1
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Li H, Li R, He S, Wang Y, Fang W, Jin Y, Yang R, Liu Y, Ye Q, Peng X. An Aptamer-Embedded Two-Dimensional DNA Nanoscale Material with the Property of Cells Recruitment. NANO LETTERS 2023; 23:8399-8405. [PMID: 37339058 DOI: 10.1021/acs.nanolett.3c01240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Stem cells possess exceptional proliferation and differentiation abilities, making them highly promising for targeted recruitment research in tissue engineering and other clinical applications. DNA is a naturally water-soluble, biocompatible, and highly editable material that is widely used in cell recruitment research. However, DNA nanomaterials face challenges, such as poor stability, complex synthesis processes, and demanding storage conditions, which limit their potential applications. In this study, we designed a highly stable DNA nanomaterial that embeds nucleic acid aptamers in the single strand region. This material has the ability to specifically bind, recruit, and capture human mesenchymal stem cells. The synthesis process involves rolling circle amplification and topological isomerization, and it can be stored for extended periods under varying temperatures and humidity conditions. This DNA material offers high specificity, ease of fabrication, simple preservation, and low cost, providing a novel approach to stem cell recruitment strategies.
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Affiliation(s)
- Hongshu Li
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Rui Li
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Songlin He
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Institute of Orthopedics, the First Medical Center, Chinese PLA General Hospital; Beijing Key Lab of Regenerative Medicine in Orthopedics, Key Laboratory of Musculoskeletal Trauma & War Injuries PLA, Beijing 100853, P. R. China
| | - Yu Wang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Wenya Fang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yufeng Jin
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Rui Yang
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
| | - Xi Peng
- School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Nankai University Eye Institute, Nankai University, Tianjin 300071, P. R. China
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2
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Kalathingal M, Rhee YM. Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study. J Comput Chem 2023; 44:1129-1137. [PMID: 36625560 DOI: 10.1002/jcc.27070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Macugen is a therapeutic RNA aptamer against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for angiogenesis. It has been reported that Macugen inhibits angiogenesis by specifically binding to the heparin binding domain (HBD) of VEGF165. The mechanism of the molecular recognition between HBD and Macugen is investigated here using all-atom molecular dynamics simulations. We find that Macugen recognizes HBD by an induced-fit mechanism with major conformational changes in Macugen and almost no changes in the structure of HBD, whereas HBD recognizes Macugen by a conformational selection mechanism.
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Affiliation(s)
- Mahroof Kalathingal
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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3
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Zhao S, Li X, Wen Z, Zou M, Yu G, Liu X, Mao J, Zhang L, Xue Y, Fu R, Wang S. Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy. iScience 2022; 25:105322. [DOI: 10.1016/j.isci.2022.105322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022] Open
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4
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Cheng EL, Cardle II, Kacherovsky N, Bansia H, Wang T, Zhou Y, Raman J, Yen A, Gutierrez D, Salipante SJ, des Georges A, Jensen MC, Pun SH. Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing. J Am Chem Soc 2022; 144:13851-13864. [PMID: 35875870 PMCID: PMC10024945 DOI: 10.1021/jacs.2c05349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The clinical manufacturing of chimeric antigen receptor (CAR) T cells includes cell selection, activation, gene transduction, and expansion. While the method of T-cell selection varies across companies, current methods do not actively eliminate the cancer cells in the patient's apheresis product from the healthy immune cells. Alarmingly, it has been found that transduction of a single leukemic B cell with the CAR gene can confer resistance to CAR T-cell therapy and lead to treatment failure. In this study, we report the identification of a novel high-affinity DNA aptamer, termed tJBA8.1, that binds transferrin receptor 1 (TfR1), a receptor broadly upregulated by cancer cells. Using competition assays, high resolution cryo-EM, and de novo model building of the aptamer into the resulting electron density, we reveal that tJBA8.1 shares a binding site on TfR1 with holo-transferrin, the natural ligand of TfR1. We use tJBA8.1 to effectively deplete B lymphoma cells spiked into peripheral blood mononuclear cells with minimal impact on the healthy immune cell composition. Lastly, we present opportunities for affinity improvement of tJBA8.1. As TfR1 expression is broadly upregulated in many cancers, including difficult-to-treat T-cell leukemias and lymphomas, our work provides a facile, universal, and inexpensive approach for comprehensively removing cancerous cells from patient apheresis products for safe manufacturing of adoptive T-cell therapies.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States.,Seattle Children's Therapeutics, Seattle, Washington 98101, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Harsh Bansia
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States
| | - Yunshi Zhou
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jai Raman
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Albert Yen
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Dominique Gutierrez
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York (CUNY), New York, New York 10016, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195-7110, United States
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Michael C Jensen
- Seattle Children's Therapeutics, Seattle, Washington 98101, United States.,Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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5
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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6
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Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene. Int J Mol Sci 2021; 22:ijms22063234. [PMID: 33810132 PMCID: PMC8004769 DOI: 10.3390/ijms22063234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.
