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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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Cao VD, Luo G, Korynta S, Liu H, Liang Y, Shanklin J, Altpeter F. Intron-mediated enhancement of DIACYLGLYCEROL ACYLTRANSFERASE1 expression in energycane promotes a step change for lipid accumulation in vegetative tissues. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:153. [PMID: 37838699 PMCID: PMC10576891 DOI: 10.1186/s13068-023-02393-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/09/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Metabolic engineering for hyperaccumulation of lipids in vegetative tissues is a novel strategy for enhancing energy density and biofuel production from biomass crops. Energycane is a prime feedstock for this approach due to its high biomass production and resilience under marginal conditions. DIACYLGLYCEROL ACYLTRANSFERASE (DGAT) catalyzes the last and only committed step in the biosynthesis of triacylglycerol (TAG) and can be a rate-limiting enzyme for the production of TAG. RESULTS In this study, we explored the effect of intron-mediated enhancement (IME) on the expression of DGAT1 and resulting accumulation of TAG and total fatty acid (TFA) in leaf and stem tissues of energycane. To maximize lipid accumulation these evaluations were carried out by co-expressing the lipogenic transcription factor WRINKLED1 (WRI1) and the TAG protect factor oleosin (OLE1). Including an intron in the codon-optimized TmDGAT1 elevated the accumulation of its transcript in leaves by seven times on average based on 5 transgenic lines for each construct. Plants with WRI1 (W), DGAT1 with intron (Di), and OLE1 (O) expression (WDiO) accumulated TAG up to a 3.85% of leaf dry weight (DW), a 192-fold increase compared to non-modified energycane (WT) and a 3.8-fold increase compared to the highest accumulation under the intron-less gene combination (WDO). This corresponded to TFA accumulation of up to 8.4% of leaf dry weight, a 2.8-fold or 6.1-fold increase compared to WDO or WT, respectively. Co-expression of WDiO resulted in stem accumulations of TAG up to 1.14% of DW or TFA up to 2.08% of DW that exceeded WT by 57-fold or 12-fold and WDO more than twofold, respectively. Constitutive expression of these lipogenic "push pull and protect" factors correlated with biomass reduction. CONCLUSIONS Intron-mediated enhancement (IME) of the expression of DGAT resulted in a step change in lipid accumulation of energycane and confirmed that under our experimental conditions it is rate limiting for lipid accumulation. IME should be applied to other lipogenic factors and metabolic engineering strategies. The findings from this study may be valuable in developing a high biomass feedstock for commercial production of lipids and advanced biofuels.
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Affiliation(s)
- Viet Dang Cao
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Guangbin Luo
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Shelby Korynta
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Hui Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA
| | - Yuanxue Liang
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA.
- Biosciences Department, Brookhaven National Laboratory, Upton, NY, USA.
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA.
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3
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Marillonnet S, Grützner R. Synthetic DNA Assembly Using Golden Gate Cloning and the Hierarchical Modular Cloning Pipeline. ACTA ACUST UNITED AC 2021; 130:e115. [PMID: 32159931 DOI: 10.1002/cpmb.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods that enable the construction of recombinant DNA molecules are essential tools for biological research and biotechnology. Golden Gate cloning is used for assembly of multiple DNA fragments in a defined linear order in a recipient vector using a one-pot assembly procedure. Golden Gate cloning is based on the use of a type IIS restriction enzyme for digestion of the DNA fragments and vector. Because restriction sites for the type IIS enzyme used for assembly must be present at the ends of the DNA fragments and vector but absent from all internal sequences, special care must be taken to prepare DNA fragments and the recipient vector with a structure suitable for assembly by Golden Gate cloning. In this article, protocols are presented for preparation of DNA fragments, modules, and vectors suitable for Golden Gate assembly cloning. Additional protocols are presented for assembly of defined parts in a transcription unit, as well as the stitching together of multiple transcription units into multigene constructs by the modular cloning (MoClo) pipeline. © 2020 The Authors. Basic Protocol 1: Performing a typical Golden Gate cloning reaction Basic Protocol 2: Accommodating a vector to Golden Gate cloning Basic Protocol 3: Accommodating an insert to Golden Gate cloning Basic Protocol 4: Generating small standardized parts compatible with hierarchical modular cloning (MoClo) using level 0 vectors Alternate Protocol: Generating large standardized parts compatible with hierarchical modular cloning (MoClo) using level -1 vectors Basic Protocol 5: Assembling transcription units and multigene constructs using level 1, M, and P MoClo vectors.
