1
|
Park JW, Tian Y, Kim ST, Park C, Kim YM, Chung HK, Kim KM, Jahng GH. Oligomeric amyloid-β targeted contrast agent for MRI evaluation of Alzheimer's disease mouse models. Front Pharmacol 2024; 15:1392729. [PMID: 38895620 PMCID: PMC11184063 DOI: 10.3389/fphar.2024.1392729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
Background Oligomeric amyloid beta (oAβ) is a toxic factor that acts in the early stage of Alzheimer's disease (AD) and may initiate the pathologic cascade. Therefore, detecting oAβ has a crucial role in the early diagnosis, monitoring, and treatment of AD. Purpose The purpose of this study was to evaluate MRI signal changes in different mouse models and the time-dependent signal changes using our novel gadolinium (Gd)-dodecane tetraacetic acid (DOTA)- ob5 aptamer contrast agent. Methods We developed an MRI contrast agent by conjugating Gd-DOTA-DNA aptamer called ob5 to evaluate its ability to detect oAβ deposits in the brain using MRI. A total of 10 control mice, 9 3xTg AD mice, and 11 APP/PS/Tau AD mice were included in this study, with the age of each model being 16 or 36 weeks. A T1-weighted image was acquired at the time points before (0 min) and after injection of the contrast agent at 5, 10, 15, 20, and 25 min. The analyses were performed to compare MRI signal differences among the three groups and the time-dependent signal differences in different mouse models. Results Both 3xTg AD and APP/PS/Tau AD mouse models had higher signal enhancement than control mice at all scan-time points after injection of our contrast media, especially in bilateral hippocampal areas. In particular, all Tg AD mouse models aged 16 weeks showed a higher contrast enhancement than those aged 36 weeks. For 3xTg AD and APP/PS/Tau AD groups, the signal enhancement was significantly different among the five time points (0 min, 5 min, 10 min, 15 min, 20 min, and 25 min) in multiple ROI areas, typically in the bilateral hippocampus, left thalamus, and left amygdala. Conclusion The findings of this study suggest that the expression of the contrast agent in different AD models demonstrates its translational flexibility across different species. The signal enhancement peaked around 15-20 min after injection of the contrast agent. Therefore, our novel contrast agent targeting oAβ has the potential ability to diagnose early AD and monitor the progression of AD.
Collapse
Affiliation(s)
- Jang Woo Park
- Korea Radioisotope Center for Pharmaceuticals, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Yunan Tian
- Department of Medicine, Graduate School, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Sang-Tae Kim
- J&Pharma, Neuroscience Research Institute, Healthcare Innovation Park, Seongnam City, Republic of Korea
| | - Chanwoo Park
- Korea Radioisotope Center for Pharmaceuticals, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Yu Mi Kim
- J&Pharma, Neuroscience Research Institute, Healthcare Innovation Park, Seongnam City, Republic of Korea
| | - Hye Kyung Chung
- Korea Radioisotope Center for Pharmaceuticals, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Kyeong Min Kim
- Korea Radioisotope Center for Pharmaceuticals, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
- Research Institute of Radiological and Medical Sciences, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
- Radiological and Medico Oncological Sciences, University of Science and Technology (UST), Seoul, Republic of Korea
| | - Geon-Ho Jahng
- Department of Radiology, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| |
Collapse
|
2
|
Kim ST, Kim HG, Kim YM, Han HS, Cho JH, Lim SC, Lee T, Jahng GH. An aptamer-based magnetic resonance imaging contrast agent for detecting oligomeric amyloid-β in the brain of an Alzheimer's disease mouse model. NMR IN BIOMEDICINE 2023; 36:e4862. [PMID: 36308279 DOI: 10.1002/nbm.4862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
The oligomeric amyloid-β (oAβ) is a reliable feature for an early diagnosis of Alzheimer's disease (AD). Therefore, the objective of this study was to demonstrate imaging of oAβ deposits using our developed DNA aptamer called ob5 conjugated with gadolinium (Gd)-dodecane tetraacetic acid (DOTA) as a contrast agent for early diagnosis of AD using MRI. An oAβ-specific aptamer was developed by amide bond formation and conjugated to Gd-DOTA MRI contrast agent and/or cyanine5 (cy5). We verified the performance of our new contrast agent with an AD mouse model using in vivo and ex vivo fluorescent imaging and animal MRI experiments. The presence of soluble Aβ in 3xTg AD mice was detected using GdDOTA-ob5-cy5 probe ex vivo. Fluorescence intensities of the GdDOTA-ob5-cy5 contrast agent were high in the brains of 3xTg-AD mice, but relatively low in the brains of control mice. The GdDOTA-ob5 contrast agent had higher relaxivity than a clinically available contrast agent. T1-weighted MRI signals in 5-month-old 3xTg AD mice increased at 5 min, were prolonged until 10 min, then decreased 15 min after injecting the GdDOTA-ob5 contrast agent. Our targeted DNA aptamer GdDOTA-ob5 contrast agent could be potentially useful for validating the efficacy of a novel diagnostic contrast agent for selectively targeting neurotoxic oAβ. It could ultimately be used for early diagnosis of AD.
Collapse
Affiliation(s)
- Sang-Tae Kim
- Neuroscience of Lab., Biomedical Research Institute, Seoul National University College of Medicine, Seongnam City, Geonggido, Republic of Korea
| | - Hyug-Gi Kim
- Department of Radiology, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Yu Mi Kim
- Neuroscience of Lab., Biomedical Research Institute, Seoul National University College of Medicine, Seongnam City, Geonggido, Republic of Korea
| | - Ho-Seong Han
- Department of Surgery, Bundang Hospital of Seoul National University, Seongnam City, Kyunggeedo, Republic of Korea
| | - Jee-Hyun Cho
- Research Equipment Operations Division, Korea Basic Science Institute, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, Chosun University Medical School, Gwangju, Republic of Korea
- Department of Education & Research, Chosun University Hospital, Gwangju, Republic of Korea
| | - Taekwan Lee
- Brain Research Core Facility, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Geon-Ho Jahng
- Department of Radiology, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
- Department of Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| |
Collapse
|
3
|
Spirov AV, Myasnikova EM. Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution. PLoS One 2022; 17:e0260497. [PMID: 35085255 PMCID: PMC8794168 DOI: 10.1371/journal.pone.0260497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special problems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland's Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromolecules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland's theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of experimental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evolution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a significant increase in the efficiency of evolutionary search.
