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Ishizawa S, Tumurkhuu M, Gross EJ, Ohata J. Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids. Chem Sci 2022; 13:1780-1788. [PMID: 35282632 PMCID: PMC8826848 DOI: 10.1039/d1sc05204g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/15/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific chemical modification of unprotected DNAs through a phosphine-mediated amine–azide coupling reaction in ionic liquid.
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Affiliation(s)
- Seiya Ishizawa
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Munkhtuya Tumurkhuu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Elizabeth J. Gross
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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2
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Fatin M, Rahim Ruslinda A, Gopinath SC, Arshad MM, Hashim U, Lakshmipriya T, Tang TH, Kamarulzaman A. Co-ordinated split aptamer assembly and disassembly on Gold nanoparticle for functional detection of HIV-1 tat. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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3
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Rahimi F. Aptamers Selected for Recognizing Amyloid β-Protein-A Case for Cautious Optimism. Int J Mol Sci 2018; 19:ijms19030668. [PMID: 29495486 PMCID: PMC5877529 DOI: 10.3390/ijms19030668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/18/2018] [Accepted: 02/22/2018] [Indexed: 02/07/2023] Open
Abstract
Aptamers are versatile oligonucleotide ligands used for molecular recognition of diverse targets. However, application of aptamers to the field of amyloid β-protein (Aβ) has been limited so far. Aβ is an intrinsically disordered protein that exists in a dynamic conformational equilibrium, presenting time-dependent ensembles of short-lived, metastable structures and assemblies that have been generally difficult to isolate and characterize. Moreover, despite understanding of potential physiological roles of Aβ, this peptide has been linked to the pathogenesis of Alzheimer disease, and its pathogenic roles remain controversial. Accumulated scientific evidence thus far highlights undesirable or nonspecific interactions between selected aptamers and different Aβ assemblies likely due to the metastable nature of Aβ or inherent affinity of RNA oligonucleotides to β-sheet-rich fibrillar structures of amyloidogenic proteins. Accordingly, lessons drawn from Aβ–aptamer studies emphasize that purity and uniformity of the protein target and rigorous characterization of aptamers’ specificity are important for realizing and garnering the full potential of aptamers selected for recognizing Aβ or other intrinsically disordered proteins. This review summarizes studies of aptamers selected for recognizing different Aβ assemblies and highlights controversies, difficulties, and limitations of such studies.
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Affiliation(s)
- Farid Rahimi
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
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4
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Wang R, Zhang X, Ding H, Qiao Y, Han X, Geng W, Guan G, Cui H, Zhao B, Wu Y, Liang G, Shang H. AID recruits the RNA exosome to degrade HIV-1 nascent transcripts through interaction with the Tat-P-TEFb-TAR RNP complex. FEBS Lett 2018; 592:284-294. [PMID: 29266200 DOI: 10.1002/1873-3468.12954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/31/2017] [Accepted: 11/17/2017] [Indexed: 01/11/2023]
Abstract
Activation-induced cytidine deaminase (AID), a member of the APOBEC family that induces antibody diversification, has been shown to inhibit the replication of hepatitis B virus, Kaposi's sarcoma-associated herpesvirus, and retro-transposons. However, whether AID can inhibit human immunodeficiency virus 1 (HIV-1) replication remains unclear. Here, we report that AID impairs the synthesis of HIV-1 components by interacting with the complex of Tat. This interaction recruits the RNA exosome to degrade the nascent HIV-1 transcript. AID also targets the HIV-1-integrated genome via the Tat-P-TEFb-TAR complex. Thus, we propose a novel function for AID as an adaptor protein that represses viral transcription. Our findings provide insights into developing anti-HIV therapeutics and understanding how host cells restrict integrated virus replication.
