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Nguyen MD, Osborne MT, Prevot GT, Churcher ZR, Johnson PE, Simine L, Dauphin-Ducharme P. Truncations and in silico docking to enhance the analytical response of aptamer-based biosensors. Biosens Bioelectron 2024; 265:116680. [PMID: 39213817 DOI: 10.1016/j.bios.2024.116680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Aptamers are short oligonucleotides capable of binding specifically to various targets (i.e., small molecules, proteins, and whole cells) which have been introduced in biosensors such as in the electrochemical aptamer-based (E-AB) sensing platform. E-AB sensors are comprised of a redox-reporter-modified aptamer attached to an electrode that undergoes, upon target addition, a binding-induced change in electron transfer rates. To date, E-AB sensors have faced a limitation in the translatability of aptamers into the sensing platform presumably because sequences obtained from Systematic Evolution of Ligands by Exponential Enrichment (SELEX) are typically long (>80 nucleotides) and that obtaining structural information remains time and resource consuming. In response, we explore the utility of aptamer base truncations and in silico docking to improve their translatability into E-AB sensors. Here, we first apply this to the glucose aptamer, which we characterize in solution using NMR methods to guide design and translate truncated variants in E-AB biosensors. We further investigated the applicability of the truncation and computational approaches to four other aptamer systems (vancomycin, cocaine, methotrexate and theophylline) from which we derived functional E-AB sensors. We foresee that our strategy will increase the success rate of translating aptamers into sensing platforms to afford low-cost measurements of molecules directly in undiluted complex matrices.
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Affiliation(s)
- Minh-Dat Nguyen
- Département de chimie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Meghan T Osborne
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Guy Terence Prevot
- Département de chimie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Zachary R Churcher
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Lena Simine
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
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2
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Hang Z, Zhou L, Bian X, Liu G, Cui F, Du H, Wen Y. Potential application of aptamers combined with DNA nanoflowers in neurodegenerative diseases. Ageing Res Rev 2024; 100:102444. [PMID: 39084322 DOI: 10.1016/j.arr.2024.102444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/09/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
The efficacy of neurotherapeutic drugs hinges on their ability to traverse the blood-brain barrier and access the brain, which is crucial for treating or alleviating neurodegenerative diseases (NDs). Given the absence of definitive cures for NDs, early diagnosis and intervention become paramount in impeding disease progression. However, conventional therapeutic drugs and existing diagnostic approaches must meet clinical demands. Consequently, there is a pressing need to advance drug delivery systems and early diagnostic methods tailored for NDs. Certain aptamers endowed with specific functionalities find widespread utility in the targeted therapy and diagnosis of NDs. DNA nanoflowers (DNFs), distinctive flower-shaped DNA nanomaterials, are intricately self-assembled through rolling ring amplification (RCA) of circular DNA templates. Notably, imbuing DNFs with diverse functionalities becomes seamlessly achievable by integrating aptamer sequences with specific functions into RCA templates, resulting in a novel nanomaterial, aptamer-bound DNFs (ADNFs) that amalgamates the advantageous features of both components. This article delves into the characteristics and applications of aptamers and DNFs, exploring the potential or application of ADNFs in drug-targeted delivery, direct treatment, early diagnosis, etc. The objective is to offer prospective ideas for the clinical treatment or diagnosis of NDs, thereby contributing to the ongoing efforts in this critical field.
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Affiliation(s)
- Zhongci Hang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Liping Zhou
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xiaochun Bian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Guotao Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Fenghe Cui
- Department of Anesthesiology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangdingdong Road, Zhifu District, Yantai, Shandong 264000, China.
| | - Hongwu Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yongqiang Wen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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3
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Kong AHY, Wu AJ, Ho OKY, Leung MMK, Huang AS, Yu Y, Zhang G, Lyu A, Li M, Cheung KH. Exploring the Potential of Aptamers in Targeting Neuroinflammation and Neurodegenerative Disorders: Opportunities and Challenges. Int J Mol Sci 2023; 24:11780. [PMID: 37511539 PMCID: PMC10380291 DOI: 10.3390/ijms241411780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Neuroinflammation is the precursor for several neurodegenerative diseases (NDDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis (MS). Targeting neuroinflammation has emerged as a promising strategy to address a wide range of CNS pathologies. These NDDs still present significant challenges in terms of limited and ineffective diagnosis and treatment options, driving the need to explore innovative and novel therapeutic alternatives. Aptamers are single-stranded nucleic acids that offer the potential for addressing these challenges through diagnostic and therapeutic applications. In this review, we summarize diagnostic and therapeutic aptamers for inflammatory biomolecules, as well as the inflammatory cells in NDDs. We also discussed the potential of short nucleotides for Aptamer-Based Targeted Brain Delivery through their unique features and modifications, as well as their ability to penetrate the blood-brain barrier. Moreover, the unprecedented opportunities and substantial challenges of using aptamers as therapeutic agents, such as drug efficacy, safety considerations, and pharmacokinetics, are also discussed. Taken together, this review assesses the potential of aptamers as a pioneering approach for target delivery to the CNS and the treatment of neuroinflammation and NDDs.
