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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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2
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Jin B, Guo Z, Chen Z, Chen H, Li S, Deng Y, Jin L, Liu Y, Zhang Y, He N. Aptamers in cancer therapy: problems and new breakthroughs. J Mater Chem B 2023; 11:1609-1627. [PMID: 36744587 DOI: 10.1039/d2tb02579e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aptamers, a class of oligonucleotides that can bind with molecular targets with high affinity and specificity, have been widely applied in research fields including biosensing, imaging, diagnosing, and therapy of diseases. However, compared with the rapid development in the research fields, the clinical application of aptamers is progressing at a much slower speed, especially in the therapy of cancer. Obstructions including nuclease degradation, renal clearance, a complex selection process, and potential side effects have inhibited the clinical transformation of aptamer-conjugated drugs. To overcome these problems, taking certain measures to improve the biocompatibility and stability of aptamer-conjugated drugs in vivo is necessary. In this review, the obstructions mentioned above are thoroughly discussed and the methods to overcome these problems are introduced in detail. Furthermore, landmark research works and the most recent studies on aptamer-conjugated drugs for cancer therapy are also listed as examples, and the future directions of research for aptamer clinical transformation are discussed.
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Affiliation(s)
- Baijiang Jin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhukang Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Lian Jin
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yuan Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yuanying Zhang
- Department of Molecular Biology, Jiangsu Cancer Hospital, Nanjing 210009, P. R. China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. .,Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
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3
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Abstract
Aptamers are oligonucleotide receptors with great potential for sensing and therapeutic applications. They are isolated from random libraries through an in vitro method termed systematic evolution of ligands by exponential enrichment (SELEX). Although SELEX-based methods have been widely employed over several decades, many aspects of the experimental process remain poorly understood in terms of how to adjust the selection conditions to obtain aptamers with the desired set of binding characteristics. As a result, SELEX is often performed with arbitrary parameters that tend to produce aptamers with insufficient affinity and/or specificity. Having a better understanding of these basic principles could increase the likelihood of obtaining high-quality aptamers. Here, we have systematically investigated how altering the selection stringency in terms of target concentration─which is essentially the root source of selection pressure for aptamer isolation─affects the outcome of SELEX. By performing four separate trials of SELEX for the same small-molecule target, we experimentally prove that the use of excessively high target concentrations promotes enrichment of low-affinity binders while also suppressing the enrichment of high-affinity aptamers. These findings should be broadly applicable across SELEX methods, given that they share the same core operating principle, and will be crucial for guiding selections to obtain high-quality aptamers in the future.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina27695, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina27695, United States
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4
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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5
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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6
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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7
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Zhu C, Li L, Yang G, Qu F. Investigating the Influences of Random-Region Length on Aptamer Selection Efficiency Based on Capillary Electrophoresis-SELEX and High-Throughput Sequencing. Anal Chem 2021; 93:17030-17035. [PMID: 34908408 DOI: 10.1021/acs.analchem.1c03661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For aptamer selection, the random-region length of an ssDNA library was generally taken in a relatively arbitrary fashion, which may lead to failure for unsuitable target binding. Herein, we coupled high-efficiency capillary electrophoresis (CE)-SELEX and high-throughput sequencing (HTS) to investigate the influences of random-region length. First, one round of selection against programmed cell death-ligand 1 (PD-L1) was performed using ssDNA libraries with random-region lengths of 15, 30, 40, and 60 nt, respectively. A good correlation was observed between candidates' random-region lengths and dissociation constant (Kd), in which the longer sequences presented higher affinity, and the picked Seq 60-1 after one round notably presented a similar affinity toward a reported aptamer through eight rounds. Molecular dynamics (MD) simulation suggested, for PD-L1, the long sequence could supply more noncovalent bonds including hydrogen bonds, electrostatic interactions, and hydrophobic interactions to form a stable protein/aptamer complex. Besides, four other proteins with selective binding performances validated the importance of random-region length. To further investigate how random-region length affects the selection efficiency, a mixed library with random-region lengths ranging from 10 to 50 nt was employed for six rounds of selection against Piezo2. Sequence variations were tracked by HTS, showing the preferential evolution and PCR uncertainty with even higher impact were the main causes. This study suggested random-region length plays a crucial factor, and a mixed library with different random-region sequences can be a worthy choice for increasing the speed of high-affinity aptamer selection. Moreover, the PCR process should be given particular attention in aptamer selection.
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Affiliation(s)
- Chao Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China.,Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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8
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Schmidt M, Hamacher K, Reinhardt F, Lotz TS, Groher F, Suess B, Jager S. SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:2189-2195. [PMID: 31295116 DOI: 10.1109/tcbb.2019.2926711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
RNA aptamer selection during SELEX experiments builds on secondary structural diversity. Advanced structural comparison methods can focus this diversity. We develop SICOR, which uses probabilistic subgraph isomorphisms for graph distances between RNA secondary structure graphs. SICOR outperforms other comparison methods and is applicable to many structural comparisons in experimental design.
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9
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Chizzolini F, Passalacqua LFM, Oumais M, Dingilian AI, Szostak JW, Lupták A. Large Phenotypic Enhancement of Structured Random RNA Pools. J Am Chem Soc 2020; 142:1941-1951. [PMID: 31887027 DOI: 10.1021/jacs.9b11396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Laboratory evolution of functional RNAs has applications in many areas of chemical and synthetic biology. In vitro selections critically depend on the presence of functional molecules, such as aptamers and ribozymes, in the starting sequence pools. For selection of novel functions the pools are typically transcribed from random-sequence DNA templates, yielding a highly diverse set of RNAs that contain a multitude of folds and biochemical activities. The phenotypic potential, the frequency of functional RNAs, is very low, requiring large complexity of starting pools, surpassing 1015 different sequences, to identify highly active isolates. Furthermore, the majority of random sequences is not structured and has a high propensity for aggregation; the in vitro selection process thus involves not just enrichment of functional RNAs, but also their purification from aggregation-prone "free-riders". We reasoned that purification of the nonaggregating, monomeric subpopulation of a random-sequence RNA pool will yield pools of folded, functional RNAs. We performed six rounds of selection for monomeric sequences and show that the enriched population is compactly folded. In vitro selections originating from various mixtures of the compact pool and a fully random pool showed that sequences from the compact pool always dominate the population once a biochemical activity is detectable. A head-to-head competition of the two pools starting from a low (5 × 1012) sequence diversity revealed that the phenotypic potential of the compact pool is about 1000-times higher than the fully random pool. A selection for folded and monomeric RNA pools thus greatly increases the frequency of functional RNAs from that seen in random-sequence pools, providing a facile experimental approach to isolation of highly active functional RNAs from low-diversity populations.