Collapse
Affiliation(s)
- Alexander V. Spirov
- I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia
- The Institute of Scientific Information for Social Sciences RAS, Moscow, Russia
| | | |
Collapse
|
4
|
Jiang H, Gao Y, Zhang L, Chen D, Gan J, Murchie AIH. The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences. Nat Catal 2021. [DOI: 10.1038/s41929-021-00685-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
5
|
Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
Collapse
Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| |
Collapse
|
6
|
Flemmich L, Heel S, Moreno S, Breuker K, Micura R. A natural riboswitch scaffold with self-methylation activity. Nat Commun 2021; 12:3877. [PMID: 34162884 PMCID: PMC8222354 DOI: 10.1038/s41467-021-24193-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Methylation is a prevalent post-transcriptional modification encountered in coding and non-coding RNA. For RNA methylation, cells use methyltransferases and small organic substances as methyl-group donors, such as S-adenosylmethionine (SAM). SAM and other nucleotide-derived cofactors are viewed as evolutionary leftovers from an RNA world, in which riboswitches have regulated, and ribozymes have catalyzed essential metabolic reactions. Here, we disclose the thus far unrecognized direct link between a present-day riboswitch and its inherent reactivity for site-specific methylation. The key is O6-methyl pre-queuosine (m6preQ1), a potentially prebiotic nucleobase which is recognized by the native aptamer of a preQ1 class I riboswitch. Upon binding, the transfer of the ligand’s methyl group to a specific cytidine occurs, installing 3-methylcytidine (m3C) in the RNA pocket under release of pre-queuosine (preQ1). Our finding suggests that nucleic acid-mediated methylation is an ancient mechanism that has offered an early path for RNA epigenetics prior to the evolution of protein methyltransferases. Furthermore, our findings may pave the way for the development of riboswitch-descending methylation tools based on rational design as a powerful alternative to in vitro selection approaches. In humans, protein methyltransferase is responsible for RNA methylation using S-adenosylmethionine as a methyl group donor. Here the authors report a self-methylation activity of a bacterial riboswitch.
Collapse
Affiliation(s)
- Laurin Flemmich
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Heel
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Sarah Moreno
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Kathrin Breuker
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria
| | - Ronald Micura
- University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Innrain 80-82, Innsbruck, 6020, Austria.
| |
Collapse
|
7
|
Scheitl CPM, Ghaem Maghami M, Lenz AK, Höbartner C. Site-specific RNA methylation by a methyltransferase ribozyme. Nature 2020; 587:663-667. [PMID: 33116304 PMCID: PMC7116789 DOI: 10.1038/s41586-020-2854-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022]
Abstract
Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification, including RNA methylation. Methylated nucleotides are among the evolutionarily most-conserved features of transfer (t)RNA and ribosomal (r)RNA1,2. Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as a methyl-group donor. SAM and other nucleotide-derived cofactors are considered to be evolutionary leftovers from an RNA world, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication3. Chemically diverse ribozymes seem to have been lost in nature, but may be reconstructed in the laboratory by in vitro selection. Here we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine in a substrate RNA, using O6-methylguanine as a small-molecule cofactor. The ribozyme shows a broad RNA-sequence scope, as exemplified by site-specific adenosine methylation in various RNAs. This finding provides fundamental insights into the catalytic abilities of RNA, serves a synthetic tool to install 1-methyladenosine in RNA and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes.
Collapse
Affiliation(s)
- Carolin P M Scheitl
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Mohammad Ghaem Maghami
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ann-Kathrin Lenz
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Claudia Höbartner
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
| |
Collapse
|
8
|
In Vitro Selection of an ATP-Binding TNA Aptamer. Molecules 2020; 25:molecules25184194. [PMID: 32933142 PMCID: PMC7570665 DOI: 10.3390/molecules25184194] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Recent advances in polymerase engineering have made it possible to isolate aptamers from libraries of synthetic genetic polymers (XNAs) with backbone structures that are distinct from those found in nature. However, nearly all of the XNA aptamers produced thus far have been generated against protein targets, raising significant questions about the ability of XNA aptamers to recognize small molecule targets. Here, we report the evolution of an ATP-binding aptamer composed entirely of α-L-threose nucleic acid (TNA). A chemically synthesized version of the best aptamer sequence shows high affinity to ATP and strong specificity against other naturally occurring ribonucleotide triphosphates. Unlike its DNA and RNA counterparts that are susceptible to nuclease digestion, the ATP-binding TNA aptamer exhibits high biological stability against hydrolytic enzymes that rapidly degrade DNA and RNA. Based on these findings, we suggest that TNA aptamers could find widespread use as molecular recognition elements in diagnostic and therapeutic applications that require high biological stability.
Collapse
|
9
|
Sharma S, Zajac M, Krishnan Y. A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition. Chembiochem 2019; 21:157-162. [PMID: 31099939 DOI: 10.1002/cbic.201900259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Indexed: 12/12/2022]
Abstract
As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA-based sensor for cAMP. Herein, we describe a new, 31-base long single-stranded DNA aptamer for cAMP, denoted caDNApt-1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt-1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non-denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt-1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.
Collapse
Affiliation(s)
- Suruchi Sharma
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India
| | - Matthew Zajac
- Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA
| | - Yamuna Krishnan
- Tata Institute of Fundamental Research, GKVK, National Centre for Biological Sciences, Bellary Road, Bengaluru, 560065, India.,Present address: Department of Chemistry, The University of Chicago, GCIS E305A, 929E, 57th Street, ., Chicago, IL, 60637, USA.,Grossman Institute of Neuroscience, Quantitative Biology and, Human Behavior, University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
10
|
Plebanek A, Larnerd C, Popović M, Wei C, Pohorille A, Ditzler MA. Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication. J Mol Evol 2019; 87:240-253. [PMID: 31435687 PMCID: PMC6711949 DOI: 10.1007/s00239-019-09906-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023]
Abstract
The potential for biopolymers to evolve new structures has important consequences for their ability to optimize function and our attempts to reconstruct their evolutionary histories. Prior work with in vitro systems suggests that structural remodeling of RNA is difficult to achieve through the accumulation of point mutations or through recombination events. Sequence duplication may represent an alternative mechanism that can more readily lead to the evolution of new structures. Structural and sequence elements in many RNAs and proteins appear to be the products of duplication events, indicating that this mechanism plays a major role in molecular evolution. Despite the potential significance of this mechanism, little experimental data is available concerning the structural and evolutionary consequences of duplicating biopolymer sequences. To assess the structural consequences of sequence duplication on the evolution of RNA, we mutagenized an RNA sequence containing two copies of an ATP aptamer and subjected the resulting population to multiple in vitro evolution experiments. We identified multiple routes by which duplication, followed by the accumulation of functional point mutations, allowed our populations to sample two entirely different secondary structures. The two structures have no base pairs in common, but both structures contain two copies of the same ATP-binding motif. We do not observe the emergence of any other functional secondary structures beyond these two. Although this result suggests a limited capacity for duplication to support short-term functional innovation, major changes in secondary structure, like the one observed here, should be given careful consideration as they are likely to frustrate attempts to infer deep evolutionary histories of functional RNAs.
