1
|
Wells KCDH, Kharma N, Jaunky BB, Nie K, Aguiar-Tawil G, Berry D. BioCloneBot: A versatile, low-cost, and open-source automated liquid handler. HardwareX 2024; 18:e00516. [PMID: 38524156 PMCID: PMC10955647 DOI: 10.1016/j.ohx.2024.e00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/03/2024] [Accepted: 02/25/2024] [Indexed: 03/26/2024]
Abstract
Liquid handler systems can provide significant benefits to researchers by automating laboratory work, however, their unaffordable price provides a steep barrier to entry. Therefore, we provide the BioCloneBot, a versatile, low-cost, and open-source automated liquid handler. This system can be easily built with 3D-printed parts and readily available commercial components. The BioCloneBot is highly adaptive to user needs and facilitates various liquid handling tasks in research and diagnostics. Its user-friendly interface and programmable nature make it suitable for a wide range of applications, from small-scale experiments to larger laboratory setups. By utilizing BioCloneBot, researchers and scientists can streamline their liquid handling processes without the financial constraints posed by traditional systems. In this paper, we detail the design, construction, and validation of BioCloneBot, showcasing its precise control, accuracy, and repeatability in various liquid handling tasks. The open-source nature of the system encourages collaboration and customization, enabling researchers to contribute and adapt the technology to specific experimental requirements.
Collapse
Affiliation(s)
- Ke’Koa CDH Wells
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
| | - Nawwaf Kharma
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Brandon B. Jaunky
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Kaiyu Nie
- Department of Electrical and Computer Engineering, Concordia University, Montréal, Québec, Canada
| | | | - Daniel Berry
- Department of Mechanical, Industrial and Aerospace Engineering, Concordia University, Montréal, Québec, Canada
| |
Collapse
|
2
|
Cutler CP, Canicatti ME, Omoregie E. Evidence That Aquaporin 11 (AQP11) in the Spiny Dogfish ( Squalus acanthias) May Represent a Pseudogene. Int J Mol Sci 2024; 25:2028. [PMID: 38396705 PMCID: PMC10889150 DOI: 10.3390/ijms25042028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish (Squalus acanthias) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These primers yielded some faint bands from gill cDNA that were sequenced. Blast searches with the sequences showed they were not AQP11. An elasmobranch AQP11 nucleotide sequence alignment was produced to identify conserved regions to make further degenerate primers. One primer pair produced a short 148 bp fragment showing particularly strong amplification in gill and intestine. It was sequenced and represented a piece of the AQP11 gene. However, as the fragment may have resulted from contaminating genomic DNA (in total RNA used to make cDNA), 5' and 3' RACE were performed to amplify the two ends of the putative cDNA. Furthermore, 5' and 3' RACE amplifications depend on the presence of a 5' cap nucleotide and a poly A tail, respectively on the putative AQP11 mRNA. Hence, successful amplification was only possible from cDNA and not genomic DNA. Nested RACE amplifications were performed using gill and intestinal RACE cDNA, but none of the DNA fragments sequenced were AQP11. Consequently, the spiny dogfish AQP11 gene may represent a pseudogene.
