J5 DNA ASSEMBLY DESIGN AUTOMATION SOFTWARE PDF

Part of the Methods in Molecular Biology book series MIMB, volume Abstract Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design combinatorial scar-less DNA assembly protocols using the web-based software j5. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost—benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.

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Jay D Keasling Research Article pubs. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries.

Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E.

The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar- less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.

KEYWORDS: DNA assembly, design automation, BioCAD, combinatorial library D eveloping the ability to construct large and functionally complex DNA sequences, such as those encoding biosynthetic pathways, genetic circuits, partially synthetic however, designing optimized protocols for scar-less multipart DNA assembly methods is often tedious, laborious, and error- prone.

Toward addressing this challenge, two recent methodo- chromosomes,1 or synthetic genomes,2 will be crucial for logical developments, MoClo18 and GoldenBraid,19 report engineering microbes, plants and mammalian cells for vaccine, consistent design patterns employing standardized subcloning biofuel, and bio-based chemical production. While in DNA assembly4,5 have introduced protocols that offer elegant, these techniques introduce predetermined sets of 4 substantial time- and cost-savings over traditional multiple bp assembly junction scars, may require elaborate plasmid cloning-site approaches, especially when constructing long libraries MoClo employs approximately 35 intermediate DNA sequences that contain multiple genes.

These methods can offer benefits over assembly without prerequisite plasmid libraries. BioBrick-style assembly,16,17 for which 6 base pair scars result at every assembly junction and only two fragments can be Received: October 4, assembled per step. A Top level design task menu. For each input file, users may opt to upload a new file or to reuse the version they last updated on the server.

As the price of DNA synthesis decreases, the cost of assembly strategies to mitigate putative off-target assembly outsourcing end-to-end construction or perhaps portions products, and to enforce design specification rules. For thereof becomes comparable to that of in-house cloning. Even as inexpensive synthesis supplants single services see Supplementary Table S1. Selecting one of two N-terminal enabling alternative graphical user interfaces or third-party signal peptides, either a long or short linker sequence, and applications to exploit the full j5 feature set.

With no a priori expectation of which how-to examples, in-depth descriptions of input and output variants might fold functionally, localize correctly, and degrade files, detailed documentation of the j5 XML-RPC web-services most efficiently, one must try them all. Leveraging a API, error-message explanations, and experimental protocols combinatorial assembly approach allows the researcher to for the aforementioned DNA construction techniques.

The restriction sites. In a more ambitious example of a gene input format is a comma separated value CSV file that can be pathway with 3 orthologs for each gene or 59, manipulated by any spreadsheet e. Information online.

Each part is defined by a start and an end To the best of our knowledge, j5 is the first DNA assembly base pair within a source sequence and by an orientation on the design tool for any assembly method including BioBricks that top or bottom strand. After defining the parts to be assembled, the user then sequentially orders and sets the direction forward or reverse of each of the parts in the final target construct s as shown in Figure S1C for a single construct and in Figure S1D for a combinatorial library.

The user may also dictate Eugene biological design specification rules. For example, if prior research demonstrated that a long linker sequence must follow tag sig1 for proper GFPuv localization see Figure 3A , Eugene rules can be specified to ensure that sig1 and the long linker are always constructed together, eliminating the two of the eight possible combinations that have the tag sig1 followed by the short linker.

To determine the most cost-effective assembly strategy, j5 uses Algorithm S1, based on the user-adjustable cost analysis parameters shown in Figure S1F.

Given an ordered list of parts to assemble, Algorithm S1 utilizes alternative cost comparison and iterative DNA synthesis fragment extension to determine for each part if direct DNA synthesis, PCR, or oligo embedding i. Algorithm Figure 2. Primer3 does not return a sequence design if none of the sequences it considers meets its design specifications. When homology sequence derived from the adjacent part s. Once this happens, it is necessary to adjust the design constraint e.

Algorithm S2 removes this burden from the user, other i. If any BLAST-identified incompatible constraints issuing warning messages as it does so that lead sequences exceed a user-specified Tm threshold see Figure to the rejection of all considered sequences.

For the design shown in Figure 2A, Algorithm S2 progressively relieved S1F , Algorithm S3 identifies contiguous sets of compatible Primer3 of 6 design constraints and eliminated less optimal assembly pieces and then designs a hierarchical assembly homology sequence pairs. The flanking sequence to append to process, mitigating the risk of assembling off-target products each terminus of each part, then, is the portion of the optimized see Figure S2C and bolstering correct assembly efficiency.

