1
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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2
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Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023; 145:8560-8568. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
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Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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3
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In vitro evolution of ribonucleases from expanded genetic alphabets. Proc Natl Acad Sci U S A 2022; 119:e2208261119. [PMID: 36279447 PMCID: PMC9636917 DOI: 10.1073/pnas.2208261119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of nucleic acids to catalyze reactions (as well as store and transmit information) is important for both basic and applied science, the first in the context of molecular evolution and the origin of life and the second for biomedical applications. However, the catalytic power of standard nucleic acids (NAs) assembled from just four nucleotide building blocks is limited when compared with that of proteins. Here, we assess the evolutionary potential of libraries of nucleic acids with six nucleotide building blocks as reservoirs for catalysis. We compare the outcomes of in vitro selection experiments toward RNA-cleavage activity of two nucleic acid libraries: one built from the standard four independently replicable nucleotides and the other from six, with the two added nucleotides coming from an artificially expanded genetic information system (AEGIS). Results from comparative experiments suggest that DNA libraries with increased chemical diversity, higher information density, and larger searchable sequence spaces are one order of magnitude richer reservoirs of molecules that catalyze the cleavage of a phosphodiester bond in RNA than DNA libraries built from a standard four-nucleotide alphabet. Evolved AEGISzymes with nitro-carrying nucleobase Z appear to exploit a general acid–base catalytic mechanism to cleave that bond, analogous to the mechanism of the ribonuclease A family of protein enzymes and heavily modified DNAzymes. The AEGISzyme described here represents a new type of catalysts evolved from libraries built from expanded genetic alphabets.
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McGorman B, Fantoni NZ, O'Carroll S, Ziemele A, El-Sagheer AH, Brown T, Kellett A. Enzymatic Synthesis of Chemical Nuclease Triplex-Forming Oligonucleotides with Gene-Silencing Applications. Nucleic Acids Res 2022; 50:5467-5481. [PMID: 35640595 PMCID: PMC9177962 DOI: 10.1093/nar/gkac438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 11/12/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are short, single-stranded oligomers that hybridise to a specific sequence of duplex DNA. TFOs can block transcription and thereby inhibit protein production, making them highly appealing in the field of antigene therapeutics. In this work, a primer extension protocol was developed to enzymatically prepare chemical nuclease TFO hybrid constructs, with gene-silencing applications. Click chemistry was employed to generate novel artificial metallo-nuclease (AMN)-dNTPs, which were selectively incorporated into the TFO strand by a DNA polymerase. This purely enzymatic protocol was then extended to facilitate the construction of 5-methylcytosine (5mC) modified TFOs that displayed increased thermal stability. The utility of the enzymatically synthesised di-(2-picolyl)amine (DPA)-TFOs was assessed and compared to a specifically prepared solid-phase synthesis counterpart through gel electrophoresis, quantitative PCR, and Sanger sequencing, which revealed similar recognition and damage properties to target genes. The specificity was then enhanced through coordinated designer intercalators-DPQ and DPPZ-and high-precision DNA cleavage was achieved. To our knowledge, this is the first example of the enzymatic production of an AMN-TFO hybrid and is the largest base modification incorporated using this method. These results indicate how chemical nuclease-TFOs may overcome limitations associated with non-molecularly targeted metallodrugs and open new avenues for artificial gene-editing technology.
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Affiliation(s)
- Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nicolò Zuin Fantoni
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK
| | - Sinéad O'Carroll
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Anna Ziemele
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK.,Department of Science and Mathematics, Suez University, Faculty of Petroleum and Mining, Engineering, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, South Parks Rd, Oxford, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.,SSPC, the Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Yuhan J, Zhu L, Zhu L, Huang K, He X, Xu W. Cell-specific aptamers as potential drugs in therapeutic applications: A review of current progress. J Control Release 2022; 346:405-420. [PMID: 35489545 DOI: 10.1016/j.jconrel.2022.04.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 12/23/2022]
Abstract
Cell-specific aptamers are a promising emerging player in the field of disease therapy. This paper reviews the multidimensional research progress made in terms of their classification, modification, and application. Based on the target location of cell-specific aptamers, it is defined and classified cell-specific aptamers into three groups including aptamers for cell surface markers, aptamers for intracellular components, and aptamers for extracellular components. Moreover, the modification methods of aptamers to achieve improved stability and affinity are concluded. In addition, recent advances in the application of cell-specific aptamers are discussed, mainly focusing on the increasing research attraction of cell state improving helpers and cell recruitment mediators in the improvement of cellular microenvironments to achieve successful disease therapy. This review also highlights 11 types of clinical aptamer drugs. Finally, the challenges and future directions of potential clinical applications are presented. In summary, we believe that cell-specific aptamers are promising drugs in disease therapy.