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Affiliation(s)
- Anna Hau-Yee Kong
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Aston Jiaxi Wu
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Olivia Ka-Yi Ho
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Maggie Ming-Ki Leung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Alexis Shiying Huang
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, China
| | - Aiping Lyu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong SAR, China
| | - Min Li
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - King-Ho Cheung
- Teaching and Research Division, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
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Thevendran R, Rogini S, Leighton G, Mutombwera A, Shigdar S, Tang TH, Citartan M. The Diagnostic Potential of RNA Aptamers against the NS1 Protein of Dengue Virus Serotype 2. BIOLOGY 2023; 12:biology12050722. [PMID: 37237536 DOI: 10.3390/biology12050722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/28/2023]
Abstract
Dengue infection, caused by the dengue virus, is a global threat which requires immediate attention and appropriate disease management. The current diagnosis of dengue infection is largely based on viral isolation, RT-PCR and serology-based detection, which are time-consuming and expensive, and require trained personnel. For early diagnosis of dengue, the direct detection of a dengue antigenic target is efficacious, and one such target is NS1. NS1-based detection is primarily antibody-centric and is beset by drawbacks pertaining to antibodies such as the high cost of synthesis and large batch-to-batch variation. Aptamers are potential surrogates of antibodies and are much cheaper, without exhibiting batch-to-batch variation. Given these advantages, we sought to isolate RNA aptamers against the NS1 protein of dengue virus serotype 2. A total of 11 cycles of SELEX were carried out, resulting in two potent aptamers, DENV-3 and DENV-6, with dissociation constant values estimated at 37.57 ± 10.34 nM and 41.40 ± 9.29 nM, respectively. These aptamers can be further miniaturized to TDENV-3 and TDENV-6a with an increased LOD upon their usage in direct ELASA. Moreover, these truncated aptamers are highly specific against the dengue NS1 while showing no cross-reactivity against the NS1 of the Zika virus, the E2 protein of the Chikungunya virus or the LipL32 protein of Leptospira, with target selectivity retained even in human serum. The usage of TDENV-3 as the capturing probe and TDENV-6a as the detection probe underpinned the development of an aptamer-based sandwich ELASA for the detection of dengue NS1. The sensitivity of the sandwich ELASA was further improved with the stabilization of the truncated aptamers and the repeated incubation strategy, which enabled a LOD of 2 nM when used with the target NS1 spiked in human serum diluted at 1:2000.
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Affiliation(s)
- Ramesh Thevendran
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Sivalingam Rogini
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Glenn Leighton
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Atherton Mutombwera
- Hutano Diagnostics Ltd. BioEscalator, Innovation Building, Old Road Campus, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3217, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Thean-Hock Tang
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
| | - Marimuthu Citartan
- Department of Biomedical Science, Advanced Medical & Dental Institute (AMDI), University Sains Malaysia, Bertam, Kepala Batas 13200, Malaysia
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Singh S, Shyamal S, Panda AC. Detecting RNA-RNA interactome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1715. [PMID: 35132791 DOI: 10.1002/wrna.1715] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Center for Biotechnology, Faridabad, India
| | | | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
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6
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Liu D, Thélot FA, Piccirilli JA, Liao M, Yin P. Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Nat Methods 2022; 19:576-585. [PMID: 35501384 DOI: 10.1038/s41592-022-01455-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/09/2022] [Indexed: 12/29/2022]
Abstract
High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy-ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops)-involves installing kissing-loop sequences onto the functionally nonessential stems of RNAs for homomeric self-assembly into closed rings with multiplied molecular weights and mitigated structural flexibility. ROCK enables cryo-EM reconstruction of the Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA, including the previously unknown peripheral domains. ROCK is further applied to two smaller RNAs-the Azoarcus group I intron and the FMN riboswitch, revealing the conformational change of the former and the bound ligand in the latter. ROCK holds promise to greatly facilitate the use of cryo-EM in RNA structural studies.
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Affiliation(s)
- Di Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - François A Thélot
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joseph A Piccirilli
- Department of Chemistry, the University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL, USA
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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7
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Liu D, Shao Y, Piccirilli JA, Weizmann Y. Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. SCIENCE ADVANCES 2021; 7:eabf4459. [PMID: 34550747 PMCID: PMC8457670 DOI: 10.1126/sciadv.abf4459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.
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Affiliation(s)
- Di Liu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Yossi Weizmann
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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8
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Mills A, Gago F. Structural Landscape of the Transition from an ssDNA Dumbbell Plus Its Complementary Hairpin to a dsDNA Microcircle Via a Kissing Loop Intermediate. Molecules 2021; 26:molecules26103017. [PMID: 34069399 PMCID: PMC8158708 DOI: 10.3390/molecules26103017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 11/17/2022] Open
Abstract
The experimental construction of a double-stranded DNA microcircle of only 42 base pairs entailed a great deal of ingenuity and hard work. However, figuring out the three-dimensional structures of intermediates and the final product can be particularly baffling. Using a combination of model building and unrestrained molecular dynamics simulations in explicit solvent we have characterized the different DNA structures involved along the process. Our 3D models of the single-stranded DNA molecules provide atomic insight into the recognition event that must take place for the DNA bases in the cohesive tail of the hairpin to pair with their complementary bases in the single-stranded loops of the dumbbell. We propose that a kissing loop involving six base pairs makes up the core of the nascent dsDNA microcircle. We also suggest a feasible pathway for the hybridization of the remaining complementary bases and characterize the final covalently closed dsDNA microcircle as possessing two well-defined U-turns. Additional models of the pre-ligation complex of T4 DNA ligase with the DNA dumbbell and the post-ligation pre-release complex involving the same enzyme and the covalently closed DNA microcircle are shown to be compatible with enzyme recognition and gap ligation.
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Dutta N, Sarzynska J, Lahiri A. Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space. J Chem Inf Model 2020; 60:4995-5002. [PMID: 33030900 DOI: 10.1021/acs.jcim.0c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There are only four derivatives of pseudouridine (Ψ) that are known to occur naturally in RNA as post-transcriptional modifications. We have studied the conformational consequences of pseudouridylation and further modifications using replica exchange molecular dynamics simulations at the nucleoside level, and the simulated conformational preferences were compared with the available experimental (NMR) data. We found that the existing AMBER FF99-derived parameters for these nucleosides did not reproduce the observed experimental features and while the recommended bsc0 correction could be combined with these parameters leading to an improvement in the description of sugar pucker distributions, the χOL3 correction could not be applied to these nucleosides as such because of base isomerization. On the other hand, the revised χ torsion parameters (χIDRP) for Ψ developed earlier by us (Deb, I., J. Comput. Chem., 2016, 37, 1576-1588) in combination with the AMBER provided parameters and the revised γ torsion parameters generated conformational distributions, which generally were in better agreement with the experimental data. A significant shift of the distribution of base orientation toward the syn conformation was observed with our revised parameter sets compared to the large excess of anti conformation predicted by the FF99 parameters. Overall, our observations indicated that our revised set of parameters (χIDRP) for Ψ were also able to generate conformational distributions for all of the derivatives of Ψ in better agreement with the experimental data.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
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10
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Abi-Ghanem J, Rabin C, Porrini M, Rosu F, Gabelica V. Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2035-2043. [PMID: 32812759 DOI: 10.1021/jasms.0c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
When electrosprayed from typical native MS solution conditions, RNA hairpins and kissing complexes acquire charge states at which they get significantly more compact in the gas phase than their initial structure in solution. Here, we also show the limits of using force field molecular dynamics to interpret the structures of nucleic acid complexes in the gas phase, as the predicted CCS distributions do not fully match the experimental ones. We suggest that higher level calculation levels should be used in the future.
