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Yang G, Li W, Zhang S, Hu B, Huang Z. Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples. Talanta 2024; 266:125039. [PMID: 37604070 DOI: 10.1016/j.talanta.2023.125039] [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: 06/10/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Abstract
Nucleic acid aptamers are of great potentials in diagnostic and therapeutic applications because of their unique molecular recognition capabilities. However, satisfactory aptamers with high affinity and specificity are still in short supply. Herein, we have developed new selection methods allowing the free interactions between the targets and potential aptamers in solution. In our selection system, the protein targets (biotinylated randomly or site-specifically) were first incubated with the random DNA library, followed by the pull-down with the streptavidin magnetic beads or biolayer-interferometry (BLI) sensors. By comparing the two biotinylation strategies (random or site-specific) and two states of the targets (free or immobilized), we have found that the combination of the site-specific biotinylation and free-target strategies was most successful. Based on these highly-efficient selection strategies, HPV L1 aptamers were obtained. By designing the sandwich aptasensor assisted with RCA and CRISPR/Cas12a, we have diagnosed various HPV subtypes in clinical samples, such as easily-collected urine samples. In summary, our new strategy can allow efficient selection of aptamers with high affinity and specificity for clinical applications.
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Affiliation(s)
- Guotai Yang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Wei Li
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610000, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, 610095, PR China.
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2
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Abstract
Aptamers are synthetic DNA or RNA oligonucleotide ligands with great potential for therapeutic applications. A vast number of disease-related targets have been used to identify agonistic, antagonistic, or inhibitory aptamers, or aptamer-based targeting ligands. However, only a few aptamers have reached late-stage clinical trials so far and the commercial infrastructure is still far behind that of other therapeutic agents such as monoclonal antibodies. The desirable properties of aptamers such as selectivity, chemical flexibility, or cost-efficiency are faced by challenges, including a short half-life in vivo, immunogenicity, and entrapment in cellular organelles. Aptamer research is still in an early stage, and a deeper understanding of their structure, target interactions, and pharmacokinetics is necessary to catch up to the clinical market. In this review, we will discuss the benefits and limitations in the development of therapeutic aptamers, as well as the advances and future directions of aptamer research. The progress towards effective therapies seems to be slow, but it has not stopped and the best is yet to come.
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Zhang Y, Lu Y, Wang F, An S, Zhang Y, Sun T, Zhu J, Jiang C. ATP/pH Dual Responsive Nanoparticle with d-[des-Arg 10 ]Kallidin Mediated Efficient In Vivo Targeting Drug Delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602494. [PMID: 27775872 DOI: 10.1002/smll.201602494] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/14/2016] [Indexed: 05/20/2023]
Abstract
Inflammation has been reported as one significant hallmark of breast cancer in relation to tumor development, metastasis, and invasion. The bradykinin receptor 1 (B1R) is highly expressed on inflammatory breast tumor cells thus providing a promising targeting site for tumor recognition and sufficient receptor mediated endocytosis. In this study, the authors evaluate the targeting efficiency of l-form and d-form [des-Arg10 ]kallidin both in vitro and in vivo. To further improve the drug delivery efficiency, the authors establish a dandelion like nanoparticle by combining the polymeric drug conjugates and aptamer complex together. The doxorubicin conjugated polymer is complexed with adenosine-5'-triphosphate (ATP) sensitive hybridized aptamer in self-assembly process by intercalating into the double strand scaffolds. The acid labile conjugating bond and ATP sensitive aptamer endow the nanoparticle with dual responsiveness to intracellular milieu, thus triggering a quick drug release in tumor cells. Remarkable therapeutic effects and tuned in vivo pharmacokinetics profiles are shown by the aptamer complexed drug conjugates nanoparticle with B1R active targeting modification. Therefore the strategies of B1R targeting and ATP/pH dual-responsiveness nanoparticle help achieve enhanced drug accumulation within tumor cells and efficient chemotherapy for breast cancer.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Yifei Lu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Feng Wang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Sai An
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Yujie Zhang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Tao Sun
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Jianhua Zhu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Chen Jiang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
- State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
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4
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Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N. Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor. Structure 2015; 23:1293-304. [PMID: 26027732 DOI: 10.1016/j.str.2015.03.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/15/2022]
Abstract
Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed essential functions of hydrophobic aromatic side chains in the context of well-known nucleic acid motifs. Here we report a 2.45-Å resolution crystal structure of a SOMAmer complexed with nerve growth factor that lacks any known nucleic acid motifs, instead adopting a configuration akin to a triangular prism. The SOMAmer utilizes extensive hydrophobic stacking interactions, non-canonical base pairing and irregular purine glycosidic bond angles to adopt a completely non-helical, compact S-shaped structure. Aromatic side chains contribute to folding by creating an unprecedented intercalating zipper-like motif and a prominent hydrophobic core. The structure provides compelling rationale for potent inhibitory activity of the SOMAmer and adds entirely novel motifs to the repertoire of structural elements uniquely available to SOMAmers.