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Affiliation(s)
- Jieyu Yuhan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyun He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
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Rusling DA. Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH. Nucleic Acids Res 2021; 49:7256-7266. [PMID: 34233006 PMCID: PMC8287925 DOI: 10.1093/nar/gkab572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
The sequence-specific recognition of duplex DNA by unmodified parallel triplex-forming oligonucleotides is restricted to low pH conditions due to a necessity for cytosine protonation in the third strand. This has severely restricted their use as gene-targeting agents, as well as for the detection and/or functionalisation of synthetic or genomic DNA. Here I report that the nucleobase 6-amino-5-nitropyridin-2-one (Z) finally overcomes this constraint by acting as an uncharged mimic of protonated cytosine. Synthetic TFOs containing the nucleobase enabled stable and selective triplex formation at oligopurine-oligopyrimidine sequences containing multiple isolated or contiguous GC base pairs at neutral pH and above. Moreover, I demonstrate a universal strategy for the enzymatic assembly of Z-containing TFOs using its commercially available deoxyribonucleotide triphosphate. These findings seek to improve not only the recognition properties of TFOs but also the cost and/or expertise associated with their chemical syntheses.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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He H, Luo G, Zhang J, Tang L, Zhou Y, Hu B, Dai J, Huang Z. Signal Extraction, Transformation, and Magnification for Ultrasensitive and Specific Detection of Nucleic Acids. Anal Chem 2021; 93:10611-10618. [PMID: 34297543 DOI: 10.1021/acs.analchem.1c01812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid noises caused by the background and nonspecificity amplifications can jeopardize accurate polymerization and detection of nucleic acids, especially when they are analyzed in low copies. We hypothesize to reduce the noises by designing a system for specific signal extraction, transformation, and magnification to improve the specificity and sensitivity. Herein, by developing an extractor-trigger complex (ET-Combo) for the system, we have established isothermal and hybridizing combined amplifications: a one-pot detection system with two-step amplification coupled by ET-Combo. To our surprise, the signal extraction is only successful when ET-Combo is included in the first amplification. Our signal extracting, filtering, and relaying system with ET-Combo is rapid and specific, removing the noises generated during the isothermal amplification under elevated temperatures. To match the first amplification, we have designed and established a hybridizing chain reaction at high temperature. This one-pot system can resist disruption of background noises and allow detection of DNA up to five copies (single digit). With the high sensitivity, specificity, and noise resistance, our system has been successfully used to diagnose clinical samples of human papillomavirus (HPV) with the genotyping specificity.
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Affiliation(s)
- Hongfei He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yan Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Jianyuan Dai
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610000, Sichuan, China
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8
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Zumrut H, Yang Z, Williams N, Arizala J, Batool S, Benner SA, Mallikaratchy P. Ligand-Guided Selection with Artificially Expanded Genetic Information Systems against TCR-CD3ε. Biochemistry 2020; 59:552-562. [PMID: 31880917 PMCID: PMC7025805 DOI: 10.1021/acs.biochem.9b00919] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here we are reporting, for the first time, a ligand-guided selection (LIGS) experiment using an artificially expanded genetic information system (AEGIS) to successfully identify an AEGIS-DNA aptamer against T cell receptor-CD3ε expressed on Jurkat.E6 cells. Thus, we have effectively combined the enhanced diversity of an AEGIS DNA library with LIGS to develop a superior screening platform to discover superior aptamers. Libraries of DNA molecules from highly diversified building blocks will provide better ligands due to more functional diversity and better-controlled folding. Thus, a DNA library with AEGIS components (dZ and dP) was used in LIGS experiments against TCR-CD3ε in its native state using two clinically relevant monoclonal antibodies to identify an aptamer termed JZPO-10, with nanomolar affinity. Multiple specificity assays using knockout cells, and competition experiments using monoclonal antibodies utilized in LIGS, show unprecedented specificity of JZPO-10, suggesting that the combination of LIGS with AEGIS-DNA libraries will provide a superior screening platform to discover artificial ligands against critical cellular targets.