Collapse
Affiliation(s)
- Andrew Plebanek
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Caleb Larnerd
- NASA Internship Program, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Milena Popović
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Blue Marble Space Institute of Science, Seattle, WA, 98145, USA
| | - Chenyu Wei
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Andrew Pohorille
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Mark A Ditzler
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA. .,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| |
Collapse
|
11
|
Pereira RL, Nascimento IC, Santos AP, Ogusuku IEY, Lameu C, Mayer G, Ulrich H. Aptamers: novelty tools for cancer biology. Oncotarget 2018; 9:26934-26953. [PMID: 29928493 PMCID: PMC6003562 DOI: 10.18632/oncotarget.25260] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Although the term ‘cancer’ was still over two thousand years away of being coined, the first known cases of the disease date back to about 3000BC, in ancient Egypt. Five thousand years later, still lacking a cure, it has become one of the leading causes of death, killing over half a dozen million people yearly. So far, monoclonal antibodies are the most successful immune-therapy tools when it comes to fighting cancer. The number of clinical trials that use them has been increasing steadily during the past few years, especially since the Food and Drug Administration greenlit the use of the first immune-checkpoint blockade antibodies. However, albeit successful, this approach does come with the cost of auto-inflammatory toxicity. Taking this into account, the development of new therapeutic reagents with low toxicity becomes evident, particularly ones acting in tandem with the tools currently at our disposal. Ever since its discovery in the early nineties, aptamer technology has been used for a wide range of diagnostic and therapeutic applications. With similar properties to those of monoclonal antibodies, such as high-specificity of recognition and high-affinity binding, and the advantages of being developed using in vitro selection procedures, aptamers quickly became convenient building blocks for the generation of multifunctional constructs. In this review, we discuss the steps involved in the in vitro selection process that leads to functional aptamers - known as Systematic Evolution of Ligands by Exponential Enrichment - as well as the most recent applications of this technology in diagnostic and treatment of oncological illnesses. Moreover, we also suggest ways to improve such use.
Collapse
Affiliation(s)
- Ricardo L Pereira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isis C Nascimento
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Ana P Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Isabella E Y Ogusuku
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Claudiana Lameu
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| | - Günter Mayer
- Chemical Biology and Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research and Development (CARD), University of Bonn, 53121, Bonn, Germany
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-900, Brazil
| |
Collapse
|
12
|
Abdelsayed MM, Ho BT, Vu MMK, Polanco J, Spitale RC, Lupták A. Multiplex Aptamer Discovery through Apta-Seq and Its Application to ATP Aptamers Derived from Human-Genomic SELEX. ACS Chem Biol 2017; 12:2149-2156. [PMID: 28661647 DOI: 10.1021/acschembio.7b00001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Laboratory-evolved RNAs bind a wide variety of targets and serve highly diverse functions, including as diagnostic and therapeutic aptamers. The majority of aptamers have been identified using in vitro selection (SELEX), a molecular evolution technique based on selecting target-binding RNAs from highly diverse pools through serial rounds of enrichment and amplification. In vitro selection typically yields multiple distinct motifs of highly variable abundance and target-binding affinities. The discovery of new aptamers is often limited by the difficulty of characterizing the selected motifs, because testing of individual sequences tends to be a tedious process. To facilitate the discovery of new aptamers within in vitro selected pools, we developed Apta-Seq, a multiplex analysis based on quantitative, ligand-dependent 2' acylation of solvent-accessible regions of the selected RNA pools, followed by reverse transcription (SHAPE) and deep sequencing. The method reveals, in a single sequencing experiment, the identity, structural features, and target dissociation constants for aptamers present in the selected pool. Application of Apta-Seq to a human genomic pool enriched for ATP-binding RNAs yielded three new aptamers, which together with previously identified human aptamers suggest that ligand-binding RNAs may be common in mammals.
Collapse
Affiliation(s)
- Michael M. Abdelsayed
- Department
of Molecular Biology and Biochemistry, University of California—Irvine, Irvine, California 92697, United States
| | - Bao T. Ho
- Department
of Pharmaceutical Sciences, University of California—Irvine, Irvine, California 92697, United States
| | - Michael M. K. Vu
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697, United States
| | - Julio Polanco
- Department
of Molecular Biology and Biochemistry, University of California—Irvine, Irvine, California 92697, United States
| | - Robert C. Spitale
- Department
of Pharmaceutical Sciences, University of California—Irvine, Irvine, California 92697, United States
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697, United States
| | - Andrej Lupták
- Department
of Molecular Biology and Biochemistry, University of California—Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of California—Irvine, Irvine, California 92697, United States
- Department
of Chemistry, University of California—Irvine, Irvine, California 92697, United States
| |
Collapse
|
13
|
Poudyal RR, Benslimane M, Lokugamage MP, Callaway MK, Staller S, Burke DH. Selective Inactivation of Functional RNAs by Ribozyme-Catalyzed Covalent Modification. ACS Synth Biol 2017; 6:528-534. [PMID: 28139121 DOI: 10.1021/acssynbio.6b00222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diverse functions of RNA provide numerous opportunities for programming biological circuits. We describe a new strategy that uses ribozyme K28min to covalently tag a specific nucleobase within an RNA or DNA target strand to regulate and selectively inactivate those nucleic acids. K28min variants with appropriately reprogrammed internal guide sequences efficiently tagged multiple sites from an mRNA and from aptamer and ribozyme targets. Upon covalent modification by the corresponding K28min variant, an ATP-binding aptamer lost all affinity for ATP, and the fluorogenic Mango aptamer lost its ability to activate fluorescence of its dye ligand. Modifying a hammerhead ribozyme near the catalytic core led to loss of almost all of its substrate-cleaving activity, but modifying the same hammerhead ribozyme within a tertiary stabilizing element that reduces magnesium dependence only impaired substrate cleavage at low magnesium concentration. Thus, ribozyme-mediated covalent modification can be used both to selectively inactivate and to fine-tune the activities of targeted functional RNAs, analogous to the effects of post-translational modifications of proteins. Ribozyme-catalyzed covalent modification could therefore be developed to regulate nucleic acids components of synthetic and natural circuits.
Collapse
Affiliation(s)
- Raghav R. Poudyal
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Malak Benslimane
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Melissa P. Lokugamage
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Mackenzie K. Callaway
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Seth Staller
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| | - Donald H. Burke
- Department of Biochemistry, ‡Genetics Area Program, §Department of Biological
Engineering, ∥Department of Molecular
Microbiology and Immunology, and ⊥Bond Life Sciences Center, University of Missouri Columbia, Coumbia, Missouri, 65211, United States
| |
Collapse
|
14
|
Rudchenko MN, Zamyatnin AA. Prospects for using self-assembled nucleic acid structures. BIOCHEMISTRY (MOSCOW) 2016; 80:391-9. [PMID: 25869355 DOI: 10.1134/s000629791504001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
According to the central dogma in molecular biology, nucleic acids are assigned with key functions on storing and executing genetic information in any living cell. However, features of nucleic acids are not limited only with properties providing template-dependent biosynthetic processes. Studies of DNA and RNA unveiled unique features of these polymers able to make various self-assembled three-dimensional structures that, among other things, use the complementarity principle. Here, we review various self-assembled nucleic acid structures as well as application of DNA and RNA to develop nanomaterials, molecular automata, and nanodevices. It can be expected that in the near future results of these developments will allow designing novel next-generation diagnostic systems and medicinal drugs.
Collapse
Affiliation(s)
- M N Rudchenko
- Research Division, Hospital for Special Surgery, New York, NY 10021, USA.
| | | |
Collapse
|
15
|
Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet 2015; 16:567-82. [PMID: 26347030 DOI: 10.1038/nrg3937] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.