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Affiliation(s)
- Sylvestre Marillonnet
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Halle, Germany
| | - Ramona Grützner
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Halle, Germany
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4
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Boute N, Lowe P, Berger S, Malissard M, Robert A, Tesar M. NanoLuc Luciferase - A Multifunctional Tool for High Throughput Antibody Screening. Front Pharmacol 2016; 7:27. [PMID: 26924984 PMCID: PMC4758271 DOI: 10.3389/fphar.2016.00027] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Based on the recent development of NanoLuc luciferase (Nluc), a small (19 kDa), highly stable, ATP independent, bioluminescent protein, an extremely robust and ultra high sensitivity screening system has been developed whereby primary hits of therapeutic antibodies and antibody fragments could be characterized and quantified without purification. This system is very versatile allowing cellular and solid phase ELISA but also homogeneous BRET based screening assays, relative affinity determinations with competition ELISA and direct Western blotting. The new Nluc protein fusion represents a “swiss army knife solution” for today and future high throughput antibody drug screenings.
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Affiliation(s)
- Nicolas Boute
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Peter Lowe
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Sven Berger
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Martine Malissard
- Biochemistry Department, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en Genevois, France
| | - Alain Robert
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
| | - Michael Tesar
- Molecular and Cellular Biology Unit, Institut de Recherche Pierre Fabre, Centre d'Immunologie Pierre Fabre Saint-Julien-en-Genevois, France
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5
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Tóth E, Huszár K, Bencsura P, Kulcsár PI, Vodicska B, Nyeste A, Welker Z, Tóth S, Welker E. Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning. PLoS One 2014; 9:e90896. [PMID: 24618593 PMCID: PMC3949710 DOI: 10.1371/journal.pone.0090896] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/06/2014] [Indexed: 11/25/2022] Open
Abstract
The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease - a Body Double of the Type IIP enzyme - is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.
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Affiliation(s)
- Eszter Tóth
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Huszár
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petra Bencsura
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter István Kulcsár
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Barbara Vodicska
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Antal Nyeste
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsombor Welker
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Szilvia Tóth
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ervin Welker
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Institute of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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6
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Abstract
DNA assembly methods are essential tools for biological research and biotechnology. Therefore various methods have been developed to clone DNA fragments of interest. Conventional methods usually require several cloning steps to generate a construct of interest. At each step, a single DNA fragment is transferred from a donor plasmid or PCR product to a recipient vector. In the past few years, a number of methods have been developed to facilitate and speed up this process. One of these methods, Golden Gate cloning, allows assembling up to nine fragments at a time in a recipient plasmid. Cloning is performed by pipetting in a single tube all plasmid donors, the recipient vector, a type IIS restriction enzyme and ligase, and incubating the mix in a thermal cycler. Despite the simplicity of the cloning procedure, the majority of clones obtained after transformation contain the expected construct. Using Golden Gate cloning however requires the use of carefully designed donor and recipient plasmids. We provide here a protocol describing how to design these plasmids and also describe the conditions necessary to perform the assembly reaction.
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7
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Sun Q, Liu J, Li Y, Zhang Q, Shan S, Li X, Qi B. Creation and validation of a widely applicable multiple gene transfer vector system for stable transformation in plant. PLANT MOLECULAR BIOLOGY 2013; 83:391-404. [PMID: 23839253 DOI: 10.1007/s11103-013-0096-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 06/16/2013] [Indexed: 05/09/2023]
Abstract
Multiple gene transfer (MGT) technology has become a powerful tool for basic and applied plant biology research in recent years. Despite some notable successes in obtaining plant lines harbouring multiple transgenes, these methods are still generally unwieldy and costly. We report here a straightforward and cost effective strategy, utilizing commonly available restriction enzymes for the transfer of multiple genes into plants, hence greatly widening the accessibility of MGT. This methodology exploits the specific 'nested' arrangement of a pair of isocaudomer restriction enzymes (for example XbaI-AvrII-XbaI) so that through the alternate use of these two enzymes in a reiterative fashion multiple genes/constructs (up to five in this study) could be 'stacked' together with ease. In a proof-of-concept experiment, we constructed a plant transformation vector containing three reporter gene expression cassettes flanked by two matrix attachment region sequences. The expression of all three genes was confirmed in transgenic Arabidopsis thaliana. The usefulness of this technology was further validated by the construction of a plant transformation vector containing five transgenes for the production of eicosapentaenoic acid (EPA, C20∆⁵,⁸,¹¹,¹⁴,¹⁷), a polyunsaturated essential fatty acid found in fish oils that is beneficial for health. In addition, we constructed four more vectors, incorporating one seed specific and three promoters conferring constitutive expression. These expression cassettes are flanked by a different isocaudomer pair (AvrII-SpeI-AvrII) and four other unique restriction sites, allowing the exchange of promoters and terminators of choice.