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Affiliation(s)
- Josephine Abi-Ghanem
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Clémence Rabin
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Massimiliano Porrini
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Frédéric Rosu
- Univ Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
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11
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Osmer PS, Singh G, Boris-Lawrie K. A New Approach to 3D Modeling of Inhomogeneous Populations of Viral Regulatory RNA. Viruses 2020; 12:v12101108. [PMID: 33003639 PMCID: PMC7650772 DOI: 10.3390/v12101108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/17/2022] Open
Abstract
Tertiary structure (3D) is the physical context of RNA regulatory activity. Retroviruses are RNA viruses that replicate through the proviral DNA intermediate transcribed by hosts. Proviral transcripts form inhomogeneous populations due to variable structural ensembles of overlapping regulatory RNA motifs in the 5′-untranslated region (UTR), which drive RNAs to be spliced or translated, and/or dimerized and packaged into virions. Genetic studies and structural techniques have provided fundamental input constraints to begin predicting HIV 3D conformations in silico. Using SimRNA and sets of experimentally-determined input constraints of HIVNL4-3 trans-activation responsive sequence (TAR) and pairings of unique-5′ (U5) with dimerization (DIS) or AUG motifs, we calculated a series of 3D models that differ in proximity of 5′-Cap and the junction of TAR and PolyA helices; configuration of primer binding site (PBS)-segment; and two host cofactors binding sites. Input constraints on U5-AUG pairings were most compatible with intramolecular folding of 5′-UTR motifs in energetic minima. Introducing theoretical constraints predicted metastable PolyA region drives orientation of 5′-Cap with TAR, U5 and PBS-segment helices. SimRNA and the workflow developed herein provides viable options to predict 3D conformations of inhomogeneous populations of large RNAs that have been intractable to conventional ensemble methods.
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Affiliation(s)
- Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
- Correspondence: ; Tel.: +1-612-625-2100
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12
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Sett A, Zara L, Dausse E, Toulmé JJ. Engineering Light-Up Aptamers for the Detection of RNA Hairpins through Kissing Interaction. Anal Chem 2020; 92:9113-9117. [PMID: 32498509 DOI: 10.1021/acs.analchem.0c01378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aptasensors are biosensors that include aptamers for detecting a target of interest. We engineered signaling aptasensors for the detection of RNA hairpins from the previously described malachite green (MG) RNA aptamer. The top part of this imperfect hairpin aptamer was modified in such a way that it can engage loop-loop (so-called kissing) interactions with RNA hairpins displaying partly complementary apical loops. These newly derived oligonucleotides named malaswitches bind their cognate fluorogenic ligand (MG) exclusively when RNA-RNA kissing complexes are formed, whereas MG does not bind to malaswitches alone. Consequently, the formation of the ternary target RNA-malaswitch RNA-MG complex results in fluorescence emission, and malaswitches constitute sensors for detecting RNA hairpins. Malaswitches were designed that specifically detect precursors of microRNAs let7b and miR-206.
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Affiliation(s)
- Arghya Sett
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France
| | - Lorena Zara
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France.,Novaptech, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, 33076 Bordeaux, France.,Novaptech, 146 rue Léo Saignat, 33076 Bordeaux, France
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13
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Angelova MT, Dimitrova DG, Da Silva B, Marchand V, Jacquier C, Achour C, Brazane M, Goyenvalle C, Bourguignon-Igel V, Shehzada S, Khouider S, Lence T, Guerineau V, Roignant JY, Antoniewski C, Teysset L, Bregeon D, Motorin Y, Schaefer MR, Carré C. tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. Nucleic Acids Res 2020; 48:2050-2072. [PMID: 31943105 PMCID: PMC7038984 DOI: 10.1093/nar/gkaa002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022] Open
Abstract
2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.
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Affiliation(s)
- Margarita T Angelova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Caroline Jacquier
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Cyrinne Achour
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Mira Brazane
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Catherine Goyenvalle
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Valérie Bourguignon-Igel
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.,Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Salman Shehzada
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Souraya Khouider
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Tina Lence
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Guerineau
- Institut de Chimie de Substances Naturelles, Centre de Recherche de Gif CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Yves Roignant
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Damien Bregeon
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Yuri Motorin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Clément Carré
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
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14
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Abstract
Surface plasmon resonance (SPR)-based instruments have become gold-standard tools for investigating molecular interactions involving macromolecules. The major advantage is that the measured signal is sensitive to changes in mass. Therefore, all kinds of complexes can be analyzed including those with compounds as small as cations. SPR is mainly used to determine the dissociation equilibrium constant and the binding rates of a reaction if slow enough. SPR is well suited for analysis molecular interactions with nucleic acids because these negatively charged macromolecules do not have a tendency to stick to the sensor chip surface as some proteins can do. To illustrate the use of SPR with RNA molecules, we describe methods that we used for monitoring the interaction between the protein Rop from E. coli and two RNA-RNA loop-loop complexes. One is derived from the natural target of Rop, RNAI-RNAII. The other one is an RNA-RNA complex formed between a shortened version of the TAR element of HIV-1 and a structured RNA, TAR* rationally designed to interact with TAR through loop-loop interactions. These methods can be easily adapted to other complexes involving RNA molecules and to other SPR instruments.
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Affiliation(s)
- Carmelo Di Primo
- Laboratoire ARNA, University of Bordeaux, Bordeaux, France.
- INSERM U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, Pessac, France.
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15
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Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019; 25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yao Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xunxun Wang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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16
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Dimitrova DG, Teysset L, Carré C. RNA 2'-O-Methylation (Nm) Modification in Human Diseases. Genes (Basel) 2019; 10:E117. [PMID: 30764532 PMCID: PMC6409641 DOI: 10.3390/genes10020117] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/24/2022] Open
Abstract
Nm (2'-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects.