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7
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Allemailem KS, Almatroudi A, Alsahli MA, Basfar GT, Alrumaihi F, Rahmani AH, Khan AA. Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents. 3 Biotech 2020; 10:551. [PMID: 33269185 PMCID: PMC7686427 DOI: 10.1007/s13205-020-02546-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A. Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ghaiyda Talal Basfar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
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8
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Churcher ZR, Garaev D, Hunter HN, Johnson PE. Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer. Biophys J 2020; 119:1147-1156. [PMID: 32882188 DOI: 10.1016/j.bpj.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022] Open
Abstract
We have used magnetization transfer NMR experiments to measure the exchange rate constant (kex) of the imino protons in the unbound, cocaine-bound, and quinine-bound forms of the cocaine-binding DNA aptamer. Both long-stem 1 (MN4) and short-stem 1 (MN19) variants were analyzed, corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions of this aptamer, respectively. The kex values were measured as a function of temperature from 5 to 45°C to determine the thermodynamics of the base pair opening for MN4. We find that the base pairs close to the ligand-binding site become stronger upon ligand binding, whereas those located away from the binding site do not strengthen. With the buffer conditions used in this study, we observe imino 1H signals in MN19 not previously seen, which leads us to conclude that in the free form, both stem 2 and parts of stem 3 are formed and that the base pairs in stem 1 become structured or more rigid upon binding. This is consistent with the kex values for MN19 decreasing in both stem 1 and at the ligand-binding site. Based on the temperature dependence of the kex values, we find that MN19 is more dynamic than MN4 in the free and both ligand-bound forms. For MN4, ligand-binding results in the reduction of dynamics that are localized to the binding site. These results demonstrate that an aptamer in which the base pairs are preformed also experiences a reduction in dynamics with ligand binding.
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Affiliation(s)
- Zachary R Churcher
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Devid Garaev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Howard N Hunter
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada.
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9
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Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function. Comput Struct Biotechnol J 2019; 17:797-804. [PMID: 31312417 PMCID: PMC6607312 DOI: 10.1016/j.csbj.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
Base-pair opening is a conformational transition that is required for proper biological function of nucleic acids. Hydrogen exchange, observed by NMR spectroscopic experiments, is a widely used method to study the thermodynamics and kinetics of base-pair opening in nucleic acids. The hydrogen exchange data of imino protons are analyzed based on a two-state (open/closed) model for the base-pair, where hydrogen exchange only occurs from the open state. In this review, we discuss examples of how hydrogen exchange data provide insight into several interesting biological processes involving functional interactions of nucleic acids: i) selective recognition of DNA by proteins; ii) regulation of RNA cleavage by site-specific mutations; iii) intermolecular interaction of proteins with their target DNA or RNA; iv) formation of PNA:DNA hybrid duplexes. This review systematically summarizes hydrogen exchange theory for base-paired imino protons of nucleic acids. Base-pair opening kinetics explain how the DNA can be selectively recognized by its target proteins. Base-pair opening kinetics explain the mechanisms by which site-specific mutations regulate RNA cleavage. Hydrogen exchange studies can elucidate the intermolecular interaction of proteins with their target DNA or RNA.
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10
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Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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11
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Boussebayle A, Groher F, Suess B. RNA-based Capture-SELEX for the selection of small molecule-binding aptamers. Methods 2019; 161:10-15. [PMID: 30953759 DOI: 10.1016/j.ymeth.2019.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 11/16/2022] Open
Abstract
Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Moreover, we provide a comparative overview of our proposed methodology versus alternative in vitro selection protocols with a special focus on the design of the pool. Finally, we have included detailed notes to point out useful tips and pitfalls for future application.
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Affiliation(s)
- Adrien Boussebayle
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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12
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Yamasaki S, Amemiya T, Yabuki Y, Horimoto K, Fukui K. ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow. J Comput Aided Mol Des 2019; 33:497-507. [PMID: 30840170 PMCID: PMC7088279 DOI: 10.1007/s10822-019-00195-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Recent progress in molecular biology has revealed that many non-coding RNAs regulate gene expression or catalyze biochemical reactions in tumors, viruses and several other diseases. The tertiary structure of RNA molecules and RNA–RNA/protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. Current RNA drugs are split into two groups: antisense RNA molecules and aptamers. In this report, we present a novel workflow to predict RNA tertiary structures and RNA–RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. In this study, three analytical workflows for comprehensive structural analysis of RNA are introduced: (1) prediction of the tertiary structure of RNA; (2) prediction of the structure of RNA–RNA complexes and analysis of their interactions; and (3) prediction of the structure of RNA–protein complexes and analysis of their interactions. In an RNA–protein case study, we modeled the tertiary structure of pegaptanib, an aptamer drug, and performed docking calculations of the pegaptanib-vascular endothelial growth factor complex using a fragment of the interaction site of the aptamer. We also present molecular dynamics simulations of the RNA–protein complex to evaluate the affinity of the complex by mutating bases at the interaction interface. The results provide valuable information for designing novel features of aptamer-protein complexes.
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Affiliation(s)
- Satoshi Yamasaki
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo (IMSUT), 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Takayuki Amemiya
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yukimitsu Yabuki
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,IMSBIO Co., Ltd, 4-21-1-601 Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan
| | - Katsuhisa Horimoto
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuhiko Fukui
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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13
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Sakamoto T, Ennifar E, Nakamura Y. Thermodynamic study of aptamers binding to their target proteins. Biochimie 2017; 145:91-97. [PMID: 29054802 DOI: 10.1016/j.biochi.2017.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023]
Abstract
Aptamers are nucleic acids that bind to a target molecule with high affinity and specificity, which are selected from systematic evolution of ligands by exponential enrichment (SELEX). Aptamers feature high affinity and specificity to their target molecule and a large structural diversity; biophysical tools, together with structural studies, are essential to reveal the mechanism of aptamers recognition. Furthermore, understanding the mechanism of action would also contribute to their development for therapeutic applications. Isothermal titration calorimetry (ITC) is a fast and robust method to study the physical basis of molecular interactions. In a single experiment, it provides all thermodynamic parameters of a molecular interaction, including dissociation constant, Kd; Gibbs free energy change, ΔG; enthalpy change, ΔH; entropy change, ΔS; and stoichiometry, N. The development of modern microcalorimeters significantly contributed to the expansion of the ITC use in biological systems. Therefore, ITC has been applied to the development of small therapeutic agents that bind to target proteins and is increasingly being used to study aptamer-target protein interactions. This review focuses on thermodynamic approaches for understanding the molecular principles of aptamer-target interactions.
