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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Mazo M, Khudobin R, Balabaev N, Belov N, Ryzhikh V, Nikiforov R, Chatterjee R, Banerjee S. Structure and free volume of fluorine-containing polyetherimides with pendant di-tert-butyl groups investigated by molecular dynamics simulation. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR. Molecular recognition of nucleosomes by binding partners. Curr Opin Struct Biol 2019; 56:164-170. [PMID: 30991239 PMCID: PMC6656623 DOI: 10.1016/j.sbi.2019.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022]
Abstract
Nucleosomes represent the elementary units of chromatin packing and hubs in epigenetic signaling pathways. Across the chromatin and over the lifetime of the eukaryotic cell, nucleosomes experience a broad repertoire of alterations that affect their structure and binding with various chromatin factors. Dynamics of the histone core, nucleosomal and linker DNA, and intrinsic disorder of histone tails add further complexity to the nucleosome interaction landscape. In light of our understanding through the growing number of experimental and computational studies, we review the emerging patterns of molecular recognition of nucleosomes by their binding partners and assess the basic mechanisms of its regulation.
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Affiliation(s)
- Seyit Kale
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yaroslav Markov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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4
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Linking chromatin composition and structural dynamics at the nucleosome level. Curr Opin Struct Biol 2019; 56:46-55. [DOI: 10.1016/j.sbi.2018.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
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Structure and Properties of High and Low Free Volume Polymers Studied by Molecular Dynamics Simulation. COMPUTATION 2019. [DOI: 10.3390/computation7020027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Using molecular dynamics, a comparative study was performed of two pairs of glassy polymers, low permeability polyetherimides (PEIs) and highly permeable Si-containing polytricyclononenes. All calculations were made with 32 independent models for each polymer. In both cases, the accessible free volume (AFV) increases with decreasing probe size. However, for a zero-size probe, the curves for both types of polymers cross the ordinate in the vicinity of 40%. The size distribution of free volume in PEI and highly permeable polymers differ significantly. In the former case, they are represented by relatively narrow peaks, with the maxima in the range of 0.5–1.0 Å for all the probes from H2 to Xe. In the case of highly permeable Si-containing polymers, much broader peaks are observed to extend up to 7–8 Å for all the gaseous probes. The obtained size distributions of free volume and accessible volume explain the differences in the selectivity of the studied polymers. The surface area of AFV is found for PEIs using Delaunay tessellation. Its analysis and the chemical nature of the groups that form the surface of free volume elements are presented and discussed.
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