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Affiliation(s)
- Dilyana G Dimitrova
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Laure Teysset
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Clément Carré
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
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17
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Zhu G, Chen X. Aptamer-based targeted therapy. Adv Drug Deliv Rev 2018; 134:65-78. [PMID: 30125604 PMCID: PMC6239901 DOI: 10.1016/j.addr.2018.08.005] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 07/12/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022]
Abstract
Precision medicine holds great promise to harness genetic and epigenetic cues for targeted treatment of a variety of diseases, ranging from many types of cancers, neurodegenerative diseases, to cardiovascular diseases. The proteomic profiles resulting from the unique genetic and epigenetic signatures represent a class of relatively well accessible molecular targets for both interrogation (e.g., diagnosis, prognosis) and intervention (e.g., targeted therapy) of these diseases. Aptamers are promising for such applications by specific binding with cognate disease biomarkers. Nucleic acid aptamers are a class of DNA or RNA with unique three-dimensional conformations that allow them to specifically bind with target molecules. Aptamers can be relatively easily screened, reproducibly manufactured, programmably designed, and chemically modified for various biomedical applications, including targeted therapy. Aptamers can be chemically modified to resist enzymatic degradation or optimize their pharmacological behaviors, which ensured their chemical integrity and bioavailability under physiological conditions. In this review, we will focus on recent progress and discuss the challenges and opportunities in the research areas of aptamer-based targeted therapy in the forms of aptamer therapeutics and aptamer-drug conjugates (ApDCs).
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Affiliation(s)
- Guizhi Zhu
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Takeuchi Y, Endo M, Suzuki Y, Hidaka K, Durand G, Dausse E, Toulmé JJ, Sugiyama H. Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure. Biomater Sci 2017; 4:130-5. [PMID: 26438892 DOI: 10.1039/c5bm00274e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.
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Affiliation(s)
- Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Guillaume Durand
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
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19
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Dausse E, Barré A, Aimé A, Groppi A, Rico A, Ainali C, Salgado G, Palau W, Daguerre E, Nikolski M, Toulmé JJ, Di Primo C. Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation. Biosens Bioelectron 2016; 80:418-425. [PMID: 26874109 DOI: 10.1016/j.bios.2016.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 01/02/2023]
Abstract
A surface plasmon resonance (SPR)-based SELEX approach has been used to raise RNA aptamers against a structured RNA, derived from XBP1 pre-mRNA, that folds as two contiguous hairpins. Thanks to the design of the internal microfluidic cartridge of the instrument, the selection was performed during the dissociation phase of the SPR analysis by recovering the aptamer candidates directly from the target immobilized onto the sensor chip surface. The evaluation of the pools was performed by SPR, simultaneously, during the association phase, each time the amplified and transcribed candidates were injected over the immobilized target. SPR coupled with SELEX from the first to the last round allowed identifying RNA aptamers that formed highly stable loop-loop complexes (KD equal to 8nM) with the hairpin located on the 5' side of the target. High throughput sequencing of two key rounds confirmed the evolution observed by SPR and also revealed the selection of hairpins displaying a loop not fully complementary to the loop of its target. These candidates were selected mainly because they bound 79 times faster to the target than those having a complementary loop. SELEX coupled with SPR is expected to speed up the selection process because selection and evaluation are performed simultaneously.
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Affiliation(s)
- Eric Dausse
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Aurélien Barré
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Ahissan Aimé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Alexis Groppi
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Alain Rico
- Thermo Fisher Scientific, Saint Aubin F-91190, France
| | | | - Gilmar Salgado
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - William Palau
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | | | - Macha Nikolski
- University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France
| | - Carmelo Di Primo
- University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
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20
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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21
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Ma H, Liu J, Ali MM, Mahmood MAI, Labanieh L, Lu M, Iqbal SM, Zhang Q, Zhao W, Wan Y. Nucleic acid aptamers in cancer research, diagnosis and therapy. Chem Soc Rev 2015; 44:1240-56. [PMID: 25561050 DOI: 10.1039/c4cs00357h] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligomers, identified from a random sequence pool, with the ability to form unique and versatile tertiary structures that bind to cognate molecules with superior specificity. Their small size, excellent chemical stability and low immunogenicity enable them to rival antibodies in cancer imaging and therapy applications. Their facile chemical synthesis, versatility in structural design and engineering, and the ability for site-specific modifications with functional moieties make aptamers excellent recognition motifs for cancer biomarker discovery and detection. Moreover, aptamers can be selected or engineered to regulate cancer protein functions, as well as to guide anti-cancer drug design or screening. This review summarizes their applications in cancer, including cancer biomarker discovery and detection, cancer imaging, cancer therapy, and anti-cancer drug discovery. Although relevant applications are relatively new, the significant progress achieved has demonstrated that aptamers can be promising players in cancer research.
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Affiliation(s)
- Haitao Ma
- The Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
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22
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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23
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Abstract
Western medicine often aims to specifically treat diseased tissues or organs. However, the majority of current therapeutics failed to do so owing to their limited selectivity and the consequent "off-target" side effects. Targeted therapy aims to enhance the selectivity of therapeutic effects and reduce adverse side effects. One approach toward this goal is to utilize disease-specific ligands to guide the delivery of less-specific therapeutics, such that the therapeutic effects can be guided specifically to diseased tissues or organs. Among these ligands, aptamers, also known as chemical antibodies, have emerged over the past decades as a novel class of targeting ligands that are capable of specific binding to disease biomarkers. Compared with other types of targeting ligands, aptamers have an array of unique advantageous features, which make them promising for developing aptamer-drug conjugates (ApDCs) for targeted therapy. In this Review, we will discuss ApDCs for targeted drug delivery in chemotherapy, gene therapy, immunotherapy, photodynamic therapy, and photothermal therapy, primarily of cancer.