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Affiliation(s)
- Taiichi Sakamoto
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan.
| | - Eric Ennifar
- Structure and Dynamics of Biomolecular Machines, Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, F-67000 Strasbourg, France
| | - Yoshikazu Nakamura
- RIBOMIC Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan; The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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14
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Bhat J, Mondal S, Sengupta P, Chatterjee S. In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of c-MYC Oncogene. ACS OMEGA 2017; 2:4382-4397. [PMID: 30023722 PMCID: PMC6044917 DOI: 10.1021/acsomega.6b00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/20/2017] [Indexed: 06/08/2023]
Abstract
Overexpression of c-MYC oncogene is associated with cancer pathology. Expression of c-MYC is regulated by the G-quadruplex structure formed in the G-rich segment of nuclease hypersensitive element (NHE III1), that is, "Pu27", which is localized in the promoter region. Ligand-induced stabilization of the Pu27 structure has been identified as a novel target for cancer therapeutics. Here, we have explored the library of synthetic compounds against the predefined binding site of Pu27. Three compounds were selected based on the docking analyses; they were further scrutinized using all atom molecular dynamics simulations in an explicit water model. Simulated trajectories were scrutinized for conformational stability and ligand binding free energy estimation; essential dynamic behavior was determined using principal component analysis. One of the molecules, "TPP (1-(3-(4-(1,2,3-thiadiazol-4-yl)phenoxy)-2-hydroxypropyl)-4-carbamoylpiperidinium)", with the best results was considered for further evaluation. The theoretical observations are supported well by biophysical analysis using circular dichroism, isothermal titration calorimetry, and high-resolution NMR spectroscopy indicating association of TPP with Pu27. The in vitro studies were then translated into c-MYC overexpression in the T47D breast cancer cell line. Biological evaluation through the MTT assay, flow cytometric assay, RT-PCR, and reporter luciferase assay suggests that TPP downregulates the expression of c-MYC oncogene by arresting its promoter region. In silico and in vitro observations cumulatively suggest that the novel skeleton of TPP could be a potential anticancer agent by stabilizing the G-quadruplex formed in the Pu27 and consequently downregulating the expression of c-MYC oncogene. Derivation of new molecules on its skeleton may confer anticancer therapeutics for the next generation.
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15
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Wu X, Shaikh AB, Yu Y, Li Y, Ni S, Lu A, Zhang G. Potential Diagnostic and Therapeutic Applications of Oligonucleotide Aptamers in Breast Cancer. Int J Mol Sci 2017; 18:ijms18091851. [PMID: 28841163 PMCID: PMC5618500 DOI: 10.3390/ijms18091851] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is one of the most common causes of cancer related deaths in women. Currently, with the development of early detection, increased social awareness and kinds of treatment options, survival rate has improved in nearly every type of breast cancer patients. However, about one third patients still have increased chances of recurrence within five years and the five-year relative survival rate in patients with metastasis is less than 30%. Breast cancer contains multiple subtypes. Each subtype could cause distinct clinical outcomes and systemic interventions. Thereby, new targeted therapies are of particular importance to solve this major clinical problem. Aptamers, often termed “chemical antibodies”, are functionally similar to antibodies and have demonstrated their superiority of recognizing target with high selectivity, affinity and stability. With these intrinsic properties, aptamers have been widely studied in cancer biology and some are in clinical trials. In this review, we will firstly discuss about the global impacts and mechanisms of breast cancer, then briefly highlight applications of aptamers that have been developed for breast cancer and finally summarize various challenges in clinical translation of aptamers.
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Affiliation(s)
| | - Atik Badshah Shaikh
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yongshu Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Shuaijian Ni
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
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16
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Churcher ZR, Neves MAD, Hunter HN, Johnson PE. Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer. JOURNAL OF BIOMOLECULAR NMR 2017; 68:33-39. [PMID: 28477231 DOI: 10.1007/s10858-017-0112-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k ex ) of the DNA imino protons in the cocaine-binding aptamer have been determined for the free, cocaine-bound, and quinine-bound states. The secondary structure of the cocaine-binding aptamer is composed of three stems built around a three-way junction. In the free aptamer the slowest exchanging imino protons are located in the middle of the stems. The highest k ex values were found for a nucleotide in the GAA loop of stem 3 and for nucleotides at the end of the stems that form the three-way junction structure and in the tandem GA mismatch. Upon ligand binding, the k ex values of nucleotides at the ligand binding site are reduced, indicating that these base pairs become more stable or less solvent accessible in the bound state. The imino proton k ex values of nucleotides located away from the binding site are only minimally affected by ligand binding.