Collapse
|
16
|
Ho B, Polanco J, Jimenez R, Lupták A. Discovering human RNA aptamers by structure-based bioinformatics and genome-based in vitro selection. Methods Enzymol 2015; 549:29-46. [PMID: 25432743 DOI: 10.1016/b978-0-12-801122-5.00002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In vitro selection and structure-based searches have emerged as useful techniques for the discoveries of structurally complex RNAs with high affinity and specificity toward metabolites. Here, we focus on the design of a human genomic library that serves as the DNA template for in vitro selection of RNA aptamers. In addition, the structural solutions obtained from the in vitro selection can be used for structure-based searches for discovery of analogous aptamers in various genomic databases.
Collapse
Affiliation(s)
- Bao Ho
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA; Department of Chemistry, University of California, Irvine, California, USA
| | - Julio Polanco
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA; Department of Chemistry, University of California, Irvine, California, USA
| | - Randi Jimenez
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA; Department of Chemistry, University of California, Irvine, California, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA; Department of Chemistry, University of California, Irvine, California, USA.
| |
Collapse
|
17
|
Vollmer S, Richert C. Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org Biomol Chem 2015; 13:5734-42. [PMID: 25902412 DOI: 10.1039/c5ob00508f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.
Collapse
Affiliation(s)
- S Vollmer
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | | |
Collapse
|
18
|
Le TT, Chumphukam O, Cass AEG. Determination of minimal sequence for binding of an aptamer. A comparison of truncation and hybridization inhibition methods. RSC Adv 2014. [DOI: 10.1039/c4ra08243e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A thermodynamic analysis of the effects of truncation or competitive hybridisation of an aptamer on target binding is presented.
Collapse
Affiliation(s)
- Thao T. Le
- Department of Chemistry
- Imperial College London
- UK
| | | | | |
Collapse
|
19
|
Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG. RAPID-SELEX for RNA aptamers. PLoS One 2013; 8:e82667. [PMID: 24376564 PMCID: PMC3869713 DOI: 10.1371/journal.pone.0082667] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 01/11/2023] Open
Abstract
Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX approach. High-throughput sequencing of the enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5×1015 sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance.
Collapse
Affiliation(s)
- Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David R Latulippe
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
20
|
Vu MMK, Jameson NE, Masuda SJ, Lin D, Larralde-Ridaura R, Lupták A. Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX. ACTA ACUST UNITED AC 2013; 19:1247-54. [PMID: 23102219 DOI: 10.1016/j.chembiol.2012.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/04/2012] [Accepted: 08/07/2012] [Indexed: 02/07/2023]
Abstract
Aptamers are structured macromolecules in vitro evolved to bind molecular targets, whereas in nature they form the ligand-binding domains of riboswitches. Adenosine aptamers of a single structural family were isolated several times from random pools, but they have not been identified in genomic sequences. We used two unbiased methods, structure-based bioinformatics and human genome-based in vitro selection, to identify aptamers that form the same adenosine-binding structure in a bacterium, and several vertebrates, including humans. Two of the human aptamers map to introns of RAB3C and FGD3 genes. The RAB3C aptamer binds ATP with dissociation constants about 10 times lower than physiological ATP concentration, while the minimal FGD3 aptamer binds ATP only cotranscriptionally.
Collapse
Affiliation(s)
- Michael M K Vu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | | | | | | | | | | |
Collapse
|
21
|
Schill M, Koslowski T. Sensing organic molecules by charge transfer through aptamer-target complexes: theory and simulation. J Phys Chem B 2013; 117:475-83. [PMID: 23227783 DOI: 10.1021/jp308042n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aptamers, i.e., short sequences of RNA and single-stranded DNA, are capable of specificilly binding objects ranging from small molecules over proteins to entire cells. Here, we focus on the structure, stability, dynamics, and electronic properties of oligonucleotides that interact with aromatic or heterocyclic targets. Large-scale molecular dynamics simulations indicate that aromatic rings such as dyes, metabolites, or alkaloides form stable adducts with their oligonucleotide host molecules at least on the simulation time scale. From molecular dynamics snapshots, the energy parameters relevant to Marcus' theory of charge transfer are computed using a modified Su-Schrieffer-Heeger Hamiltonian, permitting an estimate of the charge transfer rates. In many cases, aptamer binding seriously influences the charge transfer kinetics and the charge carrier mobility within the complex, with conductivities up to the nanoampere range for a single complex. We discuss the conductivity properties with reference to potential applications as biosensors.
Collapse
Affiliation(s)
- Maria Schill
- Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104 Freiburg im Breisgau, Germany
| | | |
Collapse
|
22
|
Analysis of protein interactions in situ by proximity ligation assays. Curr Top Microbiol Immunol 2013; 377:111-26. [PMID: 23921974 DOI: 10.1007/82_2013_334] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fate of the cell is governed by interactions among proteins, nucleic acids, and other biomolecules. It is vital to look at these interactions in a cellular environment if we want to increase our understanding of cellular processes. Herein we will describe how the in situ proximity ligation assay (in situ PLA) can be used to visualize protein interactions in fixed cells and tissues. In situ PLA is a novel technique that uses DNA, together with DNA modifying processes such as ligation, cleavage, and polymerization, as tools to create surrogate markers for protein interactions of interest. Different in situ PLA designs make it possible not only to detect protein-protein interactions but also post-translational modifications and interactions of proteins with nucleic acids. Flexibility in DNA probe design and the multitude of different DNA modifying enzymes provide the basis for modifications of the method to make it suitable to use in many applications. Furthermore, examples of how in situ PLA can be combined with other methods for a comprehensive view of the cellular activity status are discussed.
Collapse
|
23
|
Pratico ED, Sullenger BA, Nair SK. Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic Acid Ther 2012; 23:35-43. [PMID: 23113766 DOI: 10.1089/nat.2012.0388] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Induction of an effective immune response that can target and eliminate malignant cells or virus-infected cells requires the stimulation of antigen-specific effector T cells. A productive and long-lasting memory response requires 2 signals: a specific signal provided by antigen recognition through engagement of the T cell receptor and a secondary signal via engagement of costimulatory molecules (such as OX40) on these newly activated T cells. The OX40-OX40-ligand interaction is critical for the generation of productive effector and memory T cell functions. Thus agonistic antibodies that stimulate OX40 on activated T cells have been used as adjuvants to augment immune responses. We previously demonstrated that an aptamer modified to stimulate murine OX40 enhanced vaccine-mediated immune responses in a murine melanoma model. In this study, we describe the development of an agonistic aptamer that targets human OX40 (hOX40). This hOX40 aptamer was isolated using systematic evolution of ligands by exponential enrichment and binds the target purified protein with high affinity [dissociation constants (K(d))<10 nM]. Moreover, the hOX40 aptamer-streptavidin complex has an apparent binding affinity of ~50 nM for hOX40 on activated T cells as determined by flow cytometry and specifically binds activated human T cells. A multivalent version of the aptamer, but not a mutant version of the aptamer, was able to stimulate OX40 on T cells and enhance cell proliferation and interferon-gamma production. Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy.