Collapse
Affiliation(s)
- Christopher P. Cutler
- Biology Department, Georgia Southern University, P.O. Box 8042, Statesboro, GA 30460, USA
| | | | | |
Collapse
|
3
|
Liu AY, Koga H, Goya C, Kitabatake M. Quick and affordable DNA cloning by reconstitution of Seamless Ligation Cloning Extract using defined factors. Genes Cells 2023; 28:553-562. [PMID: 37132531 DOI: 10.1111/gtc.13034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/04/2023]
Abstract
The cloning of DNA fragments to plasmid vectors is at the heart of molecular biology. Recent developments have led to various methods utilizing homologous recombination of homology arms. Among them, Seamless Ligation Cloning Extract (SLiCE) is an affordable alternative solution that uses simple Escherichia coli lysates. However, the underlying molecular mechanisms remain unclear and the reconstitution of the extract by defined factors has not yet been reported. We herein show that the key factor in SLiCE is Exonuclease III (ExoIII), a double-strand (ds) DNA-dependent 3'-5' exonuclease, encoded by XthA. SLiCE prepared from the xthAΔ strain is devoid of recombination activity, whereas purified ExoIII alone is sufficient to assemble two blunt-ended dsDNA fragments with homology arms. In contrast to SLiCE, ExoIII is unable to digest (or assemble) fragments with 3' protruding ends; however, the addition of single-strand DNA-targeting Exonuclease T overcomes this issue. Through the combination of commercially available enzymes under optimized conditions, we achieved the efficient, reproducible, and affordable cocktail, "XE cocktail," for seamless DNA cloning. By reducing the cost and time required for DNA cloning, researchers will devote more resources to advanced studies and the careful validation of their own findings.
Collapse
Affiliation(s)
- Alexander Y Liu
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiroto Koga
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Chihiro Goya
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Makoto Kitabatake
- Laboratory of RNA Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| |
Collapse
|
4
|
Nawawi O, Abdullah MP, Yusuf CYL. A streamlined strategy for self-production of a commercial positive selection vector, the pJET1.2/blunt cloning vector, using common laboratory E. coli strains. 3 Biotech 2023; 13:224. [PMID: 37292140 PMCID: PMC10244300 DOI: 10.1007/s13205-023-03647-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
Positive selection vectors carry a lethal gene encoding a toxic product that is harmful to most laboratory E. coli strains. Previously, we reported a strategy for in-house production of a commercial positive selection vector, the pJET1.2/blunt cloning vector, using common laboratory E. coli strains. However, the strategy involves lengthy gel electrophoresis and extraction procedures to purify the linearized vector after digestion. Here, we streamlined the strategy to eliminate the gel-purification step. A uniquely designed short fragment called the Nawawi fragment was inserted into the coding sequence of the lethal gene of the pJET1.2 plasmid, resulting in the pJET1.2N plasmid that can be propagated in the E. coli strain DH5α. Digestion of the pJET1.2N plasmid with EcoRV released the Nawawi fragment, and the resulting blunt-ended pJET1.2/blunt cloning vector can be used directly for DNA cloning without prior purification. Cloning of a DNA fragment was not hindered by the Nawawi fragments carried over from the digestion step. After transformation, the pJET1.2N-derived pJET1.2/blunt cloning vector produced > 98% positive clones. The streamlined strategy accelerates the in-house production of the pJET1.2/blunt cloning vector and enables DNA cloning at a lower cost. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03647-3.
Collapse
Affiliation(s)
- Omar Nawawi
- Laboratory of Plant Genetic and Cell Biology, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Jasin Campus, 77300 Merlimau, Melaka Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Chong Yu Lok Yusuf
- Laboratory of Plant Genetic and Cell Biology, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Jasin Campus, 77300 Merlimau, Melaka Malaysia
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, 678000 China
| |
Collapse
|
5
|
Guo R, Zhao W, Wei L, Zhang S, Feng L, Guo Y. A variety of simple and ultra-low-cost methods preparing SLiCE extracts and their application to DNA cloning. J Microbiol Methods 2022;:106565. [PMID: 36089163 DOI: 10.1016/j.mimet.2022.106565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 12/27/2022]
Abstract
Cell lysates from a laboratory strain of Escherichia coli can be exploited for seamless DNA cloning in vitro, which is named the seamless ligation cloning extract (SLiCE) cloning method. The SLiCE method can incorporate DNA fragments into a vector to achieve conventional DNA cloning and is more cost-effective than commercially seamless DNA cloning kits. In this study, we found that the SLiCE extracts could easily be prepared with different methods, such as 3% Triton X-100 lysis buffer, 3% SDS lysis buffer, or freeze-thaw cycles. At high E. coli transformation efficiency, the SLiCE extracts prepared using different simple and ultra-low cost methods did not affect the DNA cloning efficiency. These results further revealed that the SLiCE cloning method can be efficiently used for seamless DNA cloning in vitro.