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Affiliation(s)
- Thale C Jarvis
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Douglas R Davies
- Beryllium, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA
| | - Akihiko Hisaminato
- Otsuka Pharmaceutical Co., Ltd., Institute of Biomedical Innovation, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | | | - Shashi Gupta
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Sheela M Waugh
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Akira Nagabukuro
- Otsuka Pharmaceutical Co., Ltd., Institute of Biomedical Innovation, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Takashi Wadatsu
- Otsuka Pharmaceutical Co., Ltd., Institute of Biomedical Innovation, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Haretsugu Hishigaki
- Otsuka Pharmaceutical Co., Ltd., Institute of Biomedical Innovation, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Bharat Gawande
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Chi Zhang
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Steven K Wolk
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | | | - Yuichiro Nakaishi
- Otsuka Pharmaceutical Co., Ltd., Medicinal Chemistry Research Institute, 463-10 Kagasuno, Kawauchi-cho, Tokushima 771-0192, Japan
| | - Alex B Burgin
- The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Lance J Stewart
- The Institute for Protein Design, University of Washington, 3946 West Stevens Way Northeast, Seattle, WA 98195-1655, USA
| | - Thomas E Edwards
- Beryllium, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | | | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.
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5
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Cho B. SELEX with Affinity Chromatography on RNA-RNA Interaction. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2015. [DOI: 10.5012/jkcs.2015.59.1.93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc Natl Acad Sci U S A 2014; 111:E663-71. [PMID: 24469808 DOI: 10.1073/pnas.1400126111] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the 5' UTR of genes involved in the biosynthesis and transport of preQ1, a precursor of the modified base queuosine universally found in four tRNAs. The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translational level. We present the solution NMR structure and conformational dynamics of the 59 nucleotide Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1. Unlike in the preQ1 class I (preQ1-I) riboswitch, divalent cations are required for high-affinity binding. The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, which forms a three-way junction with the other two stems. (13)C relaxation and residual dipolar coupling experiments revealed interhelical flexibility of P4. We found that the P4 helix and flanking adenine residues play crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shine-Dalgarno sequence. Aided by divalent cations, P4 is poised to act as a "screw cap" on preQ1 recognition to block ligand exit and stabilize the binding pocket. Comparison of preQ1-I and preQ1-II riboswitch structures reveals that whereas both form H-type pseudoknots and recognize preQ1 using one A, C, or U nucleotide from each of three loops, these nucleotides interact with preQ1 differently, with preQ1 inserting into different grooves. Our studies show that the preQ1-II riboswitch uses an unusual mechanism to harness exquisite control over queuosine metabolism.
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7
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Choi SY, Cho B. Identification of a Conserved Sequence Motif of an RNA Aptamer Binding to a G-rich Sequence RNA with Structural Probes. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.11.3471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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9
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Thiel WH, Bair T, Peek AS, Liu X, Dassie J, Stockdale KR, Behlke MA, Miller FJ, Giangrande PH. Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS One 2012; 7:e43836. [PMID: 22962591 PMCID: PMC3433472 DOI: 10.1371/journal.pone.0043836] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/30/2012] [Indexed: 01/05/2023] Open
Abstract
Background The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers. Methodology/Principal Findings We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs. Conclusions and Significance We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies.