Collapse
Affiliation(s)
- Elizabeth D Pratico
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA.
| | | | | |
Collapse
|
24
|
Zhu C, Liu J, Ling Y, Yang H, Liu Z, Zheng R, Qin L, Hu Z. Evaluation of the clinical value of ELISA based on MPT64 antibody aptamer for serological diagnosis of pulmonary tuberculosis. BMC Infect Dis 2012; 12:96. [PMID: 22520654 PMCID: PMC3410803 DOI: 10.1186/1471-2334-12-96] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 04/20/2012] [Indexed: 12/16/2022] Open
Abstract
Background Presently, tuberculosis (TB) poses a global threat to human health. The development of reliable laboratory tools is vital to the diagnosis and treatment of TB. MPT64, a protein secreted by Mycobacterium tuberculosis complex, is highly specific for TB, making antibody to MPT64 a reagent specific for the diagnosis of TB. Method Antibody to MPT64 was obtained by a combination of genetic engineering and immunization by the system evolution of ligands by exponential enrichment. A high-affinity aptamer of antibody to MPT64 was selected from a random single-stranded DNA library, and a sandwich ELISA method based on this aptamer was developed. This ELISA method was used to detect TB in 328 serum samples, 160 from patients with pulmonary TB (PTB) and 168 from non-tuberculous controls. Results The minimum limit of detection of the ELISA method was 2.5 mg/L, and its linear range varied from 10 mg/L to 800 mg/L. Its sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and area under the curve, with 95 % confidence intervals, were 64.4 % (56.7 %–71.4 %), 99.4 % (96.7 %–99.9 %), 108.2 (15.3–765.9), 0.350 (0.291–0.442) and 0.819 (0.770–0.868), respectively. No significant difference in sensitivity was observed between sputum smear positive (73/112, 65.2 %) and negative (30/48, 62.5 %) individuals. Conclusions This sandwich ELISA based on an MPT64 antibody aptamer may be useful for the serological diagnosis of PTB, both in sputum smear positive and negative patients.
Collapse
Affiliation(s)
- Changtai Zhu
- Department of Medical Laboratory, Changzhou Tumor Hospital Soochow University, Changzhou 213001, China
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Marimuthu C, Tang TH, Tominaga J, Tan SC, Gopinath SCB. Single-stranded DNA (ssDNA) production in DNA aptamer generation. Analyst 2012; 137:1307-15. [PMID: 22314701 DOI: 10.1039/c2an15905h] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However, the success of the DNA selection process through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments is very much dependent on its most critical step, which is the conversion of the dsDNA to ssDNA. There is a plethora of methods available in generating ssDNA from the corresponding dsDNA. These include asymmetric PCR, biotin-streptavidin separation, lambda exonuclease digestion and size separation on denaturing-urea PAGE. Herein, different methods of ssDNA generation following the PCR amplification step in SELEX are reviewed.
Collapse
Affiliation(s)
- Citartan Marimuthu
- Infectious Disease Cluster, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200, Kepala Batas, Penang, Malaysia
| | | | | | | | | |
Collapse
|
26
|
Abstract
Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities.
Collapse
Affiliation(s)
- Jagat R Kanwar
- Nanomedicine Laboratory of Immunology and Molecular Biomedical Research (LIMBR), Centre for Biotechnology and Interdisciplinary Biosciences (BioDeakin), Institute for Technology and Research Innovation (ITRI), Geelong Technology Precinct (GTP), Deakin University, Victoria, Australia.
| | | | | |
Collapse
|
27
|
Liew FF, Hasegawa T, Fukuda M, Nakata E, Morii T. Construction of dopamine sensors by using fluorescent ribonucleopeptide complexes. Bioorg Med Chem 2011; 19:4473-81. [PMID: 21742507 DOI: 10.1016/j.bmc.2011.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/18/2022]
Abstract
A facile strategy of stepwise molding of a ribonucleopeptide (RNP) complex affords fluorescent RNP sensors with selective dopamine recognition. In vitro selection of a RNA-derived RNP library, a complex of the Rev peptide and its binding site Rev Responsive Element (RRE) RNA appended with random nucleotides in variable lengths, afforded RNP receptors specific for dopamine. The modular structure of the RNP receptor enables conversion of dopamine-binding RNP receptors to fluorescent dopamine sensors. Application of conditional selection schemes, such as the variation of salt concentrations and application of a counter-selection step by using a competitor ligand norepinephrine resulted in isolation of RNP receptors with defined dopamine-binding characteristics. Increasing the salt condition at the in vitro selection stage afforded RNP receptors with higher dopamine affinity, while addition of norepinephrine in the in vitro selection milieu at the counter-selection step reinforced the selectivity of RNP receptors to dopamine against norepinephrine. Thermodynamic analyses and circular dichroismic studies of the dopamine-RNP complexes suggest that the dopamine-binding RNP with higher selectivity against norepinephrine forms a pre-organized binding pocket and that the dopamine-binding RNP with higher affinity binds dopamine through the induced-fit mechanism. These results indicate that the selection condition controls the ligand-binding mechanism of RNP receptors.
Collapse
Affiliation(s)
- Fong Fong Liew
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
| | | | | | | | | |
Collapse
|
28
|
Abstract
Gaps in the central strand of oligonucleotide triplexes bind nucleoside phosphates tightly. Watson-Crick and Hoogsteen base pairing as design principle yield motifs with high affinity for nucleoside phosphates with A or G as nucleobase, including ATP. The second messenger 3',5'-cAMP is bound with nanomolar affinity. A designed DNA motif accommodates seven nucleotides at a time. The design was implemented for both DNA and RNA.
Collapse
Affiliation(s)
- Christoph Kröner
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | | | | |
Collapse
|
29
|
Nakano S, Mashima T, Matsugami A, Inoue M, Katahira M, Morii T. Structural aspects for the recognition of ATP by ribonucleopeptide receptors. J Am Chem Soc 2011; 133:4567-79. [PMID: 21370890 DOI: 10.1021/ja110725d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A modular structure of ribonucleopeptide (RNP) affords a framework to construct macromolecular receptors and fluorescent sensors. We have isolated ATP-binding RNP with the minimum of nucleotides for ATP binding, in which the RNA consensus sequence is different from those reported for RNA aptamers against the ATP analogues. The three-dimensional structure of the substrate-binding complex of RNP was studied to understand the ATP-binding mechanism of RNP. A combination of NMR measurements, enzymatic and chemical mapping, and nucleotide mutation studies of the RNP-adenosine complex show that RNP interacts with the adenine ring of adenosine by forming a U:A:U triple with two invariant U nucleotides. The observed recognition mode for the adenine ring is different from those of RNA aptamers for ATP derivatives reported previously. The RNP-adenosine complex is folded into a particular structure by formation of the U:A:U triple and a Hoogsteen type A:U base pair. This recognition mechanism was successfully utilized to convert the substrate-binding specificity of RNP from ATP- to GTP-binding with a C(+):G:C triple recognition mode.
