronidases (PGUS-E) were obtained by our modified SELEX method. Among them, Apt5 and Apt9 were selected as representatives and covalently linked to magnetic beads, respectively. The aptamer-modified magnetic beads were characterized and successfully applied to one-step purification and immobilization of PGUS-E from the complex cell lysates. By conveniently adjusting the pH and ion strength, the PGUS-E purities reached 84% for Apt5-modified beads and 88% for Apt9-modified beads. Moreover, the maximum PGUS-E capturing capacity of the Apt5 and Apt9 modified magnetic beads were found to be 31.75μg/mg and 32.95μg/mg, respectively. The immobilized PGUS-E on aptamer-based magnetic beads showed good reusability, and the conversion of glycyrrhizin still remained more than 70% after 7 cycles. In addition, the aptamer-modified beads support can be easily regenerated, and the conversion rate of glycyrrhizin (GL) was still 62% after the 7th cycle of regeneration. This investigation can be easily extended to other enzyme systems and may help open a generic route to develop a novel enzyme immobilization technology for biocatalysis based on aptamer.
Collapse
Affiliation(s)
- Lifeng Qiao
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, Xinjiang, PR China
| | - Bo Lv
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xudong Feng
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Chun Li
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China.
| |
Collapse
|
11
|
Aptamer-based-sorbents for sample treatment--a review. Anal Bioanal Chem 2014; 407:681-98. [PMID: 25286873 DOI: 10.1007/s00216-014-8129-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
To improve selectivity during sample pretreatment, various selective tools inducing a molecular recognition mechanism during the extraction procedure have been developed, such as sorbents constituted of immobilized antibodies, i.e., immunosorbents, or molecularly imprinted polymers. More recently, as an alternative to both previous approaches, aptamers immobilized onto a solid support, i.e., oligosorbents, were proposed. Thanks to the high affinity and high selectivity of the interaction that some aptamers offer toward some target analytes, they also provide powerful techniques that make selective extraction and the concentration of a target analyte from liquid matrices in one step or sample purification of extracts from solid matrices possible. This review describes the development and the properties of these oligosorbents developed for different types of targets-pharmaceuticals, mycotoxins, proteins, cells, etc. After describing the immobilization procedures, we discuss different parameters characterizing the potential of aptamer-based supports as extraction sorbents. Close relations exist between extraction recoveries and the affinity and amounts of aptamers immobilized on the extraction device. In addition, analyte-aptamer interactions may be affected by matrix components and by additives in the samples. This may also lower extraction recoveries and affect the stability and the possible reusability of the aptamer-based sorbent. All these points are discussed and illustrated. Numerous examples of applications of these sorbents to the treatment of complex samples such as food samples, environmental samples, and biological fluids are also reported. Their association with analytical devices, from conventional to miniaturized analytical systems, is also discussed.
Collapse
|
12
|
Zhang K, Tian S, Fan E. Protein lysine acetylation analysis: current MS-based proteomic technologies. Analyst 2013; 138:1628-36. [DOI: 10.1039/c3an36837h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
|