Collapse
|
6
|
Nawawi O, Abdullah MP, Yusuf CYL. A strategy for in-house production of a positive selection cloning vector from the commercial pJET1.2/blunt cloning vector at minimal cost. 3 Biotech 2022; 12:216. [PMID: 35965659 PMCID: PMC9363543 DOI: 10.1007/s13205-022-03289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/29/2022] [Indexed: 11/01/2022] Open
Abstract
Key message In-house production of a positive selection cloning vector could be simple, efficient and low cost. Abstract DNA cloning technology requires a vector to harbour a gene of interest for multiplication of the gene in bacterial cells. Positive selection vector has become a popular type of cloning vector due to the simplicity and efficiency of the positive selection system. Due to the presence of a toxic gene, propagation of a commercial positive selection vector in common laboratory E. coli strains is infeasible. This study demonstrated a strategy for propagation and in-house production of a commercial positive selection vector, i.e., pJET1.2/blunt cloning vector, at low cost. This was done by insertion of a specially designed DNA fragment (MCS fragment), which can be easily removed later by EcoRV digestion, into the pJET1.2/blunt cloning vector to allow the propagation of the modified plasmid (termed pJET1.2M) in common E. coli strains. Removal of the MCS fragment from the pJET1.2M plasmid produces the pJET1.2/blunt cloning vector ready for gene cloning. The self-made pJET1.2/blunt cloning vector exhibited a cloning efficiency of 100%. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03289-x.
Collapse
Affiliation(s)
- Omar Nawawi
- Laboratory of Plant Genetic and Cell Biology, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Jasin Campus, 77300 Merlimau, Melaka, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Chong Yu Lok Yusuf
- Laboratory of Plant Genetic and Cell Biology, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Jasin Campus, 77300 Merlimau, Melaka, Malaysia
| |
Collapse
|
7
|
Nozaki S, Niki H. Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends. J Bacteriol 2019; 201:e00660-18. [PMID: 30530516 DOI: 10.1128/JB.00660-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/05/2018] [Indexed: 11/20/2022] Open
Abstract
Cloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently, an in vitro recombination system for DNA cloning was shown to enable the joining of multiple DNA fragments at once. Interestingly, E. coli potentially assembles multiple linear DNA fragments that are introduced into the cell. Improved protocols for this in vivo cloning have realized a high level of usability, comparable to that by in vitro recombination reactions. However, the mechanism of in vivo cloning is highly controversial. Here, we clarified the fundamental mechanism underlying in vivo cloning and also constructed a strain that was optimized for in vivo cloning. Additionally, we streamlined the procedure of in vivo cloning by using a single microcentrifuge tube. Escherichia coli has an ability to assemble DNA fragments with homologous overlapping sequences of 15 to 40 bp at each end. Several modified protocols have already been reported to improve this simple and useful DNA cloning technology. However, the molecular mechanism by which E. coli accomplishes such cloning is still unknown. In this study, we provide evidence that the in vivo cloning of E. coli is independent of both RecA and RecET recombinases but is dependent on XthA, a 3′ to 5′ exonuclease. Here, in vivo cloning of E. coli by XthA is referred to as in vivoE. coli cloning (iVEC). We also show that iVEC activity is reduced by deletion of the C-terminal domain of DNA polymerase I (PolA). Collectively, these results suggest the following mechanism of iVEC. First, XthA resects the 3′ ends of linear DNA fragments that are introduced into E. coli cells, resulting in exposure of the single-stranded 5′ overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I. Elucidation of the iVEC mechanism at the molecular level would further advance the development of in vivo DNA cloning technology. Already we have successfully demonstrated multiple-fragment assembly of up to seven fragments in combination with an effortless transformation procedure using a modified host strain for iVEC. IMPORTANCE Cloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently, an in vitro recombination system for DNA cloning was shown to enable the joining of multiple DNA fragments at once. Interestingly, E. coli potentially assembles multiple linear DNA fragments that are introduced into the cell. Improved protocols for this in vivo cloning have realized a high level of usability, comparable to that by in vitro recombination reactions. However, the mechanism of in vivo cloning is highly controversial. Here, we clarified the fundamental mechanism underlying in vivo cloning and also constructed a strain that was optimized for in vivo cloning. Additionally, we streamlined the procedure of in vivo cloning by using a single microcentrifuge tube.