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Affiliation(s)
- Fabio Chizzolini
- Department of Pharmaceutical Sciences , University of California at Irvine , Irvine , California 92697 , United States
| | - Luiz F M Passalacqua
- Department of Pharmaceutical Sciences , University of California at Irvine , Irvine , California 92697 , United States
| | - Mona Oumais
- Department of Chemistry , University of California at Irvine , Irvine , California 92697 , United States
| | - Armine I Dingilian
- Department of Pharmaceutical Sciences , University of California at Irvine , Irvine , California 92697 , United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States.,Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Andrej Lupták
- Department of Pharmaceutical Sciences , University of California at Irvine , Irvine , California 92697 , United States.,Department of Chemistry , University of California at Irvine , Irvine , California 92697 , United States.,Department of Molecular Biology and Biochemistry , University of California at Irvine , Irvine , California 92697 , United States
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10
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Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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11
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McConnell EM, Ventura K, Dwyer Z, Hunt V, Koudrina A, Holahan MR, DeRosa MC. In Vivo Use of a Multi-DNA Aptamer-Based Payload/Targeting System To Study Dopamine Dysregulation in the Central Nervous System. ACS Chem Neurosci 2019; 10:371-383. [PMID: 30160936 DOI: 10.1021/acschemneuro.8b00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The delivery of therapeutics across the blood-brain barrier remains a considerable challenge in investigating central nervous system related processes. In this work, a liposome vehicle was surface-modified with an aptamer that binds to the transferrin receptor and was loaded with two different dopamine-binding aptamer payloads. This system was effectively used to promote the delivery of the aptamer cargo from the peripheral injection site into the brain. The effect of these delivered aptamers on behavior was investigated in vivo in a locomotor task. The first dopamine binding aptamer assessed was a DNA aptamer, the binding of which had been previously validated through the aptamer-based biosensor development reported by several independent research groups. The second aptamer investigated was the result of a novel in vitro selection experiment described herein. Our data suggest that systemic administration of the modified liposomes led to delivery of the dopamine aptamers into the brain. Fluorescence microscopy revealed differential distribution of fluorescence based on the presence or absence of the transferrin receptor aptamer on the surface of fluorescently modified liposomes. In a behavioral experiment using cocaine administration to induce elevated concentrations of neural dopamine, systemic pretreatment with the dopamine aptamer-loaded liposomes reduced cocaine-induced hyperlocomotion. Multiple controls including a transferrin-negative liposome control and transferrin-positive liposomes loaded with either a nonbinding, base-substituted dopamine aptamer or a random oligonucleotide were investigated. None of these controls altered cocaine-induced hyperlocomotion. Chronic systemic administration of the modified liposomes produced no deleterious neurobehavioral or neural degenerative effects. Importantly, this work is one example of an application for this versatile multiaptamer payload/targeting system. Its general application is limited only by the availability of aptamers for specific neural targets.
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Affiliation(s)
- Erin M. McConnell
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Katelyn Ventura
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Zach Dwyer
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Vernon Hunt
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Anna Koudrina
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Matthew R. Holahan
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maria C. DeRosa
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
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12
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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Mutschler H, Taylor AI, Porebski BT, Lightowlers A, Houlihan G, Abramov M, Herdewijn P, Holliger P. Random-sequence genetic oligomer pools display an innate potential for ligation and recombination. eLife 2018; 7:43022. [PMID: 30461419 PMCID: PMC6289569 DOI: 10.7554/elife.43022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
Recombination, the exchange of information between different genetic polymer strands, is of fundamental importance in biology for genome maintenance and genetic diversification and is mediated by dedicated recombinase enzymes. Here, we describe an innate capacity for non-enzymatic recombination (and ligation) in random-sequence genetic oligomer pools. Specifically, we examine random and semi-random eicosamer (N20) pools of RNA, DNA and the unnatural genetic polymers ANA (arabino-), HNA (hexitol-) and AtNA (altritol-nucleic acids). While DNA, ANA and HNA pools proved inert, RNA (and to a lesser extent AtNA) pools displayed diverse modes of spontaneous intermolecular recombination, connecting recombination mechanistically to the vicinal ring cis-diol configuration shared by RNA and AtNA. Thus, the chemical constitution that renders both susceptible to hydrolysis emerges as the fundamental determinant of an innate capacity for recombination, which is shown to promote a concomitant increase in compositional, informational and structural pool complexity and hence evolutionary potential.
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Affiliation(s)
| | | | | | | | | | - Mikhail Abramov
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Herdewijn
- REGA Institute, Katholieke Universiteit Leuven, Leuven, Belgium
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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15
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Philippou S, Mastroyiannopoulos NP, Makrides N, Lederer CW, Kleanthous M, Phylactou LA. Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. Mol Ther Nucleic Acids 2018; 10:199-214. [PMID: 29499933 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
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Abstract
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist. Unlike the protein-based trans-regulating controllers, riboswitches can respond to their ligands faster and eliminate off-target effects. Here, we developed artificial riboswitches that activate gene expression in response to naringenin, an important flavonoid. RNA aptamers for naringenin were developed using SELEX and cloned upstream of a dual selectable marker gene to construct a riboswitch library. Two in vivo selection routes were applied separately to the library by supplementing naringenin at two different concentrations during enrichments to modulate the operational ranges of the riboswitches. The selected riboswitches were responsive to naringenin and activated gene expression up to 2.91-fold. Operational ranges of the riboswitches were distinguished on the basis of their selection route. Additionally, the specificity of the riboswitches was assessed, and their applicability as dynamic regulators was confirmed. Collectively, the naringenin riboswitches reported in this work will be valuable tools in metabolic engineering of microorganisms for the production of flavonoids.