Collapse
Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Japan
| | | | | | | | | | | |
Collapse
|
30
|
Batey RT. Recognition of S-adenosylmethionine by riboswitches. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:299-311. [PMID: 21957011 DOI: 10.1002/wrna.63] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Riboswitches are regulatory elements commonly found in the 5' leader sequences of bacterial mRNAs that bind cellular metabolites to direct expression at either the transcriptional or translational level. The effectors of these RNAs are chemically diverse, including nucleobases and nucleosides, amino acids, cofactors, and second messenger molecules. Over the last few years, a number of structures have revealed the architectural means by which RNA creates binding pockets of high affinity and specificity for these compounds. For most effectors, there is a single class of associated riboswitches. However, eight individual classes of S-adenosylmethionine (SAM) and/or S-adenosylhomocysteine (SAH) responsive riboswitches that control various aspects of sulfur metabolism have been validated, revealing a diverse set of solutions to the recognition of these ubiquitous metabolites. This review focuses upon the structures of RNAs that bind SAM and SAH and how they discriminate between these compounds.
Collapse
Affiliation(s)
- Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
| |
Collapse
|
31
|
|
32
|
Biondi E, Nickens DG, Warren S, Saran D, Burke DH. Convergent donor and acceptor substrate utilization among kinase ribozymes. Nucleic Acids Res 2010; 38:6785-95. [PMID: 20511589 PMCID: PMC2965213 DOI: 10.1093/nar/gkq433] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Accommodation of donor and acceptor substrates is critical to the catalysis of (thio)phosphoryl group transfer, but there has been no systematic study of donor nucleotide recognition by kinase ribozymes, and there is relatively little known about the structural requirements for phosphorylating internal 2′OH. To address these questions, new self-phosphorylating ribozymes were selected that utilize ATP(gammaS) or GTP(gammaS) for 2′OH (thio)phosphorylation. Eight independent sequence families were identified among 57 sequenced isolates. Kinetics, donor nucleotide recognition and secondary structures were analyzed for representatives from each family. Each ribozyme was highly specific for its cognate donor. Competition assays with nucleotide analogs showed a remarkable convergence of donor recognition requirements, with critical contributions to recognition provided by the Watson–Crick face of the nucleobase, lesser contributions from donor nucleotide ribose hydroxyls, and little or no contribution from the Hoogsteen face. Importantly, most ribozymes showed evidence of significant interaction with one or more donor phosphates, suggesting that—unlike most aptamers—these ribozymes use phosphate interactions to orient the gamma phosphate within the active site for in-line displacement. All but one of the mapped (thio)phosphorylation sites are on unpaired guanosines within internal bulges. Comparative structural analysis identified three loosely-defined consensus structural motifs for kinase ribozyme active sites.
Collapse
Affiliation(s)
- Elisa Biondi
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | | | | | | | | |
Collapse
|
33
|
Ellington AD, Chen X, Robertson M, Syrett A. Evolutionary origins and directed evolution of RNA. Int J Biochem Cell Biol 2008; 41:254-65. [PMID: 18775793 DOI: 10.1016/j.biocel.2008.08.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 07/16/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
In vitro selection experiments show first and foremost that it is possible that functional nucleic acids can arise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove to be robust binding species and catalysts, indicating that it may have been possible to transition from even the earliest self-replicators to a nascent, RNA-catalyzed metabolism. Because of the diversity of aptamers and ribozymes that can be selected, it is possible to construct a 'fossil record' of the evolution of the RNA world, with in vitro selected catalysts filling in as doppelgangers for molecules long gone. In this way a plausible pathway from simple oligonucleotide replicators to genomic polymerases can be imagined, as can a pathway from basal ribozyme activities to the ribosome. Most importantly, though, in vitro selection experiments can give a true and quantitative idea of the likelihood that these scenarios could have played out in the RNA world. Simple binding species and catalysts could have evolved into other structures and functions. As replicating sequences grew longer, new, more complex functions or faster catalytic activities could have been accessed. Some activities may have been isolated in sequence space, but others could have been approached along large, interconnected neutral networks. As the number, type, and length of ribozymes increased, RNA genomes would have evolved and eventually there would have been no area in a fitness landscape that would have been inaccessible. Self-replication would have inexorably led to life.
Collapse
Affiliation(s)
- Andrew D Ellington
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States.
| | | | | | | |
Collapse
|
34
|
Wang JX, Breaker RR. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol 2008; 86:157-68. [PMID: 18443629 DOI: 10.1139/o08-008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Numerous riboswitches have been discovered that specifically recognize metabolites and modulate gene expression. Each riboswitch class is defined either by the consensus sequence and structural features of its metabolite-binding aptamer domain, or by the distinct metabolite that the aptamer recognizes. Several distinct classes of riboswitches that respond to S-adenosylmethionine (SAM or AdoMet) have been discovered. Representatives of these classes have been shown to strongly discriminate against S-adenosylhomocystenine (SAH or AdoHcy), which is the metabolic byproduct produced when SAM is used as a cofactor for methylation reactions. However, a distinct class of riboswitches that selectively binds SAH, and strongly discriminates against SAM, also has been discovered. Herein we compare the features of SAM and SAH riboswitches, which help showcase the enormous structural diversity that RNA can harness to form precision genetic switches for compounds that are critical for fundamental metabolic processes.
Collapse
Affiliation(s)
- Joy Xin Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | | |
Collapse
|
35
|
Mairal T, Ozalp VC, Lozano Sánchez P, Mir M, Katakis I, O'Sullivan CK. Aptamers: molecular tools for analytical applications. Anal Bioanal Chem 2007; 390:989-1007. [PMID: 17581746 DOI: 10.1007/s00216-007-1346-4] [Citation(s) in RCA: 382] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 04/30/2007] [Accepted: 05/07/2007] [Indexed: 01/21/2023]
Abstract
Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.
Collapse
Affiliation(s)
- Teresa Mairal
- Nanobiotechnology and Bioanalysis Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | | | | | | | | | | |
Collapse
|
36
|
Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 931] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
Collapse
Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | | | | |
Collapse
|
37
|
Abstract
In vitro selection has proven to be a useful means of explore the molecules and catalysts that may have existed in a primordial 'RNA world'. By selecting binding species (aptamers) and catalysts (ribozymes) from random sequence pools, the relationship between biopolymer complexity and function can be better understood, and potential evolutionary transitions between functional molecules can be charted. In this review, we have focused on several critical events or transitions in the putative RNA world: RNA self-replication; the synthesis and utilization of nucleotide-based cofactors; acyl-transfer reactions leading to peptide and protein synthesis; and the basic metabolic pathways that are found in modern living systems.
Collapse
Affiliation(s)
- Xi Chen
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | |
Collapse
|
38
|
Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J. Structures of RNA Switches: Insight into Molecular Recognition and Tertiary Structure. Angew Chem Int Ed Engl 2007; 46:1212-9. [PMID: 17226886 DOI: 10.1002/anie.200604163] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA switches (riboswitches) have important functions in gene regulation. They comprise an aptamer domain, which is responsible for ligand binding, and an expression platform that transmits the ligand-binding state of the aptamer domain through a conformational change. Riboswitches can regulate gene expression either at the level of transcription or translation, and it has been proposed that riboswitch mechanisms are even used to regulate the processing of mRNA. This Minireview summarizes the current understanding of the structures and mode of action of RNA switches, with particular focus on secondary and tertiary interactions, which stabilize the global RNA structure and thus determine the function of the aptamer domain.