Collapse
|
8
|
Klimešová M, Rindi F, Škaloud P. DNA cloning demonstrates high genetic heterogeneity in populations of the subaerial green alga Trentepohlia (Trentepohliales, Chlorophyta). J Phycol 2019; 55:224-235. [PMID: 30481372 DOI: 10.1111/jpy.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/27/2018] [Indexed: 06/09/2023]
Abstract
Mats of the green alga Trentepohlia, a genus widely distributed in the tropics as well as temperate regions, have always been perceived as homogeneous (i.e., formed by only one species). As such, their general nature and specific feature play a supportive role in the species delimitation. However, the presence of morphologically dissimilar thalli was observed under the light microscope and when cultivating a piece of a single mat. To address this, we performed DNA cloning of the rbcL gene on mat fragments of T. abietina, T. annulata, T. jolithus and T. umbrina sampled in Europe to reveal if they are composed of one or more species. We revealed that more Trentepohlia haplotypes may coexist in a single mat. In consideration of this, we conclude that the use of material isolated in unialgal culture will be almost mandatory for a taxonomic reassessment of this complicated genus. Another direct implication of this problem is that herbarium specimens consisting of field-collected material should not be used for direct sequencing. We further hypothesize the reasons why multiple haplotypes of Trentepohlia occur more frequently in the tuft-like mats. Possibly, fragments and/or cells of other microalgae, including other species of Trentepohlia, might be retained in such mats more easily than in the crustose trentepohlialean mats.
Collapse
Affiliation(s)
- Michala Klimešová
- Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Pavel Škaloud
- Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| |
Collapse
|
9
|
Holmgaard A, Alsing S, Askou AL, Corydon TJ. CRISPR Gene Therapy of the Eye: Targeted Knockout of Vegfa in Mouse Retina by Lentiviral Delivery. Methods Mol Biol 2019; 1961:307-328. [PMID: 30912054 DOI: 10.1007/978-1-4939-9170-9_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome editing and knockout by virus-based delivery of CRISPR/Cas9 may provide a new option to cure inherited and acquired ocular diseases. Here we describe development and application of lentivirus-based delivery vectors enabling knockout of the Vegfa gene. We show that Streptococcus pyogenes (Sp) Cas9 and single-guide RNAs (sgRNAs) delivered by such vectors selectively can ablate the vascular endothelial growth factor A (Vegfa) gene in mouse retina following a single administration. These findings may contribute to the development of a new therapeutic path in the treatment of ocular diseases including exudative age-related macular degeneration (AMD).
Collapse
Affiliation(s)
| | - Sidsel Alsing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark.