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Affiliation(s)
- Quanxi Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271000, China
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8
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Zhou LB, Lin QQ, Zhang JX, Zhao SJ, Hu ZB. A rapid DNA assembling strategy mediated by direct full-length polymerase chain reaction. Gene 2013; 523:122-5. [DOI: 10.1016/j.gene.2013.03.140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
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9
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Abstract
A basic requirement for synthetic biology is the availability of efficient DNA assembly methods. We have previously reported the development of Golden Gate cloning, a method that allows parallel assembly of multiple DNA fragments in a one-tube reaction. Golden Gate cloning can be used for different levels of construct assembly: from gene fragments to complete gene coding sequences, from basic genetic elements to full transcription units, and finally from transcription units to multigene constructs. We provide here a protocol for DNA assembly using Golden Gate cloning, taking as an example the level of assembly of gene fragments to complete coding sequences, a level of cloning that can be used to perform DNA shuffling. Such protocol requires the following steps: (1) selecting fusion sites within parental sequences (sites at which parental sequences will be recombined), (2) amplifying all DNA fragments by PCR to add flanking restriction sites, (3) cloning the amplified fragments in intermediate constructs, and (4) assembling all or selected sets of intermediate constructs in a compatible recipient vector using a one-pot restriction-ligation.
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Affiliation(s)
- Carola Engler
- NOMAD BIOSCIENCE GMBH, Weinbergweg 22, Halle (Saale), Germany
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10
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Liang X, Peng L, Tsvetanova B, Li K, Yang JP, Ho T, Shirley J, Xu L, Potter J, Kudlicki W, Peterson T, Katzen F. Recombination-based DNA assembly and mutagenesis methods for metabolic engineering. Methods Mol Biol 2012; 834:93-109. [PMID: 22144356 DOI: 10.1007/978-1-61779-483-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In recent years there has been a growing interest in the precise and concerted assembly of multiple DNA fragments of diverse sizes, including chromosomes, and the fine tuning of gene expression levels and protein activity. Commercial DNA assembly solutions have not been conceived to support the cloning of very large or very small genetic elements or a combination of both. Here we summarize a series of protocols that allow the seamless, simultaneous, flexible, and highly efficient assembly of DNA elements of a wide range of sizes (up to hundred thousand base pairs). The protocols harness the power of homologous recombination and are performed either in vitro or within the living cells. The DNA fragments may or may not share homology at their ends. An efficient site-directed mutagenesis protocol enhanced by homologous recombination is also described.
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Affiliation(s)
- Xiquan Liang
- Life Technologies Corporation, Carlsbad, CA, USA
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11
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Tsvetanova B, Peng L, Liang X, Li K, Yang JP, Ho T, Shirley J, Xu L, Potter J, Kudlicki W, Peterson T, Katzen F. Genetic assembly tools for synthetic biology. Methods Enzymol 2011; 498:327-48. [PMID: 21601684 DOI: 10.1016/b978-0-12-385120-8.00014-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
With the completion of myriad genome sequencing projects, genetic bioengineering has expanded into many applications including the integrated analysis of complex pathways, the construction of new biological parts and the redesign of existing, natural biological systems. All these areas require the precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes, and the fine-tuning of gene expression levels and protein activity. Current commercial cloning products are not robust enough to support the assembly of very large or very small genetic elements or a combination of both. In addition, current strategies are not flexible enough to allow further modifications to the original design without having to undergo complicated cloning strategies. Here, we present a set of protocols that allow the seamless, simultaneous, flexible, and highly efficient assembly of genetic material, designed for a wide size dynamic range (10s to 100,000s base pairs). The assembly can be performed either in vitro or within the living cells and the DNA fragments may or may not share homology at their ends. A novel site-directed mutagenesis approach enhanced by in vitro recombineering is also presented.