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Affiliation(s)
- Zachary R Churcher
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada
| | - Miguel A D Neves
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, M5B 1W8, Canada
| | - Howard N Hunter
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
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17
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Boshtam M, Asgary S, Kouhpayeh S, Shariati L, Khanahmad H. Aptamers Against Pro- and Anti-Inflammatory Cytokines: A Review. Inflammation 2017; 40:340-349. [PMID: 27878687 DOI: 10.1007/s10753-016-0477-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inflammatory disorders result from continuous inflammation in injured sites. Many molecules are involved in this process; the inhibition of which could prevent the inflammation. Chemokines are a group of these biological mediators which are categorized into pro-, anti-, and pro-/anti-inflammatory. Thus, targeting these essential molecules can be an effective way for prevention and control of inflammatory diseases. Various therapeutic agents have been developed for primary and secondary prevention of these disorders, but each of them has its own limitations. Aptamers, as novel therapeutic agents, are a new generation of drugs which could replace other medications even antibodies. Aptamer can bind to its target molecule to trap it and prohibit its function. Among large group of inflammatory cytokines, only 11 aptamers have been selected either against cytokines or their related receptors. These cytokines include interleukin (IL)-2, IL-6, IL-10, IL-11, IL-17, IL-32, TGF-β, TNF-α, IFN-γ, CCL2, and IP-10. Most of the isolated aptamers are against pro-inflammatory or dual function cytokines, and it seems that they could be used for diagnosis, prevention, and treatment of the related inflammatory diseases. Most of the aptamers have been tested in vitro, but so far, none of them has been approved for in vivo use. Given a vast number of inflammatory cytokines, more aptamers against this group of biological molecules will be selected in the near future. The available aptamers will also be tested in clinical trials. Therefore, a significant improvement is expected for the prevention and control of inflammatory disorders.
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Affiliation(s)
- Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seddigheh Asgary
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Kouhpayeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Laleh Shariati
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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18
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Amano R, Aoki K, Miyakawa S, Nakamura Y, Kozu T, Kawai G, Sakamoto T. NMR monitoring of the SELEX process to confirm enrichment of structured RNA. Sci Rep 2017; 7:283. [PMID: 28325909 PMCID: PMC5428055 DOI: 10.1038/s41598-017-00273-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 01/20/2023] Open
Abstract
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
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Affiliation(s)
- Ryo Amano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Kazuteru Aoki
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Shin Miyakawa
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Yoshikazu Nakamura
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoko Kozu
- Research Institute for Clinical Oncology, Saitama Cancer Center, 818 Komuro, Ina, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba, 275-0016, Japan.
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19
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Kim HE, Kim W, Lee AR, Jin S, Jun AR, Kim NK, Lee JH, Ahn JH. Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis. Biochem Biophys Res Commun 2017; 484:839-844. [PMID: 28161630 DOI: 10.1016/j.bbrc.2017.01.185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 01/06/2023]
Abstract
Internal and environmental cues, including ambient temperature changes, regulate the timing of flowering in plants. Arabidopsis miR156 represses flowering and plays an important role in the regulation of temperature-responsive flowering. However, the molecular basis of miR156 processing at lower temperatures remains largely unknown. Here, we performed nuclear magnetic resonance studies to investigate the base-pair opening dynamics of model RNAs at 16 °C and investigated the in vivo effects of the mutant RNAs on temperature-responsive flowering. The A9C and A10CG mutations in the B5 bulge of the lower stem of pri-miR156a stabilized the C15∙G98 and U16∙A97 base-pairs at the cleavage site of pri-miR156a at 16 °C. Consistent with this, production of mature miR156 was severely affected in plants overexpressing the A9C and A10CG constructs and these plants exhibited almost no delay in flowering at 16 °C. The A10G and A9AC mutations did not strongly affect C15∙G98 and U16∙A97 base-pairs at 16 °C, and plants overexpressing A10G and A9AC mutants of miR156 produced more mature miR156 than plants overexpressing the A9C and A10CG mutants and showed a strong delay in flowering at 16 °C. Interestingly, the A9AC mutation had distinct effects on the opening dynamics of the C15∙G98 and U16∙A97 base-pairs between 16 °C and 23 °C, and plants expressing the A9AC mutant miR156 showed only a moderate delay in flowering at 16 °C. Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.
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Affiliation(s)
- Hee-Eun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| | - Wanhui Kim
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| | - Suhyun Jin
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - A Rim Jun
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea.
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea.
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20
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Kim W, Kim HE, Lee AR, Jun AR, Jung MG, Ahn JH, Lee JH. Base-pair opening dynamics of primary miR156a using NMR elucidates structural determinants important for its processing level and leaf number phenotype in Arabidopsis. Nucleic Acids Res 2016; 45:875-885. [PMID: 27574118 PMCID: PMC5314782 DOI: 10.1093/nar/gkw747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs originate from primary transcripts containing hairpin structures. The levels of mature miR156 influence the leaf number prior to flowering in the life cycle of plants. To understand the molecular mechanism of biogenesis of primary miR156a (pri-miR156a) to mature miR156, a base-pair opening dynamics study was performed using model RNAs mimicking the cleavage site of wild type and B5 bulge-stabilizing mutant pri-miR156a constructs. We also determined the mature miR156 levels and measured leaf numbers at flowering of plants overexpressing the wild type and mutant constructs. Our results suggest that the stabilities and/or opening dynamics of the C15·G98 and U16·A97 base-pairs at the cleavage site are essential for formation of the active conformation and for efficient processing of pri-miR156a, and that mutations of the B5 bulge can modulate mature miR156 levels as well as miR156-driven leaf number phenotypes via changes in the base-pair stability of the cleavage site.