| |
Collapse
|
10
|
Xu Z, Rui YN, Hagan JP, Kim DH. Precision Tagging: A Novel Seamless Protein Tagging by Combinational Use of Type II and Type IIS Restriction Endonucleases. Bio Protoc 2018; 8:e2721. [PMID: 29770347 DOI: 10.21769/bioprotoc.2721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Protein tagging is a powerful tool for performing comprehensive analyses of the biological functions of a protein of interest owing to the existence of a wide variety of tags. It becomes indispensable in some cases, such as in tracking protein dynamics in a live cell or adding a peptide epitope due to the lack of optimal antibodies. However, efficiently integrating an array of tags into the gene of interest remains a challenge. Traditional DNA recombinant technology based on type II restriction endonucleases renders protein tagging tedious and inefficient as well as the introduction of an unwanted junction sequence. In our attempt to tag Thrombospondin type 1 domain-containing 1 (THSD1) that we identified as the first intracranial aneurysm gene (Santiago-Sim et al., 2016), we developed a novel precision tagging technique by combinational use of type II and IIS restriction endonucleases (Xu et al., 2017), which generates a seamless clone with high efficiency. Here, we describe a protocol that not only provides a generalized strategy for any gene of interest but also takes its application of 11 different tags in THSD1 as a step-by-step example.
Collapse
Affiliation(s)
- Zhen Xu
- Department of Neurosurgery, the University of Texas Health Science Center at Houston, Texas, USA
| | - Yan-Ning Rui
- Department of Neurosurgery, the University of Texas Health Science Center at Houston, Texas, USA
| | - John P Hagan
- Department of Neurosurgery, the University of Texas Health Science Center at Houston, Texas, USA
| | - Dong H Kim
- Department of Neurosurgery, the University of Texas Health Science Center at Houston, Texas, USA
| |
Collapse
|
11
|
Askou AL, Corydon TJ. Development of Multigenic Lentiviral Vectors for Cell-Specific Expression of Antiangiogenic miRNAs and Protein Factors. Methods Mol Biol 2018; 1715:47-60. [PMID: 29188505 DOI: 10.1007/978-1-4939-7522-8_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Generation of lentivirus (LV)-based vectors holding multiple gene cassettes for coexpression of several therapeutic factors provides potent tools in both gene delivery studies as well as in gene therapy. Here we describe the development of such multigenic LV gene delivery vectors enabling cell-specific coexpression of antiangiogenic microRNA (miRNA) and protein factors and, if preferred, a fluorescent reporter, from RNApol(II)-driven expression cassettes orientated in a back-to-back fashion. This configuration may contribute to the development of new combination therapies for amelioration of diseases involving intraocular neovascularization including exudative age-related macular degeneration (AMD).
Collapse
|
12
|
Johnson JR, D'Amore R, Thain SC, Craig T, McCue HV, Hertz-Fowler C, Hall N, Hall AJ. GeneMill: A 21st century platform for innovation. Biochem Soc Trans 2016; 44:681-3. [PMID: 27284025 DOI: 10.1042/BST20160012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 11/17/2022]
Abstract
GeneMill officially launched on 4th February 2016 and is an open access academic facility located at The University of Liverpool that has been established for the high-throughput construction and testing of synthetic DNA constructs. GeneMill provides end-to-end design, construction and phenotypic characterization of small to large gene constructs or genetic circuits/pathways for academic and industrial applications. Thus, GeneMill is equipping the scientific community with easy access to the validated tools required to explore the possibilities of Synthetic Biology.
Collapse
|
13
|
Abstract
Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs. We used this platform to generate over 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. These AREs work as efficiently as their naturally occurring counterparts, and some of them even do not have any naturally occurring counterparts, demonstrating easy programmability, generality, versatility, and high efficiency for this new technology.
Collapse
Affiliation(s)
- Behnam Enghiad
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
14
|
Sterner A, Zehetmeier C. High-Throughput IgG Conversion of Phage Displayed Fab Antibody Fragments by AmplYFast. Methods Mol Biol 2017; 1575:121-143. [PMID: 28255877 DOI: 10.1007/978-1-4939-6857-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Phage display of antibody libraries is an invaluable strategy in antibody discovery. Many synthetic antibody library formats utilize monovalent antibody binding fragments (Fab), displayed on filamentous phage and expressed in Escherichia coli for selection and screening procedures, respectively. For most therapeutic applications, however, the final antibody candidate favors a bivalent immunoglobulin G (IgG) format, due to its particular effector function, half-life, and avidity.Here, we present an optimized subcloning method, termed AmplYFast, for the fast and convenient conversion of phage-displayed monovalent Fab fragments into full-length IgG or immunoglobulins of any other isotype. By using biotinylated primers, unique mammalian expression vectors, and multi-well plates, AmplYFast combines the rapid amplification, digestion, and ligation of recombinant Ig heavy and light chain sequences in an easy-to-operate high-throughput manner. Thus, AmplYFast improves quality and efficiency in DNA cloning and significantly minimizes timelines to antibody lead identification.