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Affiliation(s)
- Sungho Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungyeon Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Yu Xiu
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing 100191, China
| | - Taek Jin Kang
- Department
of Chemical and Biochemical Engineering, Dongguk University, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 04620, Korea
| | - Sang-Hyeup Lee
- Department
of Life Chemistry, Catholic University of Daegu, Hayang-ro 13-13,
Hayang-eup, Gyeongsan, Gyeongbuk 38430, Korea
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institutee, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School
of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
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17
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Abstract
A significant part of the genetic code likely originated via a chemical interaction, which should be experimentally verifiable. One possible verification relates bound amino acids (or perhaps their activated congeners) and ribonucleotide sequences within cognate RNA binding sites. To introduce this interaction, I first summarize how amino acids function as targets for RNA binding. Then the experimental method for selecting relevant RNA binding sites is characterized. The selection method’s characteristics are related to the investigation of the RNA binding site model treated at the outset. Finally, real binding sites from selection and also from extant natural RNAs (for example, the Sulfobacillus guanidinium riboswitch) are connected to the genetic code, and by extension, to the evolutionary progression that produced the code. During this process, peptides may have been produced directly on an instructive amino acid binding RNA (a DRT; Direct RNA Template). Combination of observed stereochemical selectivity with adaptation and co-evolutionary refinement is logically required, and also potentially sufficient, to create the striking order conserved throughout the present coding table.
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Affiliation(s)
- Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA.
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18
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Heiat M, Najafi A, Ranjbar R, Latifi AM, Rasaee MJ. Computational approach to analyze isolated ssDNA aptamers against angiotensin II. J Biotechnol 2016; 230:34-9. [PMID: 27188956 DOI: 10.1016/j.jbiotec.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022]
Abstract
Aptamers are oligonucleotides with highly structured molecules that can bind to their targets through specific 3-D conformation. Commonly, not all the nucleotides such as primer binding fixed region and some other sequences are vital for aptamers folding and interaction. Elimination of unnecessary regions needs trustworthy prediction tools to reduce experimental efforts and errors. Here we introduced a manipulated in-silico approach to predict the 3-D structure of aptamers and their target interactions. To design an approach for computational analysis of isolated ssDNA aptamers (FLC112, FLC125 and their truncated core region including CRC112 and CRC125), their secondary and tertiary structures were modeled by Mfold and RNA composer respectively. Output PDB files were modified from RNA to DNA in the discovery studio visualizer software. Using ZDOCK server, the aptamer-target interactions were predicted. Finally, the interaction scores were compared with the experimental results. In-silico interaction scores and the experimental outcomes were in the same descending arrangement of FLC112>CRC125>CRC112>FLC125 with similar intensity. The consistent results of innovative in-silico method with experimental outputs, affirmed that the present method may be a reliable approach. Also, it showed that the exact in-silico predictions can be utilized as a credible reference to find aptameric fragments binding potency.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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19
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Abstract
T4 polynucleotide kinase is widely used for 5'-phosphorylation of DNA and RNA oligonucleotide termini, but no natural protein enzyme is capable of 3'-phosphorylation. Here, we report the in vitro selection of deoxyribozymes (DNA enzymes) capable of DNA oligonucleotide 3'-phosphorylation, using a 5'-triphosphorylated RNA transcript (pppRNA) as the phosphoryl donor. The basis of selection was the capture, during each selection round, of the 3'-phosphorylated DNA substrate terminus by 2-methylimidazole activation of the 3'-phosphate (forming 3'-MeImp) and subsequent splint ligation with a 5'-amino DNA oligonucleotide. Competing and precedented DNA-catalyzed reactions were DNA phosphodiester hydrolysis or deglycosylation, each also leading to a 3'-phosphate but at a different nucleotide position within the DNA substrate. One oligonucleotide 3'-kinase deoxyribozyme, obtained from an N40 random pool and named 3'Kin1, can 3'-phosphorylate nearly any DNA oligonucleotide substrate for which the 3'-terminus has the sequence motif 5'-NKR-3', where N denotes any oligonucleotide sequence, K = T or G, and R = A or G. These results establish the viabilty of in vitro selection for identifying DNA enzymes that 3'-phosphorylate DNA oligonucleotides.
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Affiliation(s)
- Alison J Camden
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Shannon M Walsh
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sarah H Suk
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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20
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Pobanz K, Lupták A. Improving the odds: Influence of starting pools on in vitro selection outcomes. Methods 2016; 106:14-20. [PMID: 27109058 DOI: 10.1016/j.ymeth.2016.04.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 04/16/2016] [Accepted: 04/18/2016] [Indexed: 12/28/2022] Open
Abstract
As with any outcome of an evolutionary process, the success of in vitro selection experiments depends critically on the starting population. In vitro selections isolate functional nucleic acids that fold into specific structures and form unique binding and catalytic sites. The selection outcomes therefore depend on the molecular and structural diversity of the initial pools. In addition, the experiments are strongly influenced by the length of the starting pool. Longer randomized regions support the formation of more complex structures and presumably allow formation of more intricate tertiary interactions, but they also tend to misfold and aggregate, whereas shorter pools are sufficient to yield simpler motifs. Furthermore, introducing a sequence bias that promotes secondary structure formation appears to prejudice the population towards more functional macromolecules. We review the literature on the influence of the starting pools on the predicted and actual outcomes of laboratory evolution experiments.