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Affiliation(s)
- William H. Thiel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Thomas Bair
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Andrew S. Peek
- Roche Molecular Systems, San Francisco, California, United States of America
| | - Xiuying Liu
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Justin Dassie
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Katie R. Stockdale
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Mark A. Behlke
- Integrated DNA Technologies, Coralville, Iowa, United States of America
| | - Francis J. Miller
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Radiation Oncology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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10
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Cho BR. Identification of Structural Motif of RNAs Interacting with the G-rich Sequence RNA. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.8.2796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Identification of Structural Motifs of RNA Aptamers Interacting with the Stem-loop Sequence at the Gag-pol Junction of HIV-1 RNA. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.11.2227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Wochner A, Menger M, Rimmele M. Characterisation of aptamers for therapeutic studies. Expert Opin Drug Discov 2007; 2:1205-24. [DOI: 10.1517/17460441.2.9.1205] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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13
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Abstract
The SELEX technique (systematic evolution of ligands by exponential enrichment) provides a powerful tool for the in vitro selection of nucleic acid ligands (aptamers) from combinatorial oligonucleotide libraries against a target molecule. In the beginning of the technique's use, RNA molecules were identified that bind to proteins that naturally interact with nucleic acids or to small organic molecules. In the following years, the use of the SELEX technique was extended to isolate oligonucleotide ligands (aptamers) for a wide range of proteins of importance for therapy and diagnostics, such as growth factors and cell surface antigens. These oligonucleotides bind their targets with similar affinities and specificities as antibodies do. The in vitro selection of oligonucleotides with enzymatic activity, denominated aptazymes, allows the direct transduction of molecular recognition to catalysis. Recently, the use of in vitro selection methods to isolate protein inhibitors has been extended to complex targets, such as membrane-bound receptors, and even entire cells. RNA aptamers have also been expressed in living cells. These aptamers, also called intramers, can be used to dissect intracellular signal transduction pathways. The utility of RNA aptamers for in vivo experiments, as well as for diagnostic and therapeutic purposes, is considerably enhanced by chemical modifications, such as substitutions of the 2'-OH groups of the ribose backbone in order to provide resistance against enzymatic degradation in biological fluids. In an alternative approach, Spiegelmers are identified through in vitro selection of an unmodified D-RNA molecule against a mirror-image (i.e. a D-peptide) of a selection target, followed by synthesis of the unnatural nuclease-resistant L-configuration of the RNA aptamer that recognizes the natural configuration of its selection target (i.e. a L-peptide). Recently, nuclease-resistant inhibitory RNA aptamers have been developed against a great variety of targets implicated in disease. Some results have already been obtained in animal models and in clinical trials.
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Affiliation(s)
- H Ulrich
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Caixa Postal 26077, São Paulo 05513-970, Brazil.
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14
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Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 2002; 30:e108. [PMID: 12384610 PMCID: PMC137152 DOI: 10.1093/nar/gnf107] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must still individually purify protein targets. Therefore, we have attempted to select aptamers against protein targets generated by in vitro transcription and translation of individual genes. In order to specifically immobilize the protein targets for selection, they are also biotinylated in vitro. As a proof of this method, we have selected aptamers against translated human U1A, a component of the nuclear spliceosome. Selected sequences demonstrated exquisite mimicry of natural binding sequences and structures. These results not only reveal a potential path to the high throughput generation of aptamers, but also yield insights into the incredible specificity of the U1A protein for its natural RNA ligands.
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Affiliation(s)
- J Colin Cox
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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15
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Affiliation(s)
- K A Marshall
- Institute for Molecular and Cellular Biology, University of Texas, Austin 78712, USA
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16
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Kanamori H, Dodson RE, Shapiro DJ. In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein. Mol Cell Biol 1998; 18:3991-4003. [PMID: 9632784 PMCID: PMC108984 DOI: 10.1128/mcb.18.7.3991] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/1998] [Accepted: 04/07/1998] [Indexed: 02/07/2023] Open
Abstract
The function(s) and RNA binding properties of vigilin, a ubiquitous protein with 14 KH domains, remain largely obscure. We recently showed that vigilin is the estrogen-inducible protein in polysome extracts which binds specifically to a segment of the 3' untranslated region (UTR) of estrogen-stabilized vitellogenin mRNA. In order to identify consensus mRNA sequences and structures important in binding of vigilin to RNA, before vigilin was purified, we developed a modified in vitro genetic selection protocol. We subsequently validated our selection procedure, which employed crude polysome extracts, by testing natural and in vitro-selected RNAs with purified recombinant vigilin. Most of the selected up-binding mutants exhibited hypermutation of G residues leading to a largely unstructured, single-stranded region containing multiple conserved (A)nCU and UC(A)n motifs. All eight of the selected down-binding mutants contained a mutation in the sequence (A)nCU. Deletion analysis indicated that approximately 75 nucleotides are required for maximal binding. Using this information, we predicted and subsequently identified a strong vigilin binding site near the 3' end of human dystrophin mRNA. RNA sequences from the 3' UTRs of transferrin receptor and estrogen receptor, which lack strong homology to the selected sequences, did not bind vigilin. These studies describe an aproach to identifying long RNA binding sites and describe sequence and structural requirements for interaction of vigilin with RNAs.