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Affiliation(s)
- Hasan Zumrut
- Ph.D. Programs in Chemistry and Biochemistry , CUNY Graduate Center , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Zunyi Yang
- Firebird Biomolecular Sciences, LLC , Alachua , Florida 32615 , United States
| | - Nicole Williams
- Ph.D. Program in Molecular, Cellular and Developmental Biology , CUNY Graduate Center , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Joekeem Arizala
- Ph.D. Programs in Chemistry and Biochemistry , CUNY Graduate Center , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Sana Batool
- Department of Chemistry, Lehman College , The City University of New York , 250 Bedford Park Boulevard West , Bronx , New York 10468 , United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution , 13709 Progress Boulevard , Alachua , Florida 32615 , United States
- Firebird Biomolecular Sciences, LLC , Alachua , Florida 32615 , United States
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College , The City University of New York , 250 Bedford Park Boulevard West , Bronx , New York 10468 , United States
- Ph.D. Programs in Chemistry and Biochemistry , CUNY Graduate Center , 365 Fifth Avenue , New York , New York 10016 , United States
- Ph.D. Program in Molecular, Cellular and Developmental Biology , CUNY Graduate Center , 365 Fifth Avenue , New York , New York 10016 , United States
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Glushakova LG, Alto BW, Kim MS, Hutter D, Bradley A, Bradley KM, Burkett-Cadena ND, Benner SA. Multiplexed kit based on Luminex technology and achievements in synthetic biology discriminates Zika, chikungunya, and dengue viruses in mosquitoes. BMC Infect Dis 2019; 19:418. [PMID: 31088375 PMCID: PMC6518713 DOI: 10.1186/s12879-019-3998-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 04/16/2019] [Indexed: 12/22/2022] Open
Abstract
Background The global expansion of dengue (DENV), chikungunya (CHIKV), and Zika viruses (ZIKV) is having a serious impact on public health. Because these arboviruses are transmitted by the same mosquito species and co-circulate in the same area, a sensitive diagnostic assay that detects them together, with discrimination, is needed. Methods We present here a diagnostics panel based on reverse transcription-PCR amplification of viral RNA and an xMap Luminex architecture involving direct hybridization of PCRamplicons and virus-specific probes. Two DNA innovations (“artificially expanded genetic information systems”, AEGIS, and “self-avoiding molecular recognition systems”, SAMRS) increase the hybridization sensitivity on Luminex microspheres and PCR specificity of the multiplex assay compared to the standard approach (standard nucleotides). Results The diagnostics panel detects, if they are present, these viruses with a resolution of 20 genome equivalents (DENV1), or 10 (DENV3–4, CHIKV) and 80 (DENV2, ZIKV) genome equivalents per assay. It identifies ZIKV, CHIKV and DENV RNAs in a single infected mosquito, in mosquito pools comprised of 5 to 50 individuals, and mosquito saliva (ZIKV, CHIKV, and DENV2). Infected mosquitoes and saliva were also collected on a cationic surface (Q-paper), which binds mosquito and viral nucleic acids electrostatically. All samples from infected mosquitoes displayed only target-specific signals; signals from non-infected samples were at background levels. Conclusions Our results provide an efficient and multiplex tool that may be used for surveillance of emerging mosquito-borne pathogens which aids targeted mosquito control in areas at high risk for transmission. Electronic supplementary material The online version of this article (10.1186/s12879-019-3998-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA
| | - Daniel Hutter
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA
| | - Andrea Bradley
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA
| | - Kevin M Bradley
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, USA.