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Affiliation(s)
- Kelsey Pobanz
- Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Andrej Lupták
- Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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21
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Ruff P, Storici F. Genome Editing by Aptamer-Guided Gene Targeting (AGT). Advances in Experimental Medicine and Biology 2016. [DOI: 10.1007/978-1-4939-3509-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC. Analysis of In Vitro Aptamer Selection Parameters. J Mol Evol 2015; 81:150-61. [PMID: 26530075 DOI: 10.1007/s00239-015-9708-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success.
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Affiliation(s)
- Maureen McKeague
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Erin M McConnell
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Jose Cruz-Toledo
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Elyse D Bernard
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Amanda Pach
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Emily Mastronardi
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Xueru Zhang
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Michael Beking
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Tariq Francis
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Amanda Giamberardino
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ashley Cabecinha
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Annamaria Ruscito
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Rocio Aranda-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Michel Dumontier
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. .,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
| | - Maria C DeRosa
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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23
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Abstract
Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the "systematic evolution of ligands by exponential enrichment" (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.
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Affiliation(s)
- A Ganji
- a Student Research Committee , Mashhad University of Medical Sciences , Mashhad , Iran .,b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
| | - A Varasteh
- c Allergy Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran
| | - M Sankian
- b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
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24
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Abstract
![]()
Affinity
reagent pairs that recognize distinct epitopes on a target
protein can greatly improve the sensitivity and specificity of molecular
detection. Importantly, such pairs can be conjugated to generate reagents
that achieve two-site “bidentate” target recognition,
with affinities greatly exceeding either monovalent component. DNA
aptamers are especially well-suited for such constructs, because they
can be linked via standard synthesis techniques without requiring
chemical conjugation. Unfortunately, aptamer pairs are difficult to
generate, primarily because conventional selection methods preferentially
yield aptamers that recognize a dominant “hot spot”
epitope. Our array-based discovery platform for multivalent aptamers
(AD-MAP) overcomes this problem to achieve efficient discovery of
aptamer pairs. We use microfluidic selection and high-throughput sequencing
to obtain an enriched pool of aptamer sequences. Next, we synthesize
a custom array based on these sequences, and perform parallel affinity
measurements to identify the highest-affinity aptamer for the target
protein. We use this aptamer to form complexes that block the primary
binding site on the target, and then screen the same array with these
complexes to identify aptamers that bind secondary epitopes. We used
AD-MAP to discover DNA aptamer pairs that bind distinct sites on human
angiopoietin-2 with high affinities, even in undiluted serum. To the
best of our knowledge, this is the first work to discover new aptamer
pairs using arrays. We subsequently conjugated these aptamers with
a flexible linker to construct ultra-high-affinity bidentate reagents,
with equilibrium dissociation constants as low as 97 pM: >200-fold
better than either component aptamer. Functional studies confirm that
both aptamers critically contribute to this ultrahigh affinity, highlighting
the promise of such reagents for research and clinical use.
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Affiliation(s)
- Minseon Cho
- Department of Mechanical Engineering, University of California-Santa Barbara , Santa Barbara, California 93106, United States
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25
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Ouellet E, Lagally ET, Cheung KC, Haynes CA. A simple method for eliminating fixed-region interference of aptamer binding during SELEX. Biotechnol Bioeng 2014; 111:2265-79. [PMID: 24895227 DOI: 10.1002/bit.25294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 01/20/2023]
Abstract
Standard libraries for systematic evolution of ligands by exponential enrichment (SELEX) typically utilize flanking regions that facilitate amplification of aptamers recovered from each selection round. Here, we show that these flanking sequences can bias the selection process, due in part to their ability to interfere with the fold or function of aptamers localized within the random region of the library sequence. We then address this problem by investigating the use of complementary oligonucleotides as a means to block aptamer interference by each flanking region. Isothermal titration calorimetry (ITC) studies are combined with fold predictions to both define the various interference mechanisms and assess the ability of added complementary oligonucleotides to ameliorate them. The proposed blocking strategy is thereby refined and then applied to standard library forms of benchmark aptamers against human α-thrombin, streptavidin, and vascular endothelial growth factor (VEGF). In each case, ITC data show that the new method effectively removes fixed-region mediated interference effects so that the natural binding affinity of the benchmark aptamer is completely restored. We further show that the binding affinities of properly functioning aptamers within a selection library are not affected by the blocking protocol, and that the method can be applied to various common library formats comprised of different flanking region sequences. Finally, we present a rapid and inexpensive qPCR-based method for determining the mean binding affinity of retained aptamer pools and use it to show that introduction of the pre-blocking method into the standard SELEX protocol results in retention of high-affinity aptamers that would otherwise be lost during the first round of selection. Significant enrichment of the available pool of high-affinity aptamers is thereby achieved in the first few rounds of selection. By eliminating single-strand (aptamer-like) structures within or involving the fixed regions, the technique is therefore shown to isolate aptamer sequence and function within the desired random region of the library members, and thereby provide a new selection method that is complementary to other available SELEX protocols.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3; Biomedical Engineering Program, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
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26
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Abstract
Gene targeting is a genetic technique to modify an endogenous DNA sequence in its genomic location via homologous recombination (HR) and is useful both for functional analysis and gene therapy applications. HR is inefficient in most organisms and cell types, including mammalian cells, often limiting the effectiveness of gene targeting. Therefore, increasing HR efficiency remains a major challenge to DNA editing. Here, we present a new concept for gene correction based on the development of DNA aptamers capable of binding to a site-specific DNA binding protein to facilitate the exchange of homologous genetic information between a donor molecule and the desired target locus (aptamer-guided gene targeting). We selected DNA aptamers to the I-SceI endonuclease. Bifunctional oligonucleotides containing an I-SceI aptamer sequence were designed as part of a longer single-stranded DNA molecule that contained a region with homology to repair an I-SceI generated double-strand break and correct a disrupted gene. The I-SceI aptamer-containing oligonucleotides stimulated gene targeting up to 32-fold in yeast Saccharomyces cerevisiae and up to 16-fold in human cells. This work provides a novel concept and research direction to increase gene targeting efficiency and lays the groundwork for future studies using aptamers for gene targeting.