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Affiliation(s)
- H Kanamori
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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17
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Vant-Hull B, Payano-Baez A, Davis RH, Gold L. The mathematics of SELEX against complex targets. J Mol Biol 1998; 278:579-97. [PMID: 9600840 DOI: 10.1006/jmbi.1998.1727] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a computer model for the simulation of simultaneous SELEX against multiple targets. The model assumes equilibrium behavior for the formation of binary ligand:target complexes, and that there is no ligand:ligand or target:target interaction. Target concentrations, ligand concentrations, and affinity distributions of the initial ligand pool for each individual target may be set by the user. We have used this program to gain an understanding of how the presence of multiple targets affects the selection process. In most cases, we find that SELEX is capable of generating different ligands for the different targets in a heterogeneous mixture, regardless of large variations in target concentrations and ligand:target affinities. A low relative partitioning efficiency (the efficiency with which ligands complexed with a target are separated from free ligands) for a target in a mixture gives a greatly reduced rate of selection of high-affinity ligands to that target. The ratio of each high-affinity ligand to its individual target within a pool of ligands selected for binding against a mixture of targets is approximately proportional to the concentration of the target multiplied by the ligand:target partitioning efficiency.
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Affiliation(s)
- B Vant-Hull
- Department of Molecular Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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18
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Kujau MJ, Siebert A, Wölfl S. Design of leader sequences that improve the efficiency of the enzymatic synthesis of 2'-amino-pyrimidine RNA for in vitro selection. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1997; 35:141-51. [PMID: 9470093 DOI: 10.1016/s0165-022x(97)00039-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The application of nucleic acids obtained by in vitro selection from a large pool of molecules with random sequences in medical diagnosis or therapy requires nucleic acids with enhanced stability in biological fluids. Chemical modifications introduced after selection are likely to alter the structure and the properties of the selected molecules. Therefore, the chemical modifications used must be present throughout the selection. This can be achieved for example by the incorporation of 2'-amino-pyrimidine nucleotides into RNA in the transcription step. Though modified molecules could be transcribed from some generally designed dsDNA templates, the efficiency of transcription and reverse transcription and reverse transcription was very low making this strategy too inefficient. Templates and primers with varying amounts of pyrimidines in the constant flanking region of the RNA molecule were designed and their efficiency in transcription and reverse transcription tested. The obtained 2'-amino-pyrimidine RNA molecules showed enhanced stability in serum and RNAse cocktails. Here we present optimized leader sequences flanking the random core-sequence and reaction conditions that allow the reliable utilization of this modification in in vitro selection.
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Affiliation(s)
- M J Kujau
- Hans-Knöll-Institut für Naturstoff-Forschung, Abt. Zell- und Molekularbiologie, Jena, Germany
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19
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Patel DJ, Suri AK, Jiang F, Jiang L, Fan P, Kumar RA, Nonin S. Structure, recognition and adaptive binding in RNA aptamer complexes. J Mol Biol 1997; 272:645-64. [PMID: 9368648 DOI: 10.1006/jmbi.1997.1281] [Citation(s) in RCA: 205] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.
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Affiliation(s)
- D J Patel
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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20
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Affiliation(s)
- Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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21
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22
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Cantor CR, Sano T, Broude NE, Smith CL. Instrumentation in molecular biomedical diagnostics: an overview. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1997; 14:31-6. [PMID: 9349936 DOI: 10.1016/s1050-3862(97)00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- C R Cantor
- Center for Advanced Biotechnology, Boston University, MA 02215, USA.
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23
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Brown D, Brown J, Kang C, Gold L, Allen P. Single-stranded RNA recognition by the bacteriophage T4 translational repressor, regA. J Biol Chem 1997; 272:14969-74. [PMID: 9169470 DOI: 10.1074/jbc.272.23.14969] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The T4 protein, RegA, is a translational repressor that blocks ribosome binding to multiple T4 messages by interacting with the mRNAs near their respective AUG start codons. Other than the AUG, there are no obvious similarities between the affected mRNAs. High affinity RNA ligands to RegA were isolated using SELEX (systematic evolution of ligands by exponential enrichment). The selected RNAs exhibited the consensus sequence 5'-AAAAUUGUUAUGUAA-3'. The AUG was invariant, suggesting that it is the primary effector of binding specificity. The UU immediately 5' to the AUG and the upstream poly(A) tract were highly conserved among the selected RNAs. Boundary and footprinting experiments are consistent with the consensus sequence defining the RegA-binding site. Interestingly, chemical modification and nuclease digestion data indicate that the RNA-binding site is single-stranded, as if RegA discriminates between targets based on their primary sequence, not their secondary structure. Minor variations from the consensus at positions other than the universally conserved AUG have little effect on RegA binding, but accumulation of mutations has a profound effect on the interaction. Comparison of the in vivo targets for RegA to the SELEX-generated consensus suggests a repression pattern whereby the translation of individual messages is sequentially halted until the least similarly affected message, the regA gene itself, is repressed.