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Affiliation(s)
- Guizhi Zhu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health , Bethesda, Maryland 20892, United States
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24
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Bhat HB, Ishitsuka R, Inaba T, Murate M, Abe M, Makino A, Kohyama-Koganeya A, Nagao K, Kurahashi A, Kishimoto T, Tahara M, Yamano A, Nagamune K, Hirabayashi Y, Juni N, Umeda M, Fujimori F, Nishibori K, Yamaji-Hasegawa A, Greimel P, Kobayashi T. Evaluation of aegerolysins as novel tools to detect and visualize ceramide phosphoethanolamine, a major sphingolipid in invertebrates. FASEB J 2015; 29:3920-34. [PMID: 26060215 DOI: 10.1096/fj.15-272112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/26/2015] [Indexed: 12/13/2022]
Abstract
Ceramide phosphoethanolamine (CPE), a sphingomyelin analog, is a major sphingolipid in invertebrates and parasites, whereas only trace amounts are present in mammalian cells. In this study, mushroom-derived proteins of the aegerolysin family—pleurotolysin A2 (PlyA2; K(D) = 12 nM), ostreolysin (Oly; K(D) = 1.3 nM), and erylysin A (EryA; K(D) = 1.3 nM)—strongly associated with CPE/cholesterol (Chol)-containing membranes, whereas their low affinity to sphingomyelin/Chol precluded establishment of the binding kinetics. Binding specificity was determined by multilamellar liposome binding assays, supported bilayer assays, and solid-phase studies against a series of neutral and negatively charged lipid classes mixed 1:1 with Chol or phosphatidylcholine. No cross-reactivity was detected with phosphatidylethanolamine. Only PlyA2 also associated with CPE, independent of Chol content (K(D) = 41 μM), rendering it a suitable tool for visualizing CPE in lipid-blotting experiments and biologic samples from sterol auxotrophic organisms. Visualization of CPE enrichment in the CNS of Drosophila larvae (by PlyA2) and in the bloodstream form of the parasite Trypanosoma brucei (by EryA) by fluorescence imaging demonstrated the versatility of aegerolysin family proteins as efficient tools for detecting and visualizing CPE.
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Affiliation(s)
- Hema Balakrishna Bhat
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Reiko Ishitsuka
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Takehiko Inaba
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Motohide Murate
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Mitsuhiro Abe
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Asami Makino
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Ayako Kohyama-Koganeya
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Kohjiro Nagao
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Atsushi Kurahashi
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Takuma Kishimoto
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Michiru Tahara
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Akinori Yamano
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Kisaburo Nagamune
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Yoshio Hirabayashi
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Naoto Juni
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Masato Umeda
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Fumihiro Fujimori
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Kozo Nishibori
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Akiko Yamaji-Hasegawa
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Peter Greimel
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
| | - Toshihide Kobayashi
- *Lipid Biology Laboratory, RIKEN, and Laboratory of Molecular Membrane Neuroscience, Brain Science Institute, RIKEN, Saitama, Japan; Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan; Yukiguni Maitake Co. Ltd., Niigata, Japan; Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; Graduate School of Life and Environmental Sciences and Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan; **Department of Environmental Science and Education, Faculty of Human Life Science, Tokyo Kasei University, Tokyo, Japan; and Institut National de la Santé et de la Recherche Médicale Unité 1060, Université Lyon 1, Villeurbanne, France
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25
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Bouchard P, Legault P. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. RNA (NEW YORK, N.Y.) 2014; 20:1451-64. [PMID: 25051972 PMCID: PMC4138328 DOI: 10.1261/rna.046144.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/03/2014] [Indexed: 05/20/2023]
Abstract
Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem-loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8-3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7-8 kcal/mol than predicted for a comparable duplex containing three Watson-Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6-7 Watson-Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2-3 Watson-Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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26
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Largy E, Mergny JL. Shape matters: size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Res 2014; 42:e149. [PMID: 25143531 PMCID: PMC4231728 DOI: 10.1093/nar/gku751] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In recent years, an increasing number of reports have been focused on the structure and biological role of non-canonical nucleic acid secondary structures. Many of these studies involve the use of oligonucleotides that can often adopt a variety of structures depending on the experimental conditions, and hence change the outcome of an assay. The knowledge of the structure(s) formed by oligonucleotides is thus critical to correctly interpret the results, and gain insight into the biological role of these particular sequences. Herein we demonstrate that size-exclusion HPLC (SE-HPLC) is a simple yet surprisingly powerful tool to quickly and effortlessly assess the secondary structure(s) formed by oligonucleotides. For the first time, an extensive calibration and validation of the use of SE-HPLC to confidently detect the presence of different species displaying various structure and/or molecularity, involving >110 oligonucleotides forming a variety of secondary structures (antiparallel, parallel, A-tract bent and mismatched duplexes, triplexes, G-quadruplexes and i-motifs, RNA stem loops), is performed. Moreover, we introduce simple metrics that allow the use of SE-HPLC without the need for a tedious calibration work. We show that the remarkable versatility of the method allows to quickly establish the influence of a number of experimental parameters on nucleic acid structuration and to operate on a wide range of oligonucleotide concentrations. Case studies are provided to clearly illustrate the all-terrain capabilities of SE-HPLC for oligonucleotide secondary structure analysis. Finally, this manuscript features a number of important observations contributing to a better understanding of nucleic acid structural polymorphism.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
| | - Jean-Louis Mergny
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
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27
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Durand G, Lisi S, Ravelet C, Dausse E, Peyrin E, Toulmé JJ. Riboswitches Based on Kissing Complexes for the Detection of Small Ligands. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Durand G, Lisi S, Ravelet C, Dausse E, Peyrin E, Toulmé JJ. Riboswitches based on kissing complexes for the detection of small ligands. Angew Chem Int Ed Engl 2014; 53:6942-5. [PMID: 24916019 DOI: 10.1002/anie.201400402] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Indexed: 01/08/2023]
Abstract
Biosensors derived from aptamers were designed for which folding into a hairpin shape is triggered by binding of the cognate ligand. These aptamers (termed aptaswitches) thus switch between folded and unfolded states in the presence and absence of the ligand, respectively. The apical loop of the folded aptaswitch is recognized by a second hairpin called the aptakiss through loop-loop or kissing interactions, whereas the aptakiss does not bind the unfolded aptaswitch. Therefore, the formation of a kissing complex signals the presence of the ligand. Aptaswitches were designed that enable the detection of GTP and adenosine in a specific and quantitative manner by surface plasmon resonance when using a grafted aptakiss or in solution by anisotropy measurement with a fluorescently labeled aptakiss. This approach is generic and can potentially be extended to the detection of any molecule for which hairpin aptamers have been identified, as long as the apical loop is not involved in ligand binding.