Collapse
Affiliation(s)
- Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
| | | | | | | | | |
Collapse
|
39
|
Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J. Strukturen von RNA-Schaltern: Einblick in molekulare Erkennung und Tertiärstruktur. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604163] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
40
|
Hughes RA, Robertson MP, Ellington AD, Levy M. The importance of prebiotic chemistry in the RNA world. Curr Opin Chem Biol 2005; 8:629-33. [PMID: 15556407 DOI: 10.1016/j.cbpa.2004.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In vitro selection experiments have clearly demonstrated that RNA can perform many of the functions necessary to support an RNA world. Moreover, it appears that novel functions could have readily evolved from existing functional RNA molecules. Therefore, diverse molecular ecosystems could potentially have arisen from an initial, small population of functional replicators. These findings suggest that the sequences of living systems may have been determined in part by chance occurrences at origins. Any extrapolations linking sequences (as opposed to functions) obtained in the laboratory to what may have occurred ca. 4 billion years ago are tenuous at best. Thus, perhaps the best way to understand origins is not by examining relatively unconstrained sequence information, but by examining the inherent constraints imposed by prebiotic chemistry.
Collapse
Affiliation(s)
- Randall A Hughes
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | |
Collapse
|
41
|
Abstract
ATP occupies a central position in biology, for it is both an elementary building block of RNA and the most widely used cofactor in all living organisms. For this reason, it has been a recurrent target for in vitro molecular evolution techniques. The exploration of ATP-binding motifs constitutes both an important step in investigating the plausibility of the 'RNA world' hypothesis and a central starting point for the development of new enzymes. To date, only two RNA motifs that bind ATP have been characterized. The first one is targeted to the adenosine moiety, while the second one recognizes the 'Hoogsteen' face of the base. To isolate aptamers that bind ATP in different orientations, we selected RNAs on an affinity resin that presents ATP in three different orientations. We obtained five new motifs that were characterized and subsequently submitted to a secondary selection protocol designed to isolate aptamers specific for cordycepin. Interestingly, all the ATP-binding motifs selected specifically recognize the sugar-phosphate backbone region of the nucleotides. Three of the aptamers show some selectivity for adenine derivatives, while the remainder recognize any of the four nucleotides with similar efficiency. The characteristics of these aptamers are discussed along with implications for in vitro molecular evolution.
Collapse
Affiliation(s)
- Laure Weill
- Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91190 Gif sur Yvette, France
| | | | | |
Collapse
|
42
|
Clark SL, Remcho VT. Electrochromatographic retention studies on a flavin-binding RNA aptamer sorbent. Anal Chem 2004; 75:5692-6. [PMID: 14588007 DOI: 10.1021/ac030156s] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamers are oligonucleotides that are isolated and amplified on the basis of their recognition of a target molecule. In this study, an RNA aptamer isolated and amplified on the basis of its affinity for flavin mononucleotide (FMN) was covalently bound to the inner walls of fused-silica capillaries. This aptamer recognizes the flavin moiety of both FMN and flavin adenine dinucleotide (FAD). When an attempt was made to evaluate these capillaries according to existing theory, the theory proved to be insufficient. We describe a new method to evaluate capillaries for use in open-tubular capillary electrochromatography (OTCEC) of charged analytes, which combines OTCEC and flow-counterbalanced capillary electrophoresis. This method enabled us to extract k' and evaluate k(CEC) values for these capillaries, and the dependence of these values on Mg(2+) concentration was explored. The k' values for these capillaries ranged from 0.0951 to 0.2530 and from 0.0255 to 0.1118 for FMN and FAD, respectively.
Collapse
Affiliation(s)
- Stacey L Clark
- Department of Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, Oregon 97331-4003, USA
| | | |
Collapse
|
43
|
Saran D, Frank J, Burke DH. The tyranny of adenosine recognition among RNA aptamers to coenzyme A. BMC Evol Biol 2003; 3:26. [PMID: 14687414 PMCID: PMC317284 DOI: 10.1186/1471-2148-3-26] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2002] [Accepted: 12/19/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the diversity of interactions between RNA aptamers and nucleotide cofactors promises both to facilitate the design of new RNA enzymes that utilize these cofactors and to constrain models of RNA World evolution. In previous work, we isolated six pools of high affinity RNA aptamers to coenzyme A (CoA), the principle cofactor in biological acyltransfer reactions. Interpretation of the evolutionary significance of those results was made difficult by the fact that the affinity resin attachment strongly influenced the outcome of those selections. Here we describe the selection of four new pools isolated on a disulfide-linked CoA affinity matrix to minimize context-dependent recognition imposed by the attachment to the solid support. RESULTS The four new aptamer libraries show no sequence or structural relation to a previously dominant CoA-binding species, even though they were isolated from the same initial random libraries. Recognition appears to be limited to the adenosine portion of the CoA--in particular the Höogsteen edge--for most isolates surveyed, even when a counter selection was employed to remove such RNAs. Two of the recovered isolates are eluted with intact CoA more efficiently than with AMP alone suggesting a possible pantotheine interaction. However, a detailed examination of recognition specificity revealed that the 3' phosphate of CoA, and not the pantotheine arm, determined recognition by these two isolates. CONCLUSION Most aptamers that have been targeted towards cofactors containing adenosine recognize only the adenosine portion of the cofactor. They do not distinguish substituents on the 5' carbon, even when those substituents have offered hydrogen bonding opportunities and the selection conditions discouraged adenosine recognition. Beyond hydrogen bonding, additional factors that guide the selection towards adenosine recognition include aromatic stacking interactions and relatively few rotational degrees of freedom. In the present work, a sterically accessible, disulfide-linked CoA affinity resin afforded the selection of a more diverse aptamer collection then previous work with a N6 linked CoA resin.
Collapse
Affiliation(s)
- Dayal Saran
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Joseph Frank
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Donald H Burke
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| |
Collapse
|
44
|
Clark SL, Remcho VT. Open tubular liquid chromatographic separations using an aptamer stationary phase. J Sep Sci 2003. [DOI: 10.1002/jssc.200301512] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
45
|
Vaish NK, Larralde R, Fraley AW, Szostak JW, McLaughlin LW. A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality. Biochemistry 2003; 42:8842-51. [PMID: 12873145 DOI: 10.1021/bi027354i] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An analogue of uridine triphosphate containing a cationic functional group was incorporated into a degenerate RNA library by enzymatic polymerization. In vitro selection experiments using this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner completely dependent on the presence of the cationic functionality. The consensus sequence and a secondary structure model for the ATP binding site were obtained by the analysis of functional sequences selected from a partially randomized pool based on the minimal parental sequence. Mutational studies of this receptor indicated that several of the modified uridines are critical for ATP binding. Analysis of the binding of ATP analogues revealed that the modified RNA receptor makes numerous contacts with ATP, including interactions with the triphosphate group. In contrast, the aptamer repeatedly isolated from natural RNA libraries does not interact with the triphosphate group of ATP. The incorporation of a cationic amine into nucleic acids clearly allows novel interactions to occur during the molecular recognition of ligands, which carries interesting implications for the RNA world hypothesis. In addition, new materials generated from such functionalized nucleic acids could be useful tools in research and diagnostics.