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Affiliation(s)
- Ruixuan Wang
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Xiaowei Zhang
- The Core Laboratory for Public Health Science and Practice, China Medical University, Shenyang, China
| | - Haibo Ding
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Ying Qiao
- The Core Laboratory for Public Health Science and Practice, China Medical University, Shenyang, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Wenqing Geng
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Gefei Guan
- Department of Neurosurgery, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Hualu Cui
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Bin Zhao
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Yuntao Wu
- National Center for Biodefense and Infectious Diseases, Department of Molecular and Microbiology, George Mason University, Manassas, VA, USA
| | - Guoxin Liang
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
| | - Hong Shang
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, China Medical University, Shenyang, China
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5
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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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6
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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: 64] [Impact Index Per Article: 7.1] [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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7
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Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26199940 PMCID: PMC4493287 DOI: 10.1155/2015/419318] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.
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Aptamer-based therapeutics: new approaches to combat human viral diseases. Pharmaceuticals (Basel) 2013; 6:1507-42. [PMID: 24287493 PMCID: PMC3873675 DOI: 10.3390/ph6121507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/18/2022] Open
Abstract
Viruses replicate inside the cells of an organism and continuously evolve to contend with an ever-changing environment. Many life-threatening diseases, such as AIDS, SARS, hepatitis and some cancers, are caused by viruses. Because viruses have small genome sizes and high mutability, there is currently a lack of and an urgent need for effective treatment for many viral pathogens. One approach that has recently received much attention is aptamer-based therapeutics. Aptamer technology has high target specificity and versatility, i.e., any viral proteins could potentially be targeted. Consequently, new aptamer-based therapeutics have the potential to lead a revolution in the development of anti-infective drugs. Additionally, aptamers can potentially bind any targets and any pathogen that is theoretically amenable to rapid targeting, making aptamers invaluable tools for treating a wide range of diseases. This review will provide a broad, comprehensive overview of viral therapies that use aptamers. The aptamer selection process will be described, followed by an explanation of the potential for treating virus infection by aptamers. Recent progress and prospective use of aptamers against a large variety of human viruses, such as HIV-1, HCV, HBV, SCoV, Rabies virus, HPV, HSV and influenza virus, with particular focus on clinical development of aptamers will also be described. Finally, we will discuss the challenges of advancing antiviral aptamer therapeutics and prospects for future success.
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9
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Oligomeric nucleic acids as antivirals. Molecules 2011; 16:1271-96. [PMID: 21278679 PMCID: PMC6259927 DOI: 10.3390/molecules16021271] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/12/2011] [Accepted: 01/25/2011] [Indexed: 02/07/2023] Open
Abstract
Based on the natural functions and chemical characteristics of nucleic acids, a variety of novel synthetic drugs and tools to explore biological systems have become available in recent years. To date, a great number of antisense oligonucleotides, RNA interference-based tools, CpG-containing oligonucleotides, catalytic oligonucleotides, decoys and aptamers has been produced synthetically and applied successfully for understanding and manipulating biological processes and in clinical trials to treat a variety of diseases. Their versatility and potency make them equally suited candidates for fighting viral infections. Here, we describe the different types of nucleic acid-based antivirals, their mechanism of action, their advantages and limitations, and their future prospects.
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10
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Fauzi H, Agyeman A, Hines JV. T box transcription antitermination riboswitch: influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:185-91. [PMID: 19152843 PMCID: PMC2656570 DOI: 10.1016/j.bbagrm.2008.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 12/09/2008] [Accepted: 12/09/2008] [Indexed: 11/18/2022]
Abstract
Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5'-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation.
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Affiliation(s)
- Hamid Fauzi
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Akwasi Agyeman
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V. Hines
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
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11
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Abstract
Aptamers are rare nucleic acid ligands, which can be concocted in the laboratory from the randomized pool of molecules by affinity and amplification processes. Aptamers have several properties as they can be applied complementarily to antibodies and have several advantages over antibodies. In the past, several aptamers have been selected with a view to develop antiviral agents for therapeutic applications. This review summarizes potent antiviral aptamers and their strategies to prevent the viral replication.