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Affiliation(s)
- Wanhui Kim
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - A Rim Jun
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Myeong Gyo Jung
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
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21
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Lee AR, Park CJ, Cheong HK, Ryu KS, Park JW, Kwon MY, Lee J, Kim KK, Choi BS, Lee JH. Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B-Z transition. Nucleic Acids Res 2016; 44:2936-48. [PMID: 26792893 PMCID: PMC4824103 DOI: 10.1093/nar/gkw025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/06/2015] [Accepted: 01/11/2016] [Indexed: 11/23/2022] Open
Abstract
Z-DNA binding proteins (ZBPs) play important roles in RNA editing, innate immune response and viral infection. Structural and biophysical studies show that ZBPs initially form an intermediate complex with B-DNA for B-Z conversion. However, a comprehensive understanding of the mechanism of Z-DNA binding and B-Z transition is still lacking, due to the absence of structural information on the intermediate complex. Here, we report the solution structure of the Zα domain of the ZBP-containing protein kinase from Carassius auratus(caZαPKZ). We quantitatively determined the binding affinity of caZαPKZ for both B-DNA and Z-DNA and characterized its B-Z transition activity, which is modulated by varying the salt concentration. Our results suggest that the intermediate complex formed by caZαPKZ and B-DNA can be used as molecular ruler, to measure the degree to which DNA transitions to the Z isoform.
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Affiliation(s)
- Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Chin-Ju Park
- Division of Liberal Arts and Sciences and Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Jin-Wan Park
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea Division of Magnetic Resonance, KBSI, Chungbuk 28119, Republic of Korea
| | - Mun-Young Kwon
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
| | - Janghyun Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, Republic of Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Republic of Korea
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22
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Gelinas AD, Davies DR, Janjic N. Embracing proteins: structural themes in aptamer-protein complexes. Curr Opin Struct Biol 2016; 36:122-32. [PMID: 26919170 DOI: 10.1016/j.sbi.2016.01.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/17/2023]
Abstract
Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity.
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Affiliation(s)
- Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States
| | - Douglas R Davies
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States.
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23
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Drolet DW, Green LS, Gold L, Janjic N. Fit for the Eye: Aptamers in Ocular Disorders. Nucleic Acid Ther 2016; 26:127-46. [PMID: 26757406 PMCID: PMC4900223 DOI: 10.1089/nat.2015.0573] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
For any new class of therapeutics, there are certain types of indications that represent a natural fit. For nucleic acid ligands in general, and aptamers in particular, the eye has historically been an attractive site for therapeutic intervention. In this review, we recount the discovery and early development of three aptamers designated for use in ophthalmology, one approved (Macugen), and two in late-stage development (Fovista and Zimura). Every one of these molecules was originally intended for other indications. Key improvements in technology, specifically with regard to libraries used for in vitro selection and subsequent chemical optimization of aptamers, have played an important role in allowing the identification of development candidates with suitable properties. The lessons learned from the selection of these molecules are valuable for informing us about the many remaining opportunities for aptamer-based therapeutics in ophthalmology as well as for identifying additional indications for which aptamers as a class of therapeutics have distinct advantages.
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Eriksson ESE, Joshi L, Billeter M, Eriksson LA. De novo tertiary structure prediction using RNA123--benchmarking and application to Macugen. J Mol Model 2014; 20:2389. [PMID: 25107358 DOI: 10.1007/s00894-014-2389-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Abstract
The present benchmarking study utilizes the RNA123 program for de novo prediction of tertiary structures of a set of 50 RNA molecules for which X-ray/NMR structures are available, based on the nucleic acid sequence only. All molecules contain a hairpin loop motif and a helical structure of canonical and non-canonical base pairs, interrupted by bulges and internal loops to various degrees. RNA molecules with double helices made up purely by canonical base pairing, and molecules containing symmetric internal loops of non-canonical base pairing are, overall, very well predicted. Structures containing bulges and asymmetric internal loops, and more complex structures containing multiple bulges and internal loops in the same molecule, result in larger deviations from their X-ray/NMR predicted structures due to higher degree of flexibility of the nucleotide bases in these regions. In a majority of the molecules included herein, the RNA123 program was, however, able to predict the tertiary structure with a heavy atom RMSD of less than 5 Å to the X-ray/NMR structure, and the models were in most cases structurally closer to the X-ray/NMR structures than models predicted by MC-Fold and MC-Sym. A set of RNA molecules containing pseudoknot tertiary structure motifs were included, but neither of the programs was able to predict the folding of the single-stranded stem onto the helix without additional structural input. The RNA123 program was then applied to predict the tertiary structure of the RNA segment of Macugen®, the first RNA aptamer approved for clinical use, and for which no tertiary structure has yet been solved. Four possible tertiary structures were predicted for this 27-nucleic-acid-long RNA molecule, which will be used in constructing a full model of the PEGylated aptamer and its interaction with the vascular endothelial growth factor target.
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Affiliation(s)
- Emma S E Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden,
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25
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Jeong M, Lee AR, Kim HE, Choi YG, Choi BS, Lee JH. NMR study of the Z-DNA binding mode and B-Z transition activity of the Zα domain of human ADAR1 when perturbed by mutation on the α3 helix and β-hairpin. Arch Biochem Biophys 2014; 558:95-103. [PMID: 25010446 DOI: 10.1016/j.abb.2014.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 01/23/2023]
Abstract
The Zα domains of human ADAR1 (ZαADAR1) bind to Z-DNA via interaction mediated by the α3-core and β-hairpin. Five residues in the α3 helix and four residues in the β-hairpin play important roles in Zα function, forming direct or water-mediated hydrogen bonds with DNA backbone phosphates or interacting hydrophobically with DNA bases. To understand the roles of these residues during B-Z transition of duplex DNA, we performed NMR experiments on complexes of various ZαADAR1 mutants with a 6-bp DNA duplex at various protein-to-DNA molar ratios. Our study suggests that single mutations at residues K169, N173, or Y177 cause unusual conformational changes in the hydrophobic faces of helices α1, α2, and α3, which dramatically decrease the Z-DNA binding affinity. 1D imino proton spectra and chemical shift perturbation showed that single mutations at residues K170, R174, T191, P192, P193, or W195 slightly affected the Z-DNA binding affinity. A hydrogen exchange study proved that the K170A- and R174A-ZαADAR1 proteins could efficiently change B-DNA to left-handed Z-DNA via an active B-Z transition pathway, whereas the G2·C5 base pair was significantly destabilized compared to wild-type ZαADAR1.