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Affiliation(s)
- Patrick Ruff
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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27
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Cho M, Soo Oh S, Nie J, Stewart R, Eisenstein M, Chambers J, Marth JD, Walker F, Thomson JA, Soh HT. Quantitative selection and parallel characterization of aptamers. Proc Natl Acad Sci U S A 2013; 110:18460-5. [PMID: 24167271 DOI: 10.1073/pnas.1315866110] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aptamers are promising affinity reagents that are potentially well suited for high-throughput discovery, as they are chemically synthesized and discovered via completely in vitro selection processes. Recent advancements in selection, sequencing, and the use of modified bases have improved aptamer quality, but the overall process of aptamer generation remains laborious and low-throughput. This is because binding characterization remains a critical bottleneck, wherein the affinity and specificity of each candidate aptamer are measured individually in a serial manner. To accelerate aptamer discovery, we devised the Quantitative Parallel Aptamer Selection System (QPASS), which integrates microfluidic selection and next-generation sequencing with in situ-synthesized aptamer arrays, enabling simultaneous measurement of affinity and specificity for thousands of candidate aptamers in parallel. After using QPASS to select aptamers for the human cancer biomarker angiopoietin-2 (Ang2), we in situ synthesized arrays of the selected sequences and obtained equilibrium dissociation constants (Kd) for every aptamer in parallel. We thereby identified over a dozen high-affinity Ang2 aptamers, with Kd as low as 20.5 ± 7.3 nM. The same arrays enabled us to quantify binding specificity for these aptamers in parallel by comparing relative binding of differentially labeled target and nontarget proteins, and by measuring their binding affinity directly in complex samples such as undiluted serum. Finally, we show that QPASS offers a compelling avenue for exploring structure-function relationships for large numbers of aptamers in parallel by coupling array-based affinity measurements with next-generation sequencing data to identify nucleotides and motifs within the aptamer that critically affect Ang2 binding.
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28
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Jiménez JI, Xulvi-Brunet R, Campbell GW, Turk-MacLeod R, Chen IA. Comprehensive experimental fitness landscape and evolutionary network for small RNA. Proc Natl Acad Sci U S A 2013; 110:14984-9. [PMID: 23980164 DOI: 10.1073/pnas.1307604110] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural selection for the first functional sequences. Fitness landscapes are the subject of much speculation, but their structure is essentially unknown. Here we describe a comprehensive map of a fitness landscape, exploring nearly all of sequence space, for short RNAs surviving selection in vitro. With the exception of a small evolutionary network, we find that fitness peaks are largely isolated from one another, highlighting the importance of historical contingency and indicating that natural selection would be constrained to local exploration in the RNA world.
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29
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Reba A, Meyer AG, Barrick JE. Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection. Artif Life 13 (2012) 2013; 13:473-480. [PMID: 36129423 PMCID: PMC9484335 DOI: 10.7551/978-0-262-31050-5-ch062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The dual information-function nature of nucleic acids has been exploited in the laboratory to isolate novel receptors and catalysts from random DNA and RNA sequences by cycles of in vitro selection and amplification. This strategy is particularly effective because, unlike polypeptides with random amino acid sequences, nucleic acids with random base sequences are often capable of stably folding into defined three-dimensional structures. However, the pervasive base-pairing potential of nucleic acids is also known to lead to kinetic traps in their folding landscapes. That is, the same DNA or RNA sequence can often adopt alternative base-paired structures that are local energy minima, and these folds may interconvert very slowly. We have used simulations with nucleic acid folding algorithms to evaluate the effect of misfolding on in vitro selection experiments. We demonstrate that kinetic traps can prevent the recovery of novel families of complex functional motifs by two mechanisms. First, misfolding can lead to the stochastic loss of unique sequences in the first round of selection. Second, frequent misfolding can reduce the average activity of multiple copies of a sequence to such an extent that it will be outcompeted after multiple rounds of selection. In these simulations, adding thermal cycling to sample multiple folds of one sequence during a selection for a self-modifying catalytic activity can improve the recovery of rare examples of more complex structures. Although newly isolated sequences may fold poorly, they can represent footholds in sequence space that can be improved to reliably fold after a few mutations. Thus, it is plausible that thermal cycling by day-night cycles or other mechanisms on the primordial earth may have been important for the evolution of the first RNA catalysts, and a fold sampling strategy might be used to search for more effective nucleic acid catalysts in the laboratory today.
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Affiliation(s)
- Aaron Reba
- Department of Chemistry and Biochemistry, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin
| | - Austin G Meyer
- Department of Chemistry and Biochemistry, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin
| | - Jeffrey E Barrick
- Department of Chemistry and Biochemistry, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin
- Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin
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30
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Velez TE, Singh J, Xiao Y, Allen EC, Wong OY, Chandra M, Kwon SC, Silverman SK. Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length. ACS Comb Sci 2012; 14:680-7. [PMID: 23088677 DOI: 10.1021/co300111f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Functional nucleic acids are DNA and RNA aptamers that bind targets, or they are deoxyribozymes and ribozymes that have catalytic activity. These functional DNA and RNA sequences can be identified from random-sequence pools by in vitro selection, which requires choosing the length of the random region. Shorter random regions allow more complete coverage of sequence space but may not permit the structural complexity necessary for binding or catalysis. In contrast, longer random regions are sampled incompletely but may allow adoption of more complicated structures that enable function. In this study, we systematically examined random region length (N(20) through N(60)) for two particular deoxyribozyme catalytic activities, DNA cleavage and tyrosine-RNA nucleopeptide linkage formation. For both activities, we previously identified deoxyribozymes using only N(40) regions. In the case of DNA cleavage, here we found that shorter N(20) and N(30) regions allowed robust catalytic function, either by DNA hydrolysis or by DNA deglycosylation and strand scission via β-elimination, whereas longer N(50) and N(60) regions did not lead to catalytically active DNA sequences. Follow-up selections with N(20), N(30), and N(40) regions revealed an interesting interplay of metal ion cofactors and random region length. Separately, for Tyr-RNA linkage formation, N(30) and N(60) regions provided catalytically active sequences, whereas N(20) was unsuccessful, and the N(40) deoxyribozymes were functionally superior (in terms of rate and yield) to N(30) and N(60). Collectively, the results indicate that with future in vitro selection experiments for DNA and RNA catalysts, and by extension for aptamers, random region length should be an important experimental variable.