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12
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Weber E, Gruetzner R, Werner S, Engler C, Marillonnet S. Assembly of designer TAL effectors by Golden Gate cloning. PLoS One 2011; 6:e19722. [PMID: 21625552 PMCID: PMC3098256 DOI: 10.1371/journal.pone.0019722] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/08/2011] [Indexed: 12/25/2022] Open
Abstract
Generation of customized DNA binding domains targeting unique sequences in complex genomes is crucial for many biotechnological applications. The recently described DNA binding domain of the transcription activator-like effectors (TALEs) from Xanthomonas consists of a series of repeats arranged in tandem, each repeat binding a nucleotide of the target sequence. We present here a strategy for engineering of TALE proteins with novel DNA binding specificities based on the 17.5 repeat-containing AvrBs3 TALE as a scaffold. For each of the 17 full repeats, four module types were generated, each with a distinct base preference. Using this set of 68 repeat modules, recognition domains for any 17 nucleotide DNA target sequence of choice can be constructed by assembling selected modules in a defined linear order. Assembly is performed in two successive one-pot cloning steps using the Golden Gate cloning method that allows seamless fusion of multiple DNA fragments. Applying this strategy, we assembled designer TALEs with new target specificities and tested their function in vivo.
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13
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Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS One 2011; 6:e16765. [PMID: 21364738 PMCID: PMC3041749 DOI: 10.1371/journal.pone.0016765] [Citation(s) in RCA: 776] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/03/2011] [Indexed: 11/19/2022] Open
Abstract
The field of synthetic biology promises to revolutionize biotechnology through the design of organisms with novel phenotypes useful for medicine, agriculture and industry. However, a limiting factor is the ability of current methods to assemble complex DNA molecules encoding multiple genetic elements in various predefined arrangements. We present here a hierarchical modular cloning system that allows the creation at will and with high efficiency of any eukaryotic multigene construct, starting from libraries of defined and validated basic modules containing regulatory and coding sequences. This system is based on the ability of type IIS restriction enzymes to assemble multiple DNA fragments in a defined linear order. We constructed a 33 kb DNA molecule containing 11 transcription units made from 44 individual basic modules in only three successive cloning steps. This modular cloning (MoClo) system can be readily automated and will be extremely useful for applications such as gene stacking and metabolic engineering.
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14
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Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS One 2011. [PMID: 21364738 DOI: 10.1371/journal.pone.016765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
The field of synthetic biology promises to revolutionize biotechnology through the design of organisms with novel phenotypes useful for medicine, agriculture and industry. However, a limiting factor is the ability of current methods to assemble complex DNA molecules encoding multiple genetic elements in various predefined arrangements. We present here a hierarchical modular cloning system that allows the creation at will and with high efficiency of any eukaryotic multigene construct, starting from libraries of defined and validated basic modules containing regulatory and coding sequences. This system is based on the ability of type IIS restriction enzymes to assemble multiple DNA fragments in a defined linear order. We constructed a 33 kb DNA molecule containing 11 transcription units made from 44 individual basic modules in only three successive cloning steps. This modular cloning (MoClo) system can be readily automated and will be extremely useful for applications such as gene stacking and metabolic engineering.
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15
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Engler C, Marillonnet S. Generation of families of construct variants using golden gate shuffling. Methods Mol Biol 2011; 729:167-81. [PMID: 21365490 DOI: 10.1007/978-1-61779-065-2_11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Current standard cloning methods based on the use of restriction enzymes and ligase are very versatile, but are not well suited for high-throughput cloning projects or for assembly of many DNA fragments from several parental plasmids in a single step. We have previously reported the development of an efficient cloning method based on the use of type IIs restriction enzymes and restriction-ligation. Such method allows seamless assembly of multiple fragments from several parental plasmids with high efficiency, and also allows performing DNA shuffling if fragments prepared from several homologous genes are assembled together in a single restriction-ligation. Such protocol, called Golden Gate shuffling, requires performing the following steps: (1) sequences from several homologous genes are aligned, and recombination sites defined on conserved sequences; (2) modules defined by the position of these recombination sites are amplified by PCR with primers designed to equip them with flanking BsaI sites; (3) the amplified fragments are cloned as intermediate constructs and sequenced; and (4) finally, the intermediate modules are assembled together in a compatible recipient vector in a one-pot restriction-ligation. Depending on the needs of the user, and because of the high cloning efficiency, the resulting constructs can either be screened and analyzed individually, or, if required in larger numbers, directly used in functional screens to detect improved protein variants.