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Affiliation(s)
- Minjee Jeong
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Ae-Ree Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Yong-Geun Choi
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea
| | - Byong-Seok Choi
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju, Gyeongnam 660-701, Republic of Korea.
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26
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Comprehensive experimental fitness landscape and evolutionary network for small RNA. Proc Natl Acad Sci U S A 2013; 110:14984-9. [PMID: 23980164 DOI: 10.1073/pnas.1307604110] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural selection for the first functional sequences. Fitness landscapes are the subject of much speculation, but their structure is essentially unknown. Here we describe a comprehensive map of a fitness landscape, exploring nearly all of sequence space, for short RNAs surviving selection in vitro. With the exception of a small evolutionary network, we find that fitness peaks are largely isolated from one another, highlighting the importance of historical contingency and indicating that natural selection would be constrained to local exploration in the RNA world.
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Lee YM, Kim HE, Park CJ, Lee AR, Ahn HC, Cho SJ, Choi KH, Choi BS, Lee JH. NMR Study on the B–Z Junction Formation of DNA Duplexes Induced by Z-DNA Binding Domain of Human ADAR1. J Am Chem Soc 2012; 134:5276-83. [DOI: 10.1021/ja211581b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yeon-Mi Lee
- Department of Chemistry and
RINS, Gyeongsang National University, Jinju,
Gyeongnam 660-701, Republic of Korea
| | - Hee-Eun Kim
- Department of Chemistry and
RINS, Gyeongsang National University, Jinju,
Gyeongnam 660-701, Republic of Korea
| | - Chin-Ju Park
- School of General Studies, Gwangju Institute of Science and Technology, Gwangju
500-712, Republic of Korea
| | - Ae-Ree Lee
- Department of Chemistry and
RINS, Gyeongsang National University, Jinju,
Gyeongnam 660-701, Republic of Korea
| | - Hee-Chul Ahn
- College of Pharmacy, Dongguk University, Goyang, Gyeonggi 410-774, Republic
of Korea
| | - Sung Jae Cho
- Department of
Chemistry, Korea Advanced Institute of Science and Technology,
Daejeon 305-701, Republic of Korea
| | - Kwang-Ho Choi
- Department of Chemistry and
RINS, Gyeongsang National University, Jinju,
Gyeongnam 660-701, Republic of Korea
| | - Byong-Seok Choi
- Department of
Chemistry, Korea Advanced Institute of Science and Technology,
Daejeon 305-701, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and
RINS, Gyeongsang National University, Jinju,
Gyeongnam 660-701, Republic of Korea
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28
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Aptamers and their biological applications. SENSORS 2012; 12:612-31. [PMID: 22368488 PMCID: PMC3279232 DOI: 10.3390/s120100612] [Citation(s) in RCA: 452] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/31/2011] [Accepted: 01/04/2012] [Indexed: 01/09/2023]
Abstract
Recently, aptamers have attracted the attention of many scientists, because they not only have all of the advantages of antibodies, but also have unique merits, such as thermal stability, low cost, and unlimited applications. In this review, we present the reasons why aptamers are known as alternatives to antibodies. Furthermore, several types of in vitro selection processes, including nitrocellulose membrane filtration, affinity chromatography, magnetic bead, and capillary electrophoresis-based selection methods, are explained in detail. We also introduce various applications of aptamers for the diagnosis of diseases and detection of small molecules. Numerous analytical techniques, such as electrochemical, colorimetric, optical, and mass-sensitive methods, can be utilized to detect targets, due to convenient modifications and the stability of aptamers. Finally, several medical and analytical applications of aptamers are presented. In summary, aptamers are promising materials for diverse areas, not just as alternatives to antibodies, but as the core components of medical and analytical equipment.
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29
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Seo YJ, Lim J, Lee EH, Ok T, Yoon J, Lee JH, Lee HS. Base pair opening kinetics study of the aegPNA:DNA hydrid duplex containing a site-specific GNA-like chiral PNA monomer. Nucleic Acids Res 2011; 39:7329-35. [PMID: 21586589 PMCID: PMC3167616 DOI: 10.1093/nar/gkr360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Peptide nucleic acids (PNA) are one of the most widely used synthetic DNA mimics where the four bases are attached to a N-(2-aminoethyl)glycine (aeg) backbone instead of the negative-charged phosphate backbone in DNA. We have developed a chimeric PNA (chiPNA), in which a chiral GNA-like γ(3)T monomer is incorporated into aegPNA backbone. The base pair opening kinetics of the aegPNA:DNA and chiPNA:DNA hybrid duplexes were studied by NMR hydrogen exchange experiments. This study revealed that the aegPNA:DNA hybrid is much more stable duplex and is less dynamic compared to DNA duplex, meaning that base pairs are opened and reclosed much more slowly. The site-specific incorporation of γ(3)T monomer in the aegPNA:DNA hybrid can destabilize a specific base pair and its neighbors, maintaining the thermal stabilities and dynamic properties of other base pairs. Our hydrogen exchange study firstly revealed the unique kinetic features of base pairs in the aegPNA:DNA and chiPNA:DNA hybrids, which will provide an insight into the development of methodology for specific DNA recognition using PNA fragments.