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Affiliation(s)
- D Brown
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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24
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Abstract
Historically, the pharmaceutical industry has focused on proteins, rather than nucleic acids, as drug targets. But recent advances in the fields of RNA synthesis, structure determination and therapeutic target identification make the systematic exploitation of RNA as a drug target a realistic goal.
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Affiliation(s)
- N D Pearson
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, New Frontiers Science Park (North), Third Avenue, Harlow, Essex, CM19 5AW, UK.
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25
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Osborne SE, Ellington AD. Nucleic Acid Selection and the Challenge of Combinatorial Chemistry. Chem Rev 1997; 97:349-370. [PMID: 11848874 DOI: 10.1021/cr960009c] [Citation(s) in RCA: 425] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Scott E. Osborne
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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26
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Vlassov VV, Vlassova IE, Pautova LV. Oligonucleotides and polynucleotides as biologically active compounds. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 57:95-143. [PMID: 9175432 DOI: 10.1016/s0079-6603(08)60279-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- V V Vlassov
- Institute of Bioorganic Chemistry, Novosibirsk, Russia
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27
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Pagratis NC, Bell C, Chang YF, Jennings S, Fitzwater T, Jellinek D, Dang C. Potent 2'-amino-, and 2'-fluoro-2'-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor. Nat Biotechnol 1997; 15:68-73. [PMID: 9035109 DOI: 10.1038/nbt0197-68] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Reiterative in vitro selection-amplification from random oligonucleotide libraries allows the identification of molecules with specific functions such as binding to specific proteins. The therapeutic usefulness of such molecules depends on their high affinity and nuclease resistance. Libraries of RNA molecules containing 2'amino-(2'NH2)- or 2'fluoro-(2'F)-2'-deoxypyrimidines could yield ligands with similar nuclease resistance but not necessarily with similar affinities. This is because the intramolecular helices containing 2'NH2 have lower melting temperatures (Tm) compared with helices containing 2'F, giving them thermodynamically less stable structures and possibly weaker affinities. We tested these ideas by isolating high-affinity ligands to human keratinocyte growth factor from libraries containing modified RNA molecules with either 2'NH2 or 2'F pyrimidines. We demonstrated that 2'F RNA ligands have affinities (Kd approximately 0.3-3 pM) and bioactivities (Ki approximately 34 pM) superior to 2'NH2 ligands (Kd approximately 400 pM and Ki approximately 10 nM). In addition, 2'F ligands have extreme thermo-stabilities (Tm approximately 78 degrees C in low salt, and specificities).
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Affiliation(s)
- N C Pagratis
- NeXstar Pharmaceuticals, Inc., Boulder, CO 80301, USA
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28
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Abstract
Two classes of RNA ligands that bound to separate, high affinity nucleic acid binding sites on Q beta replicase were previously identified. RNA ligands to the two sites, referred to as site I and site II, were used to investigate the molecular mechanism of RNA replication employed by the four-subunit replicase. Replication inhibition by site I- and site II-specific ligands defined two subsets of replicatable RNAs. When provided with appropriate 3' ends, ligands to either site served as replication templates. UV crosslinking experiments revealed that site I is associated with the S1 subunit, site II with elongation factor Tu, and polymerization with the viral subunit of the holoenzyme. These results provide the framework for a three site model describing template recognition and product strand initiation by Q beta replicase.
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Affiliation(s)
- D Brown
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309, USA
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29
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Abstract
In vitro selection experiments are now routinely used to identify functional nucleic acid residues and structures, and have become a tool for studying molecular recognition, molecular biology, and molecular evolution. Technical innovations that have been made during the past year include the use of modified monomers to increase stability and photocross-linking reagents to improve affinity. These advances should dramatically increase the utility of aptamers in the future.
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Affiliation(s)
- K W Uphoff
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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