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10
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Glushakova LG, Alto BW, Kim MS, Wiggins K, Eastmond B, Moussatche P, Burkett-Cadena ND, Benner SA. Optimization of cationic (Q)-paper for detection of arboviruses in infected mosquitoes. J Virol Methods 2018; 261:71-79. [PMID: 30099053 PMCID: PMC6168196 DOI: 10.1016/j.jviromet.2018.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/16/2023]
Abstract
Previously (Glushakova et al. 2017), a cellulose-based cationic (Q) paper derivatized with quaternary ammonium groups was shown to be a convenient platform to collect, preserve, and store nucleic acids (NAs) derived from mosquito vectors infected with pathogens for surveillance. NAs bind electrostatically to Q-paper, but the quantity of NA bound depends on the paper's binding capacity. To optimize the original technology for mosquito surveillance, factors that affected NA absorbance on Q-paper were evaluated. Sixteen variations of Q-paper were prepared with modifications of the derivatizing reagents and derivatization temperature. The binding capacities of these variations were determined first with 1,3,5-benzenetricarboxylic (BTCA), then viral RNA (purified or in infected mosquito samples) was used for validation. For this, samples with Zika (ZIKV) and chikungunya (CHIKV) RNA or virus-infected Aedes aegypti mosquito bodies were applied to sixteen Q-paper variants. Washing the paper samples with water versus elution with aqueous salt (1 M) gave samples that were analyzed for viral RNA by a PCR-based direct Luminex hybridization assay. The comparison ranked the Q-paper binding capacities from the lowest to the highest. The Q-paper with the highest RNA binding capability was further validated with ZIKV- and CHIKV-infected mosquito saliva.
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Affiliation(s)
- Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, United States
| | - Barry W Alto
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, United States
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, United States
| | - Keenan Wiggins
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, United States
| | - Bradley Eastmond
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, United States
| | - Patricia Moussatche
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, United States
| | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, 200 9th Street SE, Vero Beach, FL, 32962, United States
| | - Steven A Benner
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL, 32615, United States.
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11
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Wang Z, Zhao J, Dai Z. A label-free fluorescent adenosine triphosphate biosensor via overhanging aptamer-triggered enzyme protection and target recycling amplification. Analyst 2018; 141:4006-9. [PMID: 27221644 DOI: 10.1039/c6an00816j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a label-free fluorescent adenosine triphosphate (ATP) aptasensor is fabricated with a DNA hairpin and an overhanging aptamer. In the presence of ATP, the overhanging sequences of the aptamer may form preferred substrates of exo III, and thus trigger the enzyme-assisted amplification, which results in the release of G-rich sequences. Free G-rich sequences subsequently generate an enhanced flourescent signal by binding with thioflavin T. However, if ATP is absent, the overhanging sequence can induce steric hindrance and protect the DNA hairpin against the digestion of exo III, significantly reducing the noise of this biosensor. Accordingly, the signal-to-noise ratio of the sensing system is greatly improved, which ensures the desirable analytical performance of the proposed aptasensor both in pure samples and real samples.
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Affiliation(s)
- Zhaoyin Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Jian Zhao
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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Gu R, Oweida T, Yingling YG, Chilkoti A, Zauscher S. Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation. Biomacromolecules 2018; 19:3525-3535. [PMID: 30011192 DOI: 10.1021/acs.biomac.8b00816] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We synthesized long, nucleobase-modified, single-stranded DNA (ssDNA) using terminal deoxynucleotidyl transferase (TdT) enzymatic polymerization. Specifically, we investigated the effect of unnatural nucleobase size and incorporation density on ssDNA resistance to exo- and endonuclease degradation. We discovered that increasing the size and density of unnatural nucleobases enhances ssDNA resistance to degradation in the presence of exonuclease I, DNase I, and human serum. We also studied the mechanism of this resistance enhancement using molecular dynamics simulations. Our results show that the presence of unnatural nucleobases in ssDNA decreases local chain flexibility and hampers nuclease access to the ssDNA backbone, which hinders nuclease binding to ssDNA and slows its degradation. Our discoveries suggest that incorporating nucleobase-modified nucleotides into ssDNA, using enzymatic polymerization, is an easy and efficient strategy to prolong and tune the half-life of DNA-based materials in nucleases-containing environments.
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Affiliation(s)
| | - Thomas Oweida
- Department of Materials Science and Engineering , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering , North Carolina State University , Raleigh , North Carolina 27695 , United States
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13
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Biondi E, Benner SA. Artificially Expanded Genetic Information Systems for New Aptamer Technologies. Biomedicines 2018; 6:E53. [PMID: 29747381 PMCID: PMC6027400 DOI: 10.3390/biomedicines6020053] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/04/2023] Open
Abstract
Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”.
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Affiliation(s)
- Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL 32615, USA.