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Affiliation(s)
- Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongnam 660-701, Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
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30
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Bioanalysis of siRNA and oligonucleotide therapeutics in biological fluids and tissues. Bioanalysis 2011; 1:595-609. [PMID: 21083155 DOI: 10.4155/bio.09.66] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This article summarizes bioanalytical avenues for the determination of siRNA and oligonucleotide therapeutics, with an emphasis on hybridization methods. Aspects of the chemistry and delivery of investigational oligonucleotide therapeutics are considered. The nature of the oligonucleotide under investigation will dictate the best analytical course of action; each method has its advantages and disadvantages, depending upon the oligonucleotide test article and the anticipated toxicokinetic and pharmacokinetic study parameters. Stringent method development and specific validation criteria are essential to attain the best quality results in support of a regulatory filing.
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31
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Kim HE, Ahn HC, Lee YM, Lee EH, Seo YJ, Kim YG, Kim KK, Choi BS, Lee JH. The Zβ domain of human DAI binds to Z-DNA via a novel B-Z transition pathway. FEBS Lett 2011; 585:772-8. [DOI: 10.1016/j.febslet.2011.01.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 01/28/2011] [Accepted: 01/29/2011] [Indexed: 11/26/2022]
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32
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NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Zα domains of yatapoxvirus E3L. FEBS Lett 2010; 584:4453-7. [DOI: 10.1016/j.febslet.2010.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 09/30/2010] [Accepted: 10/05/2010] [Indexed: 11/20/2022]
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33
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Seo YJ, Ahn HC, Lee EH, Bang J, Kang YM, Kim HE, Lee YM, Kim K, Choi BS, Lee JH. Sequence discrimination of the Zα domain of human ADAR1 during B-Z transition of DNA duplexes. FEBS Lett 2010; 584:4344-50. [PMID: 20875819 DOI: 10.1016/j.febslet.2010.09.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 09/14/2010] [Accepted: 09/20/2010] [Indexed: 10/19/2022]
Abstract
The Zα domain of human ADAR1 (Zα(ADAR1)) preferentially binds Z-DNA rather than B-DNA with high binding affinity. Zα(ADAR1) binds to the Z-conformation of both non-CG-repeat DNA duplexes and a d(CGCGCG)(2) duplex similarly. We performed NMR experiments on complexes between the Zα(ADAR1) and non-CG-repeat DNA duplexes, d(CACGTG)(2) or d(CGTACG)(2), with a variety of protein-DNA molar ratios. Comparison of these results with those from the analysis of d(CGCGCG)(2) in the previous study suggests that Zα(ADAR1) exhibits the sequence preference of d(CGCGCG)(2)≫d(CACGTG)(2)>d(CGTACG)(2) through multiple sequence discrimination steps during the B-Z transition.
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Affiliation(s)
- Yeo-Jin Seo
- Department of Chemistry, RINS, Gyeongsang National University, Jinju, Gyengnam, Republic of Korea
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34
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Base pair opening kinetics and dynamics in the DNA duplexes that specifically recognized by very short patch repair protein (Vsr). Arch Biochem Biophys 2010; 501:201-6. [PMID: 20541519 DOI: 10.1016/j.abb.2010.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 06/04/2010] [Accepted: 06/06/2010] [Indexed: 11/24/2022]
Abstract
In Escherichia coli, the very short patch (VSP) repair system is a major pathway for removal of T.G mismatches in Dcm target sequences. In the VSP repair pathway, the very short patch repair (Vsr) endonuclease selectively recognizes a T.G mismatch in Dcm target sequences and hydrolyzes the 5'-phosphate group of the mismatched thymine. The hydrogen exchange NMR studies here revealed that the T5.G18 mismatch in the Dcm target sequence significantly stabilizes own base pair but destabilizes the two neighboring G4.C19 and A6.T17 base pairs compare to other T.G mismatches. These unusual patterns of base pair stability in the Dcm target sequence can explain how the Vsr endonuclease specifically recognizes the mismatched Dcm target sequence and intercalates into the DNA.
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35
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Rinnenthal J, Klinkert B, Narberhaus F, Schwalbe H. Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution. Nucleic Acids Res 2010; 38:3834-47. [PMID: 20211842 PMCID: PMC2887971 DOI: 10.1093/nar/gkq124] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/28/2010] [Accepted: 02/10/2010] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, RNA thermometers regulate a number of heat shock and virulence genes. These temperature sensitive RNA elements are usually located in the 5'-untranslated regions of the regulated genes. They repress translation initiation by base pairing to the Shine-Dalgarno sequence at low temperatures. We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence of the imino proton exchange rates via NMR spectroscopy. Exchange rates were analyzed for the wild-type (wt) RNA and the A8C mutant. The wt RNA was found to be stabilized by the extraordinarily stable G14-C25 base pair. The mismatch base pair in the wt RNA thermometer (A8-G31) is responsible for the smaller cooperativity of the unfolding transition in the wt RNA. Enthalpy and entropy values for the base-pair opening events exhibit linear correlation for both RNAs. The slopes of these correlations coincide with the melting points of the RNAs determined by CD spectroscopy. RNA unfolding occurs at a temperature where all nucleobases have equal thermodynamic stabilities. Our results are in agreement with a consecutive zipper-type unfolding mechanism in which the stacking interaction is responsible for the observed cooperativity. Furthermore, remote effects of the A8C mutation affecting the stability of nucleobase G14 could be identified. According to our analysis we deduce that this effect is most probably transduced via the hydration shell of the RNA.