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Affiliation(s)
- Tania E. Velez
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Jaydeep Singh
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Ying Xiao
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Emily C. Allen
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - On Yi Wong
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Madhavaiah Chandra
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Sarah C. Kwon
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Scott K. Silverman
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
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31
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Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nucleic Acids Res 2012; 40:4711-22. [PMID: 22319215 PMCID: PMC3378899 DOI: 10.1093/nar/gks065] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.
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Affiliation(s)
- Julien Derr
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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32
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Abstract
Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can be limiting for certain applications, like the screening of on-bead libraries. Here, we report a method to amplify and sequence on-bead RNA libraries that requires not more than five known nucleotides. A key element is the attachment of the starting nucleoside to the synthesis resin via the nucleobase, which leaves the 3′-OH group accessible to subsequent enzymatic manipulations. After split-and-mix synthesis of the oligonucleotide library and deprotection, a poly(A)-tail can be efficiently added to this free 3′-hydroxyl terminus by Escherichia coli poly(A) polymerase that serves as an anchored primer binding site for reverse transcription. The cDNA is joined to a DNA adapter by T4 DNA ligase. PCR amplification yielded single-band products that could be cloned and sequenced starting from individual polystyrene beads. The method described here makes the selection of functional RNAs from on-bead RNA libraries more attractive due to increased flexibility in library design, higher yields of full-length sequence on bead and robust sequence determination.
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Affiliation(s)
- Anna Wiesmayr
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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33
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Illangasekare M, Turk R, Peterson GC, Lladser M, Yarus M. Chiral histidine selection by D-ribose RNA. RNA 2010; 16:2370-2383. [PMID: 20940341 PMCID: PMC2995399 DOI: 10.1261/rna.2385310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/27/2010] [Indexed: 05/30/2023]
Abstract
The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L- and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four- to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.
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Affiliation(s)
- Mali Illangasekare
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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34
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Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R. Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. RNA 2010; 16:1915-24. [PMID: 20699302 PMCID: PMC2941100 DOI: 10.1261/rna.2220210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/22/2010] [Indexed: 05/20/2023]
Abstract
Conservation is often used to define essential sequences within RNA sites. However, conservation finds only invariant sequence elements that are necessary for function, rather than finding a set of sequence elements sufficient for function. Biochemical studies in several systems-including the hammerhead ribozyme and the purine riboswitch-find additional elements, such as loop-loop interactions, required for function yet not phylogenetically conserved. Here we define a critical test of sufficiency: We embed a minimal, apparently sufficient motif for binding the amino acid tryptophan in a random-sequence background and ask whether we obtain functional molecules. After a negative result, we use a combination of three-dimensional structural modeling, selection, designed mutations, high-throughput sequencing, and bioinformatics to explore functional insufficiency. This reveals an essential unpaired G in a diverse structural context, varied sequence, and flexible distance from the invariant internal loop binding site identified previously. Addition of the new element yields a sufficient binding site by the insertion criterion, binding tryptophan in 22 out of 23 tries. Random insertion testing for site sufficiency seems likely to be broadly revealing.
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Affiliation(s)
- Irene Majerfeld
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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35
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Abstract
The in vitro selection of nucleic acid libraries has driven the discovery of RNA and DNA receptors (aptamers) and catalysts with tailor-made functional properties. Functional nucleic acids emerging from selections have been observed to possess an unusually high degree of secondary structure. In this study, we experimentally examined the relationship between the degree of secondary structure in a nucleic acid library and its ability to yield aptamers that bind protein targets. We designed a patterned nucleic acid library (denoted R*Y*) to enhance the formation of stem-loop structures without imposing any specific sequence or secondary structural requirement. This patterned library was predicted computationally to contain a significantly higher average folding energy compared to a standard, unpatterned N(60) library of the same length. We performed three different iterated selections for protein binding using patterned and unpatterned libraries competing in the same solution. In all three cases, the patterned R*Y* library was enriched relative to the unpatterned library over the course of the 9- to 10-round selection. Characterization of individual aptamer clones emerging from the three selections revealed that the highest affinity aptamer assayed arose from the patterned library for two protein targets, while in the third case, the highest affinity aptamers from the patterned and random libraries exhibited comparable affinity. We identified the binding motif requirements for the most active aptamers generated against two of the targets. The two binding motifs are 3.4- and 27-fold more likely to occur in the R*Y* library than in the N(60) library. Collectively, our findings suggest that researchers performing selections for nucleic acid aptamers and catalysts should consider patterned libraries rather than commonly used N(m) libraries to increase both the likelihood of isolating functional molecules and the potential activities of the resulting molecules.
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Affiliation(s)
- Karen M Ruff
- Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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36
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Abstract
Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.