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14
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Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes. Int J Mol Sci 2017; 18:ijms18081683. [PMID: 28767098 PMCID: PMC5578073 DOI: 10.3390/ijms18081683] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleic acid aptamers have minimal immunogenicity, high chemical synthesis production, low cost and high chemical stability when compared with antibodies. However, the susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity hindered their development as drug candidates for therapeutic applications. In this review, we will discuss methods to conquer these challenges and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.
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15
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Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
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16
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Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant. PLoS One 2017; 12:e0174163. [PMID: 28323896 PMCID: PMC5360312 DOI: 10.1371/journal.pone.0174163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/03/2017] [Indexed: 11/23/2022] Open
Abstract
One research goal for unnatural base pair (UBP) is to replicate, transcribe and translate them in vivo. Accordingly, the corresponding unnatural nucleoside triphosphates must be available at sufficient concentrations within the cell. To achieve this goal, the unnatural nucleoside analogues must be phosphorylated to the corresponding nucleoside triphosphates by a cascade of three kinases. The first step is the monophosphorylation of unnatural deoxynucleoside catalyzed by deoxynucleoside kinases (dNK), which is generally considered the rate limiting step because of the high specificity of dNKs. Here, we applied a Drosophila melanogaster deoxyribonucleoside kinase (DmdNK) to the phosphorylation of an UBP (a pyrimidine analogue (6-amino-5-nitro-3-(1’-b-d-2’-deoxyribofuranosyl)-2(1H)-pyridone, Z) and its complementary purine analogue (2-amino-8-(1’-b-d-2’-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one, P). The results showed that DmdNK could efficiently phosphorylate only the dP nucleoside. To improve the catalytic efficiency, a DmdNK-Q81E mutant was created based on rational design and structural analyses. This mutant could efficiently phosphorylate both dZ and dP nucleoside. Structural modeling indicated that the increased efficiency of dZ phosphorylation by the DmdNK-Q81E mutant might be related to the three additional hydrogen bonds formed between E81 and the dZ base. Overall, this study provides a groundwork for the biological phosphorylation and synthesis of unnatural base pair in vivo.
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17
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Winiger CB, Shaw RW, Kim MJ, Moses JD, Matsuura MF, Benner SA. Expanded Genetic Alphabets: Managing Nucleotides That Lack Tautomeric, Protonated, or Deprotonated Versions Complementary to Natural Nucleotides. ACS Synth Biol 2017; 6:194-200. [PMID: 27648724 DOI: 10.1021/acssynbio.6b00193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
2,4-Diaminopyrimidine (trivially K) and imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (trivially X) form a nucleobase pair with Watson-Crick geometry as part of an artificially expanded genetic information system (AEGIS). Neither K nor X can form a Watson-Crick pair with any natural nucleobase. Further, neither K nor X has an accessible tautomeric form or a protonated/deprotonated state that can form a Watson-Crick pair with any natural nucleobase. In vitro experiments show how DNA polymerase I from E. coli manages replication of DNA templates with one K:X pair, but fails with templates containing two adjacent K:X pairs. In analogous in vivo experiments, E. coli lacking dKTP/dXTP cannot rescue chloramphenicol resistance from a plasmid containing two adjacent K:X pairs. These studies identify bacteria able to serve as selection environments for engineering cells that replicate AEGIS pairs that lack forms that are Watson-Crick complementary to any natural nucleobase.
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Affiliation(s)
- Christian B. Winiger
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
| | - Ryan W. Shaw
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States
| | - Jennifer D. Moses
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States
| | - Mariko F. Matsuura
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States
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18
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Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW, Matsuura M, Fajardo D, Moussatche P. Alternative Watson-Crick Synthetic Genetic Systems. Cold Spring Harb Perspect Biol 2016; 8:a023770. [PMID: 27663774 PMCID: PMC5088529 DOI: 10.1101/cshperspect.a023770] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.