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Affiliation(s)
- Carola Engler
- Icon Genetics GmbH, Biozentrum Halle, Halle, Germany
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A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008; 3:e3647. [PMID: 18985154 PMCID: PMC2574415 DOI: 10.1371/journal.pone.0003647] [Citation(s) in RCA: 1501] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 10/20/2008] [Indexed: 11/19/2022] Open
Abstract
Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called ‘Golden Gate’ cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation.
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A high-throughput and single-tube recombination of crude PCR products using a DNA polymerase inhibitor and type IIS restriction enzyme. J Biotechnol 2008; 137:1-7. [DOI: 10.1016/j.jbiotec.2008.07.1816] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 06/22/2008] [Accepted: 07/07/2008] [Indexed: 11/20/2022]
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18
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An X, Lu J, Huang JD, Zhang B, Liu D, Zhang X, Chen J, Zhou Y, Tong Y. Rapid assembly of multiple-exon cDNA directly from genomic DNA. PLoS One 2007; 2:e1179. [PMID: 18000550 PMCID: PMC2048664 DOI: 10.1371/journal.pone.0001179] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 10/18/2007] [Indexed: 11/18/2022] Open
Abstract
Background Polymerase chain reaction (PCR) is extensively applied in gene cloning. But due to the existence of introns, low copy number of particular genes and high complexity of the eukaryotic genome, it is usually impossible to amplify and clone a gene as a full-length sequence directly from the genome by ordinary PCR based techniques. Cloning of cDNA instead of genomic DNA involves multiple steps: harvest of tissues that express the gene of interest, RNA isolation, cDNA synthesis (reverse transcription), and PCR amplification. To simplify the cloning procedures and avoid the problems caused by ubiquitously distributed durable RNases, we have developed a novel strategy allowing the cloning of any cDNA or open reading frame (ORF) with wild type sequence in any spliced form from a single genomic DNA preparation. Methodology Our “Genomic DNA Splicing” technique contains the following steps: first, all exons of the gene are amplified from a genomic DNA preparation, using software-optimized, highly efficient primers residing in flanking introns. Next, the tissue-specific exon sequences are assembled into one full-length sequence by overlapping PCR with deliberately designed primers located at the splicing sites. Finally, software-optimized outmost primers are exploited for efficient amplification of the assembled full-length products. Conclusions The “Genomic DNA Splicing” protocol avoids RNA preparation and reverse transcription steps, and the entire assembly process can be finished within hours. Since genomic DNA is more stable than RNA, it may be a more practical cloning strategy for many genes, especially the ones that are very large and difficult to generate a full length cDNA using oligo-dT primed reverse transcription. With this technique, we successfully cloned the full-length wild type coding sequence of human polymeric immunoglobulin receptor, which is 2295 bp in length and composed of 10 exons.
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Affiliation(s)
- Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jun Lu
- Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Jian-dong Huang
- Department of Biochemistry, The University of Hong Kong, Hong Kong Special Administrative Region (SAR), China
- * To whom correspondence should be addressed. E-mail: (JH); (YT)
| | - Baozhong Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dabin Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jinhui Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- * To whom correspondence should be addressed. E-mail: (JH); (YT)
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Li X, Qiu Y, Shen Y, Ding C, Liu P, Zhou J, Ma Z. Splicing together different regions of a gene by modified polymerase chain reaction-based site-directed mutagenesis. Anal Biochem 2007; 373:398-400. [PMID: 18022376 DOI: 10.1016/j.ab.2007.10.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/12/2007] [Accepted: 10/16/2007] [Indexed: 10/22/2022]
Abstract
A modified polymerase chain reaction (PCR)-based site-directed mutagenesis method used to splice together different regions of a gene by deleting hundreds of nucleotides of undesired sequences is described. This method was inspired by a PCR-based site-directed mutagenesis method developed by Stratagene (La Jolla, CA, USA); the procedure and primer design were modified to enable the method to generate deletions several hundreds of nucleotides in length with an efficiency of 80-100%, and to delete two DNA fragments simultaneously in a single PCR. This method should be useful for deletion of large DNA fragments from a gene.