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Affiliation(s)
- Guillaume Durand
- Univ. Bordeaux, IECB, Laboratoire ARNA, 2 rue Robert Escarpit, 33607 Pessac (France); Inserm U869, Laboratoire ARNA, 146 rue Léo Saignat, 33076 Bordeaux (France)
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29
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Mundigala H, Michaux JB, Feig AL, Ennifar E, Rueda D. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Nucleic Acids Res 2014; 42:7281-9. [PMID: 24813449 PMCID: PMC4066764 DOI: 10.1093/nar/gku332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The HIV-1 dimerization initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin motif in the 5′-untranslated region of its RNA genome. DIS hairpin plays an important role in genome dimerization by forming a ‘kissing complex’ between two complementary hairpins. Understanding the kinetics of this interaction is key to exploiting DIS as a possible human immunodeficiency virus (HIV) drug target. Here, we present a single-molecule Förster resonance energy transfer (smFRET) study of the dimerization reaction kinetics. Our data show the real-time formation and dissociation dynamics of individual kissing complexes, as well as the formation of the mature extended duplex complex that is ultimately required for virion packaging. Interestingly, the single-molecule trajectories reveal the presence of a previously unobserved bent intermediate required for extended duplex formation. The universally conserved A272 is essential for the formation of this intermediate, which is stabilized by Mg2+, but not by K+ cations. We propose a 3D model of a possible bent intermediate and a minimal dimerization pathway consisting of three steps with two obligatory intermediates (kissing complex and bent intermediate) and driven by Mg2+ ions.
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Affiliation(s)
- Hansini Mundigala
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | | | - Andrew L Feig
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - David Rueda
- Department of Chemistry, Wayne State University, Detroit, MI 48236, USA Department of Medicine, Section of Virology, Imperial College, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College, London W12 0NN, UK
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30
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Palau W, Masante C, Ventura M, Di Primo C. Direct evidence for RNA-RNA interactions at the 3' end of the Hepatitis C virus genome using surface plasmon resonance. RNA (NEW YORK, N.Y.) 2013; 19:982-991. [PMID: 23651615 PMCID: PMC3683932 DOI: 10.1261/rna.037606.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/11/2013] [Indexed: 06/02/2023]
Abstract
Surface plasmon resonance was used to investigate two previously described interactions analyzed by reverse genetics and complementation mutation experiments, involving 5BSL3.2, a stem-loop located in the NS5B coding region of HCV. 5BSL3.2 was immobilized on a sensor chip by streptavidin-biotin coupling, and its interaction either with the SL2 stem-loop of the 3' end or with an upstream sequence centered on nucleotide 9110 (referred to as Seq9110) was monitored in real-time. In contrast with previous results obtained by NMR assays with the same short RNA sequences that we used or SHAPE analysis with longer RNAs, we demonstrate that recognition between 5BSL3.2 and SL2 can occur in solution through a kissing-loop interaction. We show that recognition between Seq9110 and the internal loop of 5BSL3.2 does not prevent binding of SL2 on the apical loop of 5BSL3.2 and does not influence the rate constants of the SL2-5BSL3.2 complex. Therefore, the two binding sites of 5BSL3.2, the apical and internal loops, are structurally independent and both interactions can coexist. We finally show that the stem-loop SL2 is a highly dynamic RNA motif that fluctuates between at least two conformations: One is able to hybridize with 5BSL3.2 through loop-loop interaction, and the other one is capable of self-associating in the absence of protein, reinforcing the hypothesis of SL2 being a dimerization sequence. This result suggests also that the conformational dynamics of SL2 could play a crucial role for controlling the destiny of the genomic RNA.
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Affiliation(s)
- William Palau
- Université de Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
- INSERM, U869, Laboratoire ARNA, F-33600 Pessac, France
| | - Cyril Masante
- Université de Bordeaux, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
- CNRS UMR 5234, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
| | - Michel Ventura
- Université de Bordeaux, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
- CNRS UMR 5234, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
| | - Carmelo Di Primo
- Université de Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
- INSERM, U869, Laboratoire ARNA, F-33600 Pessac, France
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31
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Sumita M, White NA, Julien KR, Hoogstraten CG. Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis. RNA Biol 2013; 10:425-35. [PMID: 23324606 PMCID: PMC3672286 DOI: 10.4161/rna.23609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a “double conformational capture” model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding.
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Affiliation(s)
- Minako Sumita
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA
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32
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Sehdev P, Crews G, Soto AM. Effect of Helix Stability on the Formation of Loop–Loop Complexes. Biochemistry 2012; 51:9612-23. [DOI: 10.1021/bi300481v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Preeti Sehdev
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Gordon Crews
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Ana Maria Soto
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
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33
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Lambert D, Draper DE. Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values. Biochemistry 2012; 51:9014-26. [PMID: 23088364 PMCID: PMC3505219 DOI: 10.1021/bi301103j] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To investigate the mechanism by which urea destabilizes RNA structure, urea-induced unfolding of four different RNA secondary and tertiary structures was quantified in terms of an m-value, the rate at which the free energy of unfolding changes with urea molality. From literature data and our osmometric study of a backbone analogue, we derived average interaction potentials (per square angstrom of solvent accessible surface) between urea and three kinds of RNA surfaces: phosphate, ribose, and base. Estimates of the increases in solvent accessible surface areas upon RNA denaturation were based on a simple model of unfolded RNA as a combination of helical and single-strand segments. These estimates, combined with the three interaction potentials and a term to account for interactions of urea with released ions, yield calculated m-values that are in good agreement with experimental values (200 mm monovalent salt). Agreement was obtained only if single-stranded RNAs were modeled in a highly stacked, A-form conformation. The primary driving force for urea-induced denaturation is the strong interaction of urea with the large surface areas of bases that become exposed upon denaturation of either RNA secondary or tertiary structure, though interactions of urea with backbone and released ions may account for up to a third of the m-value. Urea m-values for all four RNAs are salt-dependent, which we attribute to an increased extension (or decreased charge density) of unfolded RNAs with an increased urea concentration. The sensitivity of the urea m-value to base surface exposure makes it a potentially useful probe of the conformations of RNA unfolded states.