Collapse
Affiliation(s)
- Andrea Sterner
- MorphoSys AG, Semmelweisstrasse 7, 82152, Planegg, Germany.
| | | |
Collapse
|
15
|
Park H, Lee EH, Ka KH, Eom AH. Community Structures of Arbuscular Mycorrhizal Fungi in Soils and Plant Roots Inhabiting Abandoned Mines of Korea. Mycobiology 2016; 44:277-282. [PMID: 28154485 PMCID: PMC5287160 DOI: 10.5941/myco.2016.44.4.277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
In this study, we collected rhizosphere soils and root samples from a post-mining area and a natural forest area in Jecheon, Korea. We extracted spores of arbuscular mycorrhizal fungi (AMF) from rhizospheres, and then examined the sequences of 18S rDNA genes of the AMF from the collected roots of plants. We compared the AMF communities in the post-mining area and the natural forest area by sequence analysis of the AMF spores from soils and of the AMF clones from roots. Consequently, we confirmed that the structure of AMF communities varied between the post-mining area and the natural forest area and showed significant relationship with heavy metal contents in soils. These results suggest that heavy metal contamination by mining activity significantly affects the AMF community structure.
Collapse
Affiliation(s)
- Hyeok Park
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Korea
| | - Eun-Hwa Lee
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Korea
| | - Kang-Hyeon Ka
- Division of Wood Chemistry & Microbiology, Korea Forest Research Institute, Seoul 02455, Korea
| | - Ahn-Heum Eom
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Korea
| |
Collapse
|
16
|
Šafář J, Šimková H, Doležel J. Construction of BAC Libraries from Flow-Sorted Chromosomes. Methods Mol Biol 2016; 1429:135-49. [PMID: 27511172 DOI: 10.1007/978-1-4939-3622-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.
Collapse
|
17
|
Abstract
In 1973, Cohen and coworkers published a foundational paper describing the cloning of DNA fragments into plasmid vectors. In it, they used DNA segments made by digestion with restriction enzymes and joined these in vitro with DNA ligase. These methods established working recombinant DNA technology and enabled the immediate start of the biotechnology industry. Since then, "classical" recombinant DNA technology using restriction enzymes and DNA ligase has matured. At the same time, researchers have developed numerous ways to generate large, complex, multisegment DNA constructions that offer advantages over classical techniques. Here, we provide an overview of "post-Cohen-Boyer" techniques used for cloning single segments into vectors (T/A, Topo cloning, Gateway and Recombineering) and for multisegment DNA assembly (BioBricks, Golden Gate, Gibson, yeast homologous recombination in vivo, and ligase cycling reaction). We compare and contrast these methods and also discuss issues that researchers should consider before choosing a particular multisegment DNA assembly method. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Bryan Sands
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| |
Collapse
|
18
|
Abstract
Poxvirus expression vectors were described in 1982 and quickly became widely used for vaccine development as well as research in numerous fields. Advantages of the vectors include simple construction, ability to accommodate large amounts of foreign DNA and high expression levels. Numerous poxvirus-based veterinary vaccines are currently in use and many others are in human clinical trials. The early reports of poxvirus vectors paved the way for and stimulated the development of other viral vectors and recombinant DNA vaccines.
Collapse
Affiliation(s)
- Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|