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Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main and Microbial Biology, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF06/783, 44780 Bochum, Germany
| | - Birgit Klinkert
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main and Microbial Biology, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF06/783, 44780 Bochum, Germany
| | - Franz Narberhaus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main and Microbial Biology, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF06/783, 44780 Bochum, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main and Microbial Biology, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF06/783, 44780 Bochum, Germany
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36
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Wang T, Hoy JA, Lamm MH, Nilsen-Hamilton M. Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity. J Am Chem Soc 2010; 131:14747-55. [PMID: 19778045 DOI: 10.1021/ja902719q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as "induced fit". But, it is not known to what extent this structural flexibility affects the integrity of the target-aptamer interaction. Using the malachite green aptamer (MGA) as a model system, we show that the MGA can protect its bound target, malachite green (MG), from oxidation over several days. Protection is reversed by an oligonucleotide complementary to the MGA binding pocket. Computational cavity analysis of the MGA-MG structure predicted that MG oxidation is protected because a molecule as small as an OH(-) is sterically excluded from the C1 position of the bound MG. These results suggest that, while the MGA-MG interface is sufficiently coherent to prevent OH(-) penetration, the bases involved in the interaction are sufficiently mobile that they can exchange out of the MG binding interface to hybridize with a complementary oligonucleotide. The computational predictions were confirmed experimentally using variants of the MGA with single base changes in the binding pocket. This work demonstrates the successful application of molecular dynamics simulations and cavity analysis in determining the effects of sequence variations on the structure of a small single-stranded nucleic acid. It also shows that a nucleic acid aptamer can control access to specific chemical groups on its target, which suggests that aptamers might be applied for selectively protecting small molecules from modification.
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Affiliation(s)
- Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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37
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Kang YM, Bang J, Lee EH, Ahn HC, Seo YJ, Kim KK, Kim YG, Choi BS, Lee JH. NMR spectroscopic elucidation of the B-Z transition of a DNA double helix induced by the Z alpha domain of human ADAR1. J Am Chem Soc 2009; 131:11485-91. [PMID: 19637911 DOI: 10.1021/ja902654u] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human RNA editing enzyme ADAR1 (double-stranded RNA deaminase I) deaminates adenine in pre-mRNA to yield inosine, which codes as guanine. ADAR1 has two left-handed Z-DNA binding domains, Z alpha and Z beta, at its NH(2)-terminus and preferentially binds Z-DNA, rather than B-DNA, with high binding affinity. The cocrystal structure of Z alpha(ADAR1) complexed to Z-DNA showed that one monomeric Z alpha(ADAR1) domain binds to one strand of double-stranded DNA and a second Z alpha(ADAR1) monomer binds to the opposite strand with 2-fold symmetry with respect to DNA helical axis. It remains unclear how Z alpha(ADAR1) protein specifically recognizes Z-DNA sequence in a sea of B-DNA to produce the stable Z alpha(ADAR1)-Z-DNA complex during the B-Z transition induced by Z alpha(ADAR1). In order to characterize the molecular recognition of Z-DNA by Z alpha(ADAR1), we performed circular dichroism (CD) and NMR experiments with complexes of Zalpha(ADAR1) bound to d(CGCGCG)(2) (referred to as CG6) produced at a variety of protein-to-DNA molar ratios. From this study, we identified the intermediate states of the CG6-Z alpha(ADAR1) complex and calculated their relative populations as a function of the Z alpha(ADAR1) concentration. These findings support an active B-Z transition mechanism in which the Z alpha(ADAR1) protein first binds to B-DNA and then converts it to left-handed Z-DNA, a conformation that is then stabilized by the additional binding of a second Z alpha(ADAR1) molecule.
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Affiliation(s)
- Young-Min Kang
- Department of Chemistry, RINS, and Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, Gyeongnam 660-701, Korea
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38
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Elucidation of Double Exponential Behavior in the T 1Relaxation of the Tetrahymena Group I Ribozyme. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.10.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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39
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Measurement of Hydrogen Exchange Times of the RNA Imino Protons Using by Phase-modulated CLEAN Chemical Exchange Spectroscopy. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.10.2197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Bang J, Kang YM, Park CJ, Lee JH, Choi BS. Thermodynamics and kinetics for base pair opening in the DNA decamer duplexes containing cyclobutane pyrimidine dimer. FEBS Lett 2009; 583:2037-41. [PMID: 19450588 DOI: 10.1016/j.febslet.2009.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/09/2009] [Accepted: 05/12/2009] [Indexed: 11/28/2022]
Abstract
The cyclobutane pyrimidine dimer (CPD) is one of the major classes of cytotoxic and carcinogenic DNA photoproducts induced by UV light. Hydrogen exchange rates of the imino protons were measured for various CPD-containing DNA duplexes to better understand the mechanism for CPD recognition by XPC-hHR23B. The results here revealed that double T.G mismatches in a CPD lesion significantly destabilized six consecutive base pairs compared to other DNA duplexes. This flexibility in a DNA duplex caused at the CPD lesions with double T.G mismatches might be the key factor for damage recognition by XPC-hHR23B.
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Affiliation(s)
- Jongchul Bang
- Department of Chemistry, National Creative Research Initiative Center, KAIST, Daejeon 305-701, Republic of Korea
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