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Phytobricks are standardized DNA parts for plants that can be assembled hierarchically into transcriptional units and, subsequently, into multigene constructs. Phytobricks each contain the sequences of one or more functional elements that comprise eukaryotic transcription units, with sequence features that enable them to be used interchangeably in one-step cloning reactions to facilitate combinatorial assembly. The simplicity and efficiency of this one-step reaction has enabled Phytobrick assembly to be miniaturized and automated on liquid handing platforms. In this method, we describe how to design and construct new Phytobricks as well as how to assemble them in both manual and nanoscale automated one-step reactions. Finally, we describe a high-throughput method for sequence verification of assembled plasmids.
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http://dx.doi.org/10.1007/978-1-0716-0908-8_11 | DOI Listing |
Methods Mol Biol
October 2024
Brightmont Academy, Seattle, WA, USA.
Synthetic biology, also known as engineering biology, is an interdisciplinary field that applies engineering principles to biological systems. One way to engineer biological systems is by modifying their DNA. A common workflow involves creating new DNA parts through synthesis and then using them in combination with other parts through assembly.
View Article and Find Full Text PDFACS Synth Biol
December 2023
Intelligent Software & Systems, Raytheon BBN Technologies, 10 Moulton Street, Cambridge, Massachusetts 02138, United States.
The design and construction of genetic systems, in silico, in vitro, or in vivo, often involve the handling of various pieces of DNA that exist in different forms across an assembly process: as a standalone "part" sequence, as an insert into a carrier vector, as a digested fragment, etc. Communication about these different forms of a part and their relationships is often confusing, however, because of a lack of standardized terms. Here, we present a systematic terminology and an associated set of practices for representing genetic parts at various stages of design, synthesis, and assembly.
View Article and Find Full Text PDFJ Exp Bot
July 2023
Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable.
View Article and Find Full Text PDFPlant Genome
June 2023
Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research.
View Article and Find Full Text PDFACS Synth Biol
September 2022
Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Camino de Vera s/n, Valencia 46022, Spain.
Programmable transcriptional factors based on the CRISPR architecture are becoming commonly used in plants for endogenous gene regulation. In plants, a potent CRISPR tool for gene induction is the so-called dCasEV2.1 activation system, which has shown remarkable genome-wide specificity combined with a strong activation capacity.
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