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Affiliation(s)
- Namhee Kim
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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37
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Carothers JM, Goler JA, Kapoor Y, Lara L, Keasling JD. Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity. Nucleic Acids Res 2010; 38:2736-47. [PMID: 20159999 PMCID: PMC2860116 DOI: 10.1093/nar/gkq082] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ability to generate RNA aptamers for synthetic biology using in vitro selection depends on the informational complexity (IC) needed to specify functional structures that bind target ligands with desired affinities in physiological concentrations of magnesium. We investigate how selection for high-affinity aptamers is constrained by chemical properties of the ligand and the need to bind in low magnesium. We select two sets of RNA aptamers that bind planar ligands with dissociation constants (Kds) ranging from 65 nM to 100 μM in physiological buffer conditions. Aptamers selected to bind the non-proteinogenic amino acid, p-amino phenylalanine (pAF), are larger and more informationally complex (i.e., rarer in a pool of random sequences) than aptamers selected to bind a larger fluorescent dye, tetramethylrhodamine (TMR). Interestingly, tighter binding aptamers show less dependence on magnesium than weaker-binding aptamers. Thus, selection for high-affinity binding may automatically lead to structures that are functional in physiological conditions (1–2.5 mM Mg2+). We hypothesize that selection for high-affinity binding in physiological conditions is primarily constrained by ligand characteristics such as molecular weight (MW) and the number of rotatable bonds. We suggest that it may be possible to estimate aptamer–ligand affinities and predict whether a particular aptamer-based design goal is achievable before performing the selection.
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Affiliation(s)
- James M Carothers
- California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, CA 94720, USA
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38
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Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection. ACTA ACUST UNITED AC 2009; Chapter 9:Unit 9.2. [DOI: 10.1002/0471142700.nc0902s39] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas Austin Texas
| | | | - Pooja Satya
- Freshman Research Initiative, University of Texas Austin Texas
| | - Krystal Ogle
- Freshman Research Initiative, University of Texas Austin Texas
| | - Jack Pollard
- 3rd Millennium Corporation Cambridge Massachusetts
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39
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Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, synthesis, and amplification of DNA pools for in vitro selection. ACTA ACUST UNITED AC 2009; Chapter 24:Unit 24.2. [PMID: 19816932 DOI: 10.1002/0471142727.mb2402s88] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Preparation of a random-sequence DNA pool is presented. The degree of randomization and the length of the random sequence are discussed, as is synthesis of the pool using a DNA synthesizer or via commercial synthesis companies. Purification of a single-stranded pool and conversion to a double-stranded pool are presented as step-by-step protocols. Support protocols describe determination of the complexity and skewing of the pool, and optimization of amplification conditions.
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Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
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40
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Yarus M, Widmann JJ, Knight R. RNA-amino acid binding: a stereochemical era for the genetic code. J Mol Evol 2009; 69:406-29. [PMID: 19795157 DOI: 10.1007/s00239-009-9270-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 07/28/2009] [Indexed: 12/19/2022]
Abstract
By combining crystallographic and NMR structural data for RNA-bound amino acids within riboswitches, aptamers, and RNPs, chemical principles governing specific RNA interaction with amino acids can be deduced. Such principles, which we summarize in a "polar profile", are useful in explaining newly selected specific RNA binding sites for free amino acids bearing varied side chains charged, neutral polar, aliphatic, and aromatic. Such amino acid sites can be queried for parallels to the genetic code. Using recent sequences for 337 independent binding sites directed to 8 amino acids and containing 18,551 nucleotides in all, we show a highly robust connection between amino acids and cognate coding triplets within their RNA binding sites. The apparent probability (P) that cognate triplets around these sites are unrelated to binding sites is congruent with 5.3 x 10(-45) for codons overall, and P congruent with 2.1 x 10(-46) for cognate anticodons. Therefore, some triplets are unequivocally localized near their present amino acids. Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites. Use of cognate coding triplets in RNA binding sites is nevertheless sparse, with only 21% of possible triplets appearing. Reasoning from such broad recurrent trends in our results, a majority (approximately 75%) of modern amino acids entered the code in this stereochemical era; nevertheless, a minority (approximately 21%) of modern codons and anticodons were assigned via RNA binding sites. A Direct RNA Template scheme embodying a credible early history for coded peptide synthesis is readily constructed based on these observations.
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41
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Schlosser K, Lam JCF, Li Y. A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype. Nucleic Acids Res 2009; 37:3545-57. [PMID: 19357090 PMCID: PMC2699508 DOI: 10.1093/nar/gkp222] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with selection of the target phenotype. The model population is composed of 857 DNAzyme clones representing 215 discrete sequence classes, which had previously been identified from two parallel selection experiments, conducted under an increasingly stringent, or permissive and constant selection time pressure. In this report, we determined the principal phenotypic properties (i.e. kobs, maximum cleavage yield and PCR efficiency) from a sample of 58 clones representing 46 different major and minor sequence classes from various rounds of each selection experiment. Interestingly, a positive correlation between the catalytic rate constant and the corresponding frequency and temporal position of a given DNAzyme was not consistently observed; however, the strength of the correlation was qualitatively higher under conditions of more stringent selection time pressure. These results suggest that the selective sampling paradigm on which in vitro selection is based, may underestimate the true functional capacity of any given random-sequence library.
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Affiliation(s)
- Kenny Schlosser
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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42
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Cowperthwaite MC, Ellington AD. Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J Mol Evol 2008; 67:95-102. [PMID: 18594898 DOI: 10.1007/s00239-008-9130-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 05/12/2008] [Accepted: 05/15/2008] [Indexed: 02/07/2023]
Abstract
Aptamers are nucleic acid molecules selected in vitro to bind a particular ligand. While numerous experimental studies have examined the sequences, structures, and functions of individual aptamers, considerably fewer studies have applied bioinformatics approaches to try to infer more general principles from these individual studies. We have used a large Aptamer Database to parse the contributions of both random and constant regions to the secondary structures of more than 2000 aptamers. We find that the constant, primer-binding regions do not, in general, contribute significantly to aptamer structures. These results suggest that (a) binding function is not contributed to nor constrained by constant regions; (b) in consequence, the landscape of functional binding sequences is sparse but robust, favoring scenarios for short, functional nucleic acid sequences near origins; and (c) many pool designs for the selection of aptamers are likely to prove robust.