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Affiliation(s)
- S C B Gopinath
- Functional Nucleic Acids Group, Institute for Biological Resources and Functions and Center for Applied Near Field Optics Research, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
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12
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Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 931] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
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Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Bugaut A, Toulmé JJ, Rayner B. SELEX and dynamic combinatorial chemistry interplay for the selection of conjugated RNA aptamers. Org Biomol Chem 2007; 4:4082-8. [PMID: 17312962 DOI: 10.1039/b610890c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SELEX (for Systematic Evolution of Ligands by Exponential enrichment) has proven to be extraordinarily powerful for the isolation of DNA or RNA aptamers that bind with high affinity and specificity to a wide range of molecular targets. However, the modest chemical functionality of nucleic acids poses some limits on the versatility of aptamers as binders and catalysts. To further improve the properties of aptamers, additional chemical diversity must be introduced. The design of chemical modifications is not a trivial task. Recently, dynamic combinatorial chemistry (DCC) has been introduced as an alternative to traditional combinatorial chemistry. DCC employs equilibrium shifting to effect molecular evolution of a dynamic combinatorial library of molecules. Herein, we describe an original process that combines DCC and SELEX for the in vitro selection of modified aptamers which are conjugated to chemically diverse small-molecules. Its successful application for the selection of small-molecule conjugated RNA aptamers that bind tightly to the transactivation-response (TAR) element of HIV-1 is presented.
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Affiliation(s)
- Anthony Bugaut
- INSERM U386, 146 rue Leo Saignat, 33076 BORDEAUX Cedex, France.
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Surugiu-Wärnmark I, Wärnmark A, Toresson G, Gustafsson JA, Bülow L. Selection of DNA aptamers against rat liver X receptors. Biochem Biophys Res Commun 2005; 332:512-7. [PMID: 15910755 DOI: 10.1016/j.bbrc.2005.04.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 04/29/2005] [Indexed: 10/25/2022]
Abstract
Liver X receptors alpha and beta (LXRalpha; LXRbeta) are members of the nuclear hormone receptor superfamily of ligand-activated transcription factors. LXRs play an important role in the reverse cholesterol transport and govern the expression of many of the proteins that are indispensable for the regulation of normal cholesterol levels in the body. SELEX, an in vitro selection technology, was used on a single stranded DNA library harboring a 12 randomized nucleotide sequence in order to isolate aptamers showing affinity for LXRalpha. Enzyme-linked assays and surface plasmon resonance measurements showed that the selected aptamers had strong affinities for LXRalpha with apparent dissociation constants, K(d)s, in nanomolar range. All clones carried CG-repeats, indicating a probability for a similar manner of binding to LXRalpha. Very high cross-reactivities were observed when testing the aptamers with LXRbeta (up to 700%) and RXRalpha (up to 50%). If instead we regard the aptamer sequences as selected against LXRbeta, the cross-reactivities decrease considerably, to 17% for LXRalpha and 7% for RXRalpha. Therefore, in the future we are planning to use the obtained aptamers as binders for LXRbeta.
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Affiliation(s)
- Ioana Surugiu-Wärnmark
- Department of Pure and Applied Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden.
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15
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Fauzi H, Jack KD, Hines JV. In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding. Nucleic Acids Res 2005; 33:2595-602. [PMID: 15879350 PMCID: PMC1090546 DOI: 10.1093/nar/gki546] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with four bases in a 7 nt bulge of the antiterminator RNA. In vitro selection of randomized tRNA binding to Bacillus subtilis tyrS antiterminator model RNAs was used to determine what, if any, sequence trends there are for binding beyond the known base pair complementarity. The model antiterminator RNAs were selected for the wild-type tertiary fold of tRNA. While there were no obvious sequence correlations between the selected tRNAs, there were correlations between certain tertiary structural elements and binding efficiency to different antiterminator model RNAs. In addition, one antiterminator model selected primarily for a kissing tRNA T loop-antiterminator bulge interaction, while another antiterminator model resulted in no such selection. The selection results indicate that, at the level of tertiary structure, there are ideal matches between tRNAs and antiterminator model RNAs consistent with in vivo observations and that additional recognition features, beyond base pair complementarity, may play a role in the formation of the complex.