Collapse
Affiliation(s)
- Narendra K Vaish
- Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA.
| | | | | | | | | |
Collapse
|
46
|
McDaniel BAM, Grundy FJ, Artsimovitch I, Henkin TM. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci U S A 2003; 100:3083-8. [PMID: 12626738 PMCID: PMC152250 DOI: 10.1073/pnas.0630422100] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modulation of the structure of a leader RNA to control formation of an intrinsic termination signal is a common mechanism for regulation of gene expression in bacteria. Expression of the S box genes in Gram-positive organisms is induced in response to limitation for methionine. We previously postulated that methionine availability is monitored by binding of a regulatory factor to the leader RNA and suggested that methionine or S-adenosylmethionine (SAM) could serve as the metabolic signal. In this study, we show that efficient termination of the S box leader region by bacterial RNA polymerase depends on SAM but not on methionine or other related compounds. We also show that SAM directly binds to and induces a conformational change in the leader RNA. Both binding of SAM and SAM-directed transcription termination were blocked by leader mutations that cause constitutive expression in vivo. Overproduction of SAM synthetase in Bacillus subtilis resulted in delay in induction of S box gene expression in response to methionine starvation, consistent with the hypothesis that SAM is the molecular effector in vivo. These results indicate that SAM concentration is sensed directly by the nascent transcript in the absence of a trans-acting factor.
Collapse
Affiliation(s)
- Brooke A Murphy McDaniel
- Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
47
|
Abstract
Coenzymes are small organic molecules that supply a varied set of reactive groups to protein enzymes, thereby diversifying catalysis beyond the chemistries of amino acid sidechains. As RNA structures begin with a more limited chemical diversity than proteins, it seems likely that RNA enzymes would also use functional groups from other molecules to support a complex RNA world metabolism. In fact, ribonucleotide moieties in many coenzymes have long been thought to be surviving vestiges of covalently bound coenzymes in an RNA world. The idea of coenzyme utilization by ribozymes can be explored by selection-amplification of coenzyme-binding RNAs and coenzyme-assisted ribozymes. Here, we review coenzyme-RNAs, and discuss their possible significance for RNA-mediated metabolism. In summary, a plausible route from prebiotic chemistry to ribozyme biochemistry exists for CoA, and via similar activities, likely exists for all the nucleotidyl coenzymes.
Collapse
Affiliation(s)
- Vasant R Jadhav
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | | |
Collapse
|
48
|
Morii T, Hagihara M, Sato SI, Makino K. In vitro selection of ATP-binding receptors using a ribonucleopeptide complex. J Am Chem Soc 2002; 124:4617-22. [PMID: 11971709 DOI: 10.1021/ja016569x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently described three-dimensional structure of the ribosome provides a sense of remarkable diversity of RNA-protein complexes. We have designed a new class of scaffold for artificial receptors, in which a short peptide and RNA with a randomized nucleotide region form a stable and specific complex. The randomized nucleotide region was placed next to the HIV-1 Rev response element to enable the formation of "ribonucleopeptide" pools in the presence of the Rev peptide. In vitro selection of RNA oligonucleotides from the randomized pool afforded a ribonucleopeptide receptor specific for ATP. The ATP-binding ribonucleopeptide did not share the known consensus nucleotide sequence for ATP aptamers and completely lost its ATP-binding ability in the absence of the Rev peptide. The ATP-binding activity of the ribonucleopeptide was increased by a substitution of the N-terminal amino acid of the Rev peptide. These results demonstrate directly that the peptide is incorporated in the functional structure of RNA and suggest that amino acids outside the RNA-binding region of the peptide modulate the ATP-binding of ribonucleopeptide. Our approach would provide an alternative strategy for the design of "tailor-made" ribonucleopeptide receptors and enzymes.
Collapse
Affiliation(s)
- Takashi Morii
- Institute of Advanced Energy, Kyoto University, and PRESTO, Japan Science and Technology Corporation, Uji, Kyoto 611-0011, Japan.
| | | | | | | |
Collapse
|
49
|
Abstract
Many important analytical methods are based on molecular recognition. Aptamers are oligonucleotides that exhibit molecular recognition; they are capable of specifically binding a target molecule, and have exhibited affinity for several classes of molecules. The use of aptamers as tools in analytical chemistry is on the rise due to the development of the "systematic evolution of ligands by exponential enrichment" (SELEX) procedure. This technique allows high-affinity aptamers to be isolated and amplified when starting from a large pool of oligonucleotide sequences. These molecules have been used in flow cytometry, biosensors, affinity probe electrophoresis, capillary electrochromatography, and affinity chromatography. In this paper, we will discuss applications of aptamers which have led to the development of aptamers as chromatographic stationary phases and applications of these stationary phases; and look towards future work which may benefit from the use of aptamers as stationary phases.
Collapse
Affiliation(s)
- Stacey L Clark
- Department of Chemistry, Oregon State University, Corvallis, OR 97331-4003, USA
| | | |
Collapse
|
50
|
Lato SM, Ozerova NDS, He K, Sergueeva Z, Shaw BR, Burke DH. Boron-containing aptamers to ATP. Nucleic Acids Res 2002; 30:1401-7. [PMID: 11884639 PMCID: PMC101341 DOI: 10.1093/nar/30.6.1401] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2001] [Revised: 01/02/2002] [Accepted: 01/02/2002] [Indexed: 11/12/2022] Open
Abstract
Boron neutron capture therapy (BNCT), an experimental treatment for certain cancers, destroys only cells near the boron; however, there is a need to develop highly specific delivery agents. As nucleic acid aptamers recognize specific molecular targets, we investigated the influence of boronated nucleotide analogs on RNA function and on the systematic evolution of ligands by exponential enrichment (SELEX) process. Substitution of guanosine 5'-(alpha-P-borano) triphosphate (bG) for GTP or uridine 5'-(alpha-P-borano) triphosphate (bU) for UTP in several known aptamers diminished or eliminated target recognition by those RNAs. Specifically, ATP-binding aptamers containing the zeta-fold, which appears in several selections for adenosine aptamers, became inactive upon bG substitution but were only moderately affected by bU substitution. Selections were carried out using the bG or bU analogs with C8-linked ATP agarose as the binding target. The selections with bU and normal NTP yielded some zeta-fold aptamers, while the bG selection yielded none of this type. Non-zeta aptamers from bU and bG populations tolerated the borano substitution and many required it. The borano nucleotide requirement is specific; bU could not be used in bG-dependent aptamers nor vice versa. The borano group plays an essential role, as yet undefined, in target recognition or RNA structure. We conclude that the bG and bU nucleotides are fully compatible with SELEX, and that these analogs could be used to make boronated aptamers as therapeutics for BNCT.
Collapse
Affiliation(s)
- Susan M Lato
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, IN 47405-7102, USA
| | | | | | | | | | | |
Collapse
|