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Affiliation(s)
- Matthew C Cowperthwaite
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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43
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Abstract
Aptamers are synthetic single-stranded RNA or DNA molecules capable of specific binding to other target molecules. In this review, the main aptamer properties are considered and methods for selection of aptamers against various protein targets are described. Special attention is given to the methods for directed selection of aptamers, which allow one to obtain ligands with specified properties.
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Affiliation(s)
- A V Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, pl. Kurchatova 2, 123182 Moscow, Russia.
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44
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Schlosser K, Gu J, Sule L, Li Y. Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res 2008; 36:1472-81. [PMID: 18203744 PMCID: PMC2275145 DOI: 10.1093/nar/gkm1175] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many sequence variations of the 8–17 RNA-cleaving deoxyribozyme have been isolated through in vitro selection. In an effort to understand how these sequence variations affect cleavage site selectivity, we systematically mutated the catalytic core of 8–17 and measured the cleavage activity of each mutant deoxyribozyme against all 16 possible chimeric (RNA/DNA) dinucleotide junctions. We observed sequence-function relationships that suggest how the following non-conserved positions in the catalytic core influence selectivity at the dinucleotide (5′ rN18-N1.1 3′) cleavage site: (i) positions 2.1 and 12 represent a primary determinant of the selectivity at the 3′ position (N1.1) of the cleavage site; (ii) positions 15 and 15.0 represent a primary determinant of the selectivity at the 5′ position (rN18) of the cleavage site and (iii) the sequence of the 3-bp intramolecular stem has relatively little influence on cleavage site selectivity. Furthermore, we report for the first time that 8–17 variants have the collective ability to cleave all dinucleotide junctions with rate enhancements of at least 1000-fold over background. Three optimal 8–17 variants, identified from ∼75 different sequences that were examined, can collectively cleave 10 of 16 junctions with useful rates of ≥0.1 min−1, and exhibit an overall hierarchy of reactivity towards groups of related junctions according to the order NG > NA > NC > NT.
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Affiliation(s)
- Kenny Schlosser
- Department of Biochemistry and Biomedical Sciences and Department of Chemistry, McMaster University, Hamilton, Ontario, Canada
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45
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Abstract
Although in vitro selection technology is a versatile experimental tool for discovering novel synthetic RNA molecules, finding complex RNA molecules is difficult because most RNAs identified from random sequence pools are simple motifs, consistent with recent computational analysis of such sequence pools. Thus, enriching in vitro selection pools with complex structures could increase the probability of discovering novel RNAs. Here we develop an approach for engineering sequence pools that links RNA sequence space regions with corresponding structural distributions via a "mixing matrix" approach combined with a graph theory analysis. We define five classes of mixing matrices motivated by covariance mutations in RNA; these constructs define nucleotide transition rates and are applied to chosen starting sequences to yield specific nonrandom pools. We examine the coverage of sequence space as a function of the mixing matrix and starting sequence via clustering analysis. We show that, in contrast to random sequences, which are associated only with a local region of sequence space, our designed pools, including a structured pool for GTP aptamers, can target specific motifs. It follows that experimental synthesis of designed pools can benefit from using optimized starting sequences, mixing matrices, and pool fractions associated with each of our constructed pools as a guide. Automation of our approach could provide practical tools for pool design applications for in vitro selection of RNAs and related problems.
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Affiliation(s)
- Namhee Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
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46
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Leontis NB, Lescoute A, Westhof E. The building blocks and motifs of RNA architecture. Curr Opin Struct Biol 2006; 16:279-87. [PMID: 16713707 PMCID: PMC4857889 DOI: 10.1016/j.sbi.2006.05.009] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 04/12/2006] [Accepted: 05/10/2006] [Indexed: 10/24/2022]
Abstract
RNA motifs can be defined broadly as recurrent structural elements containing multiple intramolecular RNA-RNA interactions, as observed in atomic-resolution RNA structures. They constitute the modular building blocks of RNA architecture, which is organized hierarchically. Recent work has focused on analyzing RNA backbone conformations to identify, define and search for new instances of recurrent motifs in X-ray structures. One current view asserts that recurrent RNA strand segments with characteristic backbone configurations qualify as independent motifs. Other considerations indicate that, to characterize modular motifs, one must take into account the larger structural context of such strand segments. This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences.
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Affiliation(s)
- Neocles B Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
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47
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Schlosser K, Lam JC, Li Y. Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: the effect of excess sequence elements on the outcome of in vitro selection. Nucleic Acids Res 2006; 34:2445-54. [PMID: 16682452 PMCID: PMC1458524 DOI: 10.1093/nar/gkl276] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We previously conducted an in vitro selection experiment for RNA-cleaving deoxyribozymes, using a combinatorial DNA library containing 80 random nucleotides. Ultimately, 110 different sequence classes were isolated, but the vast majority contained a short14-15 nt catalytic DNA motif commonly known as 8-17. Herein, we report extensive truncation experiments conducted on multiple sequence classes to confirm the suspected catalytic role played by 8-17 and to determine the effect of excess sequence elements on the activity of this motif and the outcome of selection. Although we observed beneficial, detrimental and neutral consequences for activity, the magnitude of the effect rarely exceeded 2-fold. These deoxyribozymes appear to have survived increasing selection pressure despite the presence of additional sequence elements, rather than because of them. A new deoxyribozyme with comparable activity, called G15-30, was approximately 2.5-fold larger and experienced a approximately 4-fold greater inhibitory effect from excess sequence elements than the average 8-17 motif. Our results suggest that 8-17 may be less susceptible to the potential inhibitory effects of excess arbitrary sequence than larger motifs, which represents a previously unappreciated selective advantage that may contribute to its widespread recurrence.
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Affiliation(s)
| | | | - Yingfu Li
- To whom correspondence should be addressed. Tel: 1 905 5259140; Fax: 1 905 522 9033;
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