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Affiliation(s)
| | | | - Jennifer V. Hines
- To whom correspondence should be addressed. Tel: +1 740 517 8482; Fax: +1 740 593 0148;
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16
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Kolb G, Reigadas S, Boiziau C, van Aerschot A, Arzumanov A, Gait MJ, Herdewijn P, Toulmé JJ. Hexitol nucleic acid-containing aptamers are efficient ligands of HIV-1 TAR RNA. Biochemistry 2005; 44:2926-33. [PMID: 15723535 DOI: 10.1021/bi048393s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transactivation responsive element (TAR) plays a crucial role in the transcription of the HIV-1 genome upon specific binding of the viral protein Tat and cellular proteins. We have previously identified a RNA hairpin aptamer forming a stable and specific kissing complex with TAR RNA (Ducongé, F., and Toulmé, J. J. (1999) RNA 5, 1605-1614). We chemically modified this aptamer with hexitol nucleic acid (HNA) residues. We demonstrate that a fully HNA-modified aptamer is a poor ligand but, in contrast, mixmers containing both HNA and unmodified RNA nucleotides display interesting properties. Two HNA-RNA mixmers bind to TAR with an equilibrium dissociation constant in the low-nanomolar range and show a reduced nuclease sensitivity. In addition, they show a moderate dependence on magnesium ions for binding to TAR. These HNA-RNA mixmers are able to inhibit transactivation of transcription in an in vitro assay.
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Affiliation(s)
- Gaëlle Kolb
- INSERM U 386; Université Victor Segalen Bordeaux 2, 146 rue Léo-Saignat, F-33076 Bordeaux Cedex, France
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17
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Jeon SH, Kayhan B, Ben-Yedidia T, Arnon R. A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J Biol Chem 2004; 279:48410-9. [PMID: 15358767 DOI: 10.1074/jbc.m409059200] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Influenza A virus infection is a major source of morbidity and mortality worldwide. Current means of control for influenza are based on prophylaxis by vaccines and on treatment by the available specific influenza neuraminidase inhibitor drugs. The approach taken in the present study is to prevent and/or ameliorate influenza infection by site-specific blocking of the viral binding to host cell receptors. We describe a novel oligonucleotide, known also as an aptamer, which has been designed to complement the receptor-binding region of the influenza hemagglutinin molecule. It was constructed by screening a DNA library and processing by the selective evolution of ligands by exponential enrichment (SELEX) procedure. We show that this DNA aptamer is indeed capable of inhibiting the hemagglutinin capacity of the virus, as well as in the prevention of viral infectivity in vitro, in tissue culture. Furthermore, it inhibits viral infection by different influenza strains in an animal model, as manifested by 90-99% reduction of virus burden in the lungs of treated mice. The mode of action of this aptamer is by blocking the binding of influenza virus to target cell receptors and consequently prevention of the virus invasion into the host cells.
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Affiliation(s)
- Sung Ho Jeon
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
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Da Rocha Gomes S, Dausse E, Toulmé JJ. Determinants of apical loop–internal loop RNA–RNA interactions involving the HCV IRES. Biochem Biophys Res Commun 2004; 322:820-6. [PMID: 15336537 DOI: 10.1016/j.bbrc.2004.07.185] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Indexed: 01/13/2023]
Abstract
Domain II of the hepatitis C virus internal ribosome entry site is a major RNA structure involved in the viral mRNA translation. It comprises four different structural domains. We performed in vitro selection against the apical loop of the domain II and we identified RNA aptamers folding as an imperfect hairpin with an internal loop of interacting with the apical loop of the domain II. This RNA-RNA interaction creates apical loop-internal loop complex. The aptamer binds the target with an apparent K(d) of 35nM. In this study, the main structural elements of the target and the aptamer involved in the formation of the complex are characterized by mutation, deletion, and RNase probing analysis. We demonstrate that a complementary loop flanked by G,C rich upper and lower stems are crucial for such RNA-RNA interactions.
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Affiliation(s)
- Sonia Da Rocha Gomes
- INSERM U386, IFR 66, Université Victor Segalen Bordeaux 2, France and Institut Européen de Chimie et Biologie, Pessac, France
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