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Affiliation(s)
- Xiangdong Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200232, People's Republic of China
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20
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Abstract
Gene fusion technology is a key tool in facilitating gene function studies. Hybrid molecules in which all the components are joined precisely, without the presence of intervening and unwanted extraneous sequences, enable accurate studies of molecules and the characterization of individual components. This article reviews situations in which seamlessly fused genes and proteins are required or desired and describes molecular approaches that are available for generating these hybrid molecules.
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Affiliation(s)
- Quinn Lu
- Gene Expression and Protein Biochemistry, Discovery Research, GlaxoSmithKline, Mail Code: UE0548, 709 Swedeland Road, King of Prussia, PA 19406, USA.
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21
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Bornhorst JA, Deibel MA, Mulnix AB. Gene amplification by PCR and subcloning into a GFP-fusion plasmid expression vector as a molecular biology laboratory course*. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 32:173-182. [PMID: 21706718 DOI: 10.1002/bmb.2004.494032030345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A novel experimental sequence for the advanced undergraduate laboratory course has been developed at Earlham College. Utilizing recent improvements in molecular techniques for a time-sensitive environment, undergraduates were able to create a chimera of a selected gene and green fluorescent protein (GFP) in a bacterial expression plasmid over the course of a single semester in a weekly 3-h laboratory period. Students designed PCR primers for amplification of the selected gene using computational DNA sequence analysis tools. During the experimental portion of the course, students amplified and ligated the target DNA into a commercially available GFP expression vector. Following transformation of the ligation product, plasmids were harvested from the resulting bacterial colonies and were analyzed by restriction digestion to confirm the creation of the chimeric GFP-DNA. This course gave students valuable experience with commonly used molecular techniques in an authentic research project. In addition, students gained experience with experimental design and execution. The techniques presented here are flexible and can be generalized for use with almost any DNA sequence and expression vector. This series also serves as an example of how faculty can adapt their ongoing research projects to the undergraduate laboratory.
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Affiliation(s)
- Joshua A Bornhorst
- Department of Biology, Earlham College, Richmond, Indiana 47374; Department of Pathology, University of Utah, Salt Lake City, Utah 84108
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22
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Abstract
Retroviruses have been used for many years as vectors for human gene therapy as well as for making transgenic animals. However, the efficient insertion of genes by retroviruses is often complicated by transcriptional inactivation of the retroviral long terminal repeats (LTRs) and by the production of replication-competent retroviruses (RCR). Solutions to these and other difficulties are being found in modular vectors, in which the desirable features of different vector systems are combined. Examples of synergistic vectors include virosomes (liposome/virus delivery), adeno-retro vectors, and MLV/VL30 chimeras. As gene delivery systems become increasingly complex, methodology is also needed for precise assembly of modular vectors. Gene self-assembly (GENSA) technology permits seamless vector construction and simultaneous, multifragment assembly.
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Affiliation(s)
- F Solaiman
- Creighton University School of Medicine, Omaha, Nebraska, USA
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23
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Birikh KR, Lebedenko EN, Boni IV, Berlin YA. A high-level prokaryotic expression system: synthesis of human interleukin 1 alpha and its receptor antagonist. Gene 1995; 164:341-5. [PMID: 7590354 DOI: 10.1016/0378-1119(95)00488-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Synthetic intronless genes, coding for human interleukin 1 alpha (IL 1 alpha) and interleukin 1 receptor antagonist (IL1ra), have been expressed efficiently in a specially designed prokaryotic vector, pGMCE (a pGEM1 derivative), where the target gene forms the second part of a two-cistron system. The first part of the system is a translation enhancer-containing mini-cistron, whose termination codon overlaps the start codon of the target gene. In the case of the IL1 alpha gene, the high expression level is largely due to the direct efficient translation initiation at the second cistron, whereas with the IL1ra gene in the same system, the proximal translation initiation region (TIR) provides a high level of coupled expression of the target gene. Thus, pGMCE is a potentially versatile vector for direct prokaryotic expression.
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Affiliation(s)
- K R Birikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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[7] PCR-mediated gene synthesis. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1043-9471(06)80085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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25
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26
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27
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Birikh KR, Plutalov OV, Schwartz EI, Devi PS, Berlin YA. A modified approach to identification of the sickle cell anemia mutation by means of allele-specific polymerase chain reaction. Hum Mutat 1992; 1:417-9. [PMID: 1301951 DOI: 10.1002/humu.1380010511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.
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Affiliation(s)
- K R Birikh
- M.M. Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
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