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Affiliation(s)
| | - David E. Draper
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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Zhu G, Ye M, Donovan MJ, Song E, Zhao Z, Tan W. Nucleic acid aptamers: an emerging frontier in cancer therapy. Chem Commun (Camb) 2012; 48:10472-80. [PMID: 22951893 PMCID: PMC3869973 DOI: 10.1039/c2cc35042d] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The last two decades have witnessed the development and application of nucleic acid aptamers in a variety of fields, including target analysis, disease therapy, and molecular and cellular engineering. The efficient and widely applicable aptamer selection, reproducible chemical synthesis and modification, generally impressive target binding selectivity and affinity, relatively rapid tissue penetration, low immunogenicity, and rapid systemic clearance make aptamers ideal recognition elements for use as therapeutics or for in vivo delivery of therapeutics. In this feature article, we discuss the development and biomedical application of nucleic acid aptamers, with emphasis on cancer cell aptamer isolation, targeted cancer therapy, oncology biomarker identification and drug discovery.
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Affiliation(s)
- Guizhi Zhu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Departments of Chemistry, Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, Center For Research at Bio/nano Interface, University of Florida, Gainesville, FL 32611-7200 (USA) Fax: (+1) 352-846-2410
| | - Mao Ye
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Michael J. Donovan
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Erqun Song
- Departments of Chemistry, Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, Center For Research at Bio/nano Interface, University of Florida, Gainesville, FL 32611-7200 (USA) Fax: (+1) 352-846-2410
- Key Laboratory of Luminescence and Real-Time Analysis of the Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zilong Zhao
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Departments of Chemistry, Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, Center For Research at Bio/nano Interface, University of Florida, Gainesville, FL 32611-7200 (USA) Fax: (+1) 352-846-2410
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Palau W, Di Primo C. Single-cycle kinetic analysis of ternary DNA complexes by surface plasmon resonance on a decaying surface. Biochimie 2012; 94:1891-9. [PMID: 22580385 DOI: 10.1016/j.biochi.2012.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/30/2012] [Indexed: 12/16/2022]
Abstract
Complexes involving three DNA strands were used to demonstrate that the single-cycle kinetics (SCK) method, which consists in injecting sequentially samples at increasing concentrations and until now used exclusively to investigate bimolecular complexes by surface plasmon resonance, can be extended to the kinetic analysis of ternary complexes. DNA targets, B, were designed with sequences of variable lengths on their 3' sides that recognise a surface-immobilized biotinylated DNA anchor, A. These targets displayed on their 5' sides sequences that recognise DNA oligonucleotides of variable lengths, C, namely the analytes. Combinations of B and C DNA oligonucleotides on A generated ternary complexes each composed of two Watson-Crick helices displaying different kinetic properties. The target-analyte B-C duplexes were formed by sequentially injecting three increasing concentrations of the analytes C during the dissociation phase of the target B from the anchor A. The sensorgrams for the target-analyte complexes dissociating from the functionalized surface were successfully fitted by the SCK method while the target dissociated from the anchor, i.e. on a decaying surface. Within the range of applicability of the method which is driven by the rate of dissociation of the target from the anchor, the rate and equilibrium constants characteristic of these target-analyte duplexes of the ternary complexes did not depend on how fast the targets dissociated from the immobilized DNA anchor. In addition the results agreed very well with those obtained when such duplexes were analysed directly as bimolecular complexes, i.e. when the target, modified with a biotin, was directly immobilized onto a streptavidin sensor chip surface rather than captured by an anchor. Therefore the method we named SCKODS (Single-Cycle Kinetics On a Decaying Surface) can also be used to investigate complexes formed during a dissociation phase, in a ternary complex context. The SCKODS method can be combined with the SCK one to fully characterize the two bimolecular complexes of a ternary complex.
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Affiliation(s)
- William Palau
- Univ. Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
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Cao S, Chen SJ. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (NEW YORK, N.Y.) 2011; 17:2130-43. [PMID: 22028361 PMCID: PMC3222126 DOI: 10.1261/rna.026658.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/12/2011] [Indexed: 05/24/2023]
Abstract
We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. From the energy landscape, we identify two minimal free energy structures, which correspond to the kissing-loop dimer and the extended-duplex dimer, respectively. The results support the two-step dimerization process for the HIV-1 replication cycle. Furthermore, based on the Vfold model and energy minimization, the theory can predict the native structure as well as the local minima in the free energy landscape. The root-mean-square deviations (RMSDs) for the predicted kissing-loop dimer and extended-duplex dimer are ~3.0 Å. The method developed here provides a new method to study the RNA/RNA kissing complex.
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Affiliation(s)
- Song Cao
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | - Shi-Jie Chen
- Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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Li TJX, Reidys CM. Combinatorial analysis of interacting RNA molecules. Math Biosci 2011; 233:47-58. [PMID: 21689666 DOI: 10.1016/j.mbs.2011.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 12/06/2010] [Accepted: 04/05/2011] [Indexed: 12/26/2022]
Abstract
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zigzag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.