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Affiliation(s)
- Steven A Benner
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Nilesh B Karalkar
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Shuichi Hoshika
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Roberto Laos
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Ryan W Shaw
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Mariko Matsuura
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Diego Fajardo
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Patricia Moussatche
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
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19
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Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA. Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen. Nucleic Acids Res 2016; 44:9565-9577. [PMID: 27701076 PMCID: PMC5175368 DOI: 10.1093/nar/gkw890] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 11/16/2022] Open
Abstract
Reported here is a laboratory in vitro evolution (LIVE) experiment based on an artificially expanded genetic information system (AEGIS). This experiment delivers the first example of an AEGIS aptamer that binds to an isolated protein target, the first whose structural contact with its target has been outlined and the first to inhibit biologically important activities of its target, the protective antigen from Bacillus anthracis. We show how rational design based on secondary structure predictions can also direct the use of AEGIS to improve the stability and binding of the aptamer to its target. The final aptamer has a dissociation constant of ∼35 nM. These results illustrate the value of AEGIS-LIVE for those seeking to obtain receptors and ligands without the complexities of medicinal chemistry, and also challenge the biophysical community to develop new tools to analyze the spectroscopic signatures of new DNA folds that will emerge in synthetic genetic systems replacing standard DNA and RNA as platforms for LIVE.
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Affiliation(s)
- Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Joshua D Lane
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Debasis Das
- School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA
| | - Saurja Dasgupta
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Bryan A Krantz
- School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA .,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
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20
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Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus. J Virol Methods 2016; 236:54-61. [PMID: 27421627 PMCID: PMC5010982 DOI: 10.1016/j.jviromet.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/17/2016] [Accepted: 07/12/2016] [Indexed: 11/21/2022]
Abstract
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA.
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21
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Anal Biochem 2015; 489:62-72. [PMID: 26299645 PMCID: PMC4733849 DOI: 10.1016/j.ab.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/23/2022]
Abstract
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.
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Affiliation(s)
| | - Nidhi Sharma
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Andrea C Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences, Alachua, FL 32615, USA; Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA.
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23
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Leal NA, Kim HJ, Hoshika S, Kim MJ, Carrigan MA, Benner SA. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components. ACS Synth Biol 2015; 4:407-13. [PMID: 25137127 DOI: 10.1021/sb500268n] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA.
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Affiliation(s)
- Nicole A. Leal
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Hyo-Joong Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Shuichi Hoshika
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Matthew A. Carrigan
- Department
of Natural Sciences, Santa Fe College, 3000 NW 83rd Street L209, Gainesville, Florida 32606, United States
| | - Steven A. Benner
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
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24
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High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology. J Virol Methods 2015; 214:60-74. [PMID: 25680538 DOI: 10.1016/j.jviromet.2015.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 01/25/2015] [Accepted: 01/26/2015] [Indexed: 11/23/2022]
Abstract
Mosquito-borne arboviruses are emerging world-wide as important human and animal pathogens. This makes assays for their accurate and rapid identification essential for public health, epidemiological, ecological studies. Over the past decade, many mono- and multiplexed assays targeting arboviruses nucleic acids have been reported. None has become established for the routine identification of multiple viruses in a "single tube" setting. With increasing multiplexing, the detection of viral RNAs is complicated by noise, false positives and negatives. In this study, an assay was developed that avoids these problems by combining two new kinds of nucleic acids emerging from the field of synthetic biology. The first is a "self-avoiding molecular recognition system" (SAMRS), which enables high levels of multiplexing. The second is an "artificially expanded genetic information system" (AEGIS), which enables clean PCR amplification in nested PCR formats. A conversion technology was used to place AEGIS component into amplicon, improving their efficiency of hybridization on Luminex beads. When Luminex "liquid microarrays" are exploited for downstream detection, this combination supports single-tube PCR amplification assays that can identify 22 mosquito-borne RNA viruses from the genera Flavivirus, Alphavirus, Orthobunyavirus. The assay differentiates between closely-related viruses, as dengue, West Nile, Japanese encephalitis, and the California serological group. The performance and the sensitivity of the assay were evaluated with dengue viruses and infected mosquitoes; as few as 6-10 dengue virions can be detected in a single mosquito.
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25
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Merritt KK, Bradley KM, Hutter D, Matsuura MF, Rowold DJ, Benner SA. Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance. Beilstein J Org Chem 2014; 10:2348-60. [PMID: 25383105 PMCID: PMC4222377 DOI: 10.3762/bjoc.10.245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 09/18/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide "letters", the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson-Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so. RESULTS We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson-Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2'-deoxyisocytidine and 2'-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted. CONCLUSION AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.
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Affiliation(s)
- Kristen K Merritt
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Daniel Hutter
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 17, Alachua, FL 32615, USA
| | - Mariko F Matsuura
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Diane J Rowold
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 17, Alachua, FL 32615, USA
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
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Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
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