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Affiliation(s)
- Thomas J X Li
- Center for Combinatorics, LPMC-TJKLC, Nankai University, Tianjin 300071, PR China
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Dausse E, Taouji S, Evadé L, Di Primo C, Chevet E, Toulmé JJ. HAPIscreen, a method for high-throughput aptamer identification. J Nanobiotechnology 2011; 9:25. [PMID: 21639912 PMCID: PMC3127992 DOI: 10.1186/1477-3155-9-25] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 06/03/2011] [Indexed: 01/24/2023] Open
Abstract
Background Aptamers are oligonucleotides displaying specific binding properties for a predetermined target. They are selected from libraries of randomly synthesized candidates through an in vitro selection process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment) alternating selection and amplification steps. SELEX is followed by cloning and sequencing of the enriched pool of oligonucleotides to enable comparison of the selected sequences. The most represented candidates are then synthesized and their binding properties are individually evaluated thus leading to the identification of aptamers. These post-selection steps are time consuming and introduce a bias to the expense of poorly amplified binders that might be of high affinity and are consequently underrepresented. A method that would circumvent these limitations would be highly valuable. Results We describe a novel homogeneous solution-based method for screening large populations of oligonucleotide candidates generated from SELEX. This approach, based on the AlphaScreen® technology, is carried out on the exclusive basis of the binding properties of the selected candidates without the needs of performing a priori sequencing. It therefore enables the functional identification of high affinity aptamers. We validated the HAPIscreen (High throughput APtamer Identification screen) methodology using aptamers targeted to RNA hairpins, previously identified in our laboratory. We then screened pools of candidates issued from SELEX rounds in a 384 well microplate format and identify new RNA aptamers to pre-microRNAs. Conclusions HAPIscreen, an Alphascreen®-based methodology for the identification of aptamers is faster and less biased than current procedures based on sequence comparison of selected oligonucleotides and sampling binding properties of few individuals. Moreover this methodology allows for screening larger number of candidates. Used here for selecting anti-premiR aptamers, HAPIscreen can be adapted to any type of tagged target and is fully amenable to automation.
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Affiliation(s)
- Eric Dausse
- Inserm U869, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33706 Pessac, France
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Di Primo C, Dausse E, Toulmé JJ. Surface plasmon resonance investigation of RNA aptamer-RNA ligand interactions. Methods Mol Biol 2011; 764:279-300. [PMID: 21748648 DOI: 10.1007/978-1-61779-188-8_19] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Instruments based on the surface plasmon resonance (SPR) principle allow label-free detection of interactions between targets immobilized at a solid-liquid interface and partners in solution. This method is well suited to determine the kinetic parameters, the equilibrium constant and the stoichiometry of a reaction. Aptamers are ligands identified from random libraries of RNA, DNA or chemically modified oligonucleotides by in vitro selection (SELEX). Aptamers can be raised against a great variety of targets (small molecules, proteins, nucleic acids, cells, viruses, bacteria). SPR is routinely used in our laboratory for the analysis of RNA aptamer-RNA target complexes. To illustrate SPR investigation of such complexes, we describe here methods that were successfully used to monitor the interaction between the trans-activating responsive element of HIV-1 and an RNA aptamer.
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Affiliation(s)
- Carmelo Di Primo
- ARNA laboratory, University of Bordeaux, F-33000 Bordeaux, France.
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Lambert D, Leipply D, Draper DE. The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration. J Mol Biol 2010; 404:138-57. [PMID: 20875423 PMCID: PMC3001104 DOI: 10.1016/j.jmb.2010.09.043] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 09/13/2010] [Accepted: 09/17/2010] [Indexed: 12/20/2022]
Abstract
The stabilization of RNA tertiary structures by ions is well known, but the neutral osmolyte trimethylamine oxide (TMAO) can also effectively stabilize RNA tertiary structure. To begin to understand the physical basis for the effects of TMAO on RNA, we have quantitated the TMAO-induced stabilization of five RNAs with known structures. So-called m values, the increment in unfolding free energy per molal of osmolyte at constant KCl activity, are ∼0 for a hairpin secondary structure and between 0.70 and 1.85 kcal mol(-1)m(-1) for four RNA tertiary structures (30-86 nt). Further analysis of two RNAs by small-angle X-ray scattering and hydroxyl radical probing shows that TMAO reduces the radius of gyration of the unfolded ensemble to the same endpoint as seen in titration with Mg(2+) and that the structures stabilized by TMAO and Mg(2+) are indistinguishable. Remarkably, TMAO induces the native conformation of a Mg(2+) ion chelation site formed in part by a buried phosphate, even though Mg(2+) is absent. TMAO interacts weakly, if at all, with KCl, ruling out the possibility that TMAO stabilizes RNA indirectly by increasing salt activity. TMAO is, however, strongly excluded from the vicinity of dimethylphosphate (unfavorable interaction free energy, +211 cal mol(-1)m(-1) for the potassium salt), an ion that mimics the RNA backbone phosphate. We suggest that formation of RNA tertiary structure is accompanied by substantial phosphate dehydration (loss of 66-173 water molecules in the RNA structures studied) and that TMAO works principally by reducing the energetic penalty associated with this dehydration. The strong parallels we find between the effects of TMAO and Mg(2+) suggest that RNA sequence is more important than specific ion interactions in specifying the native structure.
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Affiliation(s)
- Dominic Lambert
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Watrin M, Von Pelchrzim F, Dausse E, Schroeder R, Toulmé JJ. In vitro selection of RNA aptamers derived from a genomic human library against the TAR RNA element of HIV-1. Biochemistry 2009; 48:6278-84. [PMID: 19496624 DOI: 10.1021/bi802373d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The transactivating responsive (TAR) element is a RNA hairpin located in the 5' untranslated region of HIV-1 mRNA. It is essential for full-length transcription of the retroviral genome and therefore for HIV-1 replication. Hairpin aptamers that generate highly stable and specific complexes with TAR were previously identified, thus decreasing the level of TAR-dependent expression in cultured cells [Kolb, G., et al. (2006) RNA Biol. 3, 150-156]. We performed genomic SELEX against TAR using a human RNA library to identify human transcripts that might interact with the retroviral genome through loop-loop interactions and potentially contribute to the regulation of TAR-mediated processes. We identified a genomic aptamer termed a1 that folds as a hairpin with an apical loop complementary to five nucleotides of the TAR hexanucleotide loop. Surface plasmon resonance experiments performed on a truncated or mutated version of the a1 aptamer, in the presence of the Rop protein of Escherichia coli, indicate the formation of a highly stable a1-TAR kissing complex. The 5' ACCCAG loop of a1 constitutes a new motif of interaction with the TAR loop.
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Affiliation(s)
- Marguerite Watrin
- Inserm U869, European Institute of Chemistry and Biology, Pessac, France
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