The type IIs endonuclease e. For each assembly junction, there may be multiple overhang sequences to choose from that would result in the same assembly product see Figure S2E. Algorithm S4 searches through all combinations of putative overhangs and selects the set of overhang sequences that are compatible with themselves and each other, are as neutral as possible, and satisfy a user-determined maximum number of off-target overhang base-pair matches see Figures S1F, S2D.

Algorithm S4 uses a branched search strategy that is pruned to avoid redundant paths and paths that will not lead to compatible sets of overhangs. For the two-fragment two overhang combinatorial library design shown in Figure 3A, it was necessary to evaluate 25 overhang combinations before identifying the optimal compatible set of overhang sequences. We are currently pursuing a more complicated metabolic Figure 3. Combinatorial Golden Gate assembly design. A Schematic pathway combinatorial library design requiring 11 assembly of a portion of the combinatorial Golden Gate DNA assembly task.

Without the use of Algorithm S4, identifying the schematically depicted as a rectangle labeled with an arrowhead compatible set of overhang sequences for this metabolic pointing to the 4-bp Golden Gate overhang sequence, here shown in pathway design would not be possible. For the design shown in Figure 3A, Algorithm S2 tively. For those parts for which the most fragments. This is a direct synthesis fragments to be ordered see Figure S3A,B. Algorithm S5 makes it easy combinatorial variant Figure S3F.

Finally, j5 appends the for the user to take advantage of thermocycler annealing 17 dx. In preparation required to select the appropriate temperatures and place the for assessing the ClpX protease dependence of the assembled PCR reactions accordingly.

Following a previously described optimized thermocycler block annealing temperature gradients strategy24 schematically depicted in Figure S8, this deletion Figure S5D , as schematically depicted in Figure S5E. Control files for other robotics deletion efforts. The resulting strains were conditionally Plasmid Construction. To show that j5 can design assembly induced with arabinose, and the relative GFPuv fluorescence protocols for the SLIC,6 Gibson,7 and CPEC9 methods, was measured for each plasmid variant for each genetic plasmid pNJH was designed as a four fragment assembly, background for each induction condition Figure 4.

For each of the three methods, DNA electro- for any of the strains. Summary and Conclusion. The fragments to be assembled were and process optimization as part of an integrated synthetic PCR-derived, contrasting with the previously reported Golden biology platform Figures 5 and S9 , while fully preserving scar- Gate approach11,12 that utilizes plasmid-borne fragments.

DNA less and multipart assembly without prerequisite plasmid electrophoresis of the six j5-designed, PCR amplified fragments libraries. These results demonstrate that j5 can be tion. Although j5 does not currently design protocols for DNA used to design successful combinatorial Golden Gate variant Assembler,14,15 USER,13 or combinatorial assembly protocols protocols.

These data demonstrate the utility of employing a combinatorial approach to identify assemblies of genetic elements yielding a functional DNA device. Future advances in DNA assembly methodology will also significantly impact the cost-optimal Figure 4.

Experimental characterization of the assembled GFPuv process calculus and drive the continual development of j5.

In variants. The resulting variants will be cost-effective. Error bars show the services and may also make possible the integration of standard error of four biological and two technical replicates.

Inset combinatorial DNA library construction, clonal transformation, table presents the localization tag, linker, and ssrA degradation tag and functional assay into an affordable benchtop device. Finally, j5 specializes in DNA assembly protocol design and as such is not intended to facilitate the biological design of the DNA to be assembled. For example, j5 does not assist the selection of the genetic expression systems or metabolic enzymes to be assembled into functional biosynthetic pathways.

Figure 5. These algorithms could also cost to noncommercial e. Exploring the entire Commercial use is available through the Technology Transfer combinatorial space of fusion proteins, overexpression schemes, Department of Lawrence Berkeley National Laboratory ttd genetic pathways, etc.

Kinney for providing plasmid command-line interfaces are also available. Strain and Sequence Availability. Andrews-Pfannkoch, C. Supporting tables, methods, algorithms, and figures. This 5 Hillson, N. Bio-molecular Circuits Koeppl, H. E-mail: 7 Gibson, D.

Author Contributions 9 Quan, J. H and R. R cloning of complex gene libraries and pathways. PLoS One 4, e R performed all experiments, 10 Quan, J. R, and cloning for high-throughput cloning of complex and combinatorial J.

K wrote the manuscript. DNA libraries. Department of Energy one step, precision cloning method with high throughput capability. Contract No. Nucleic Acids Res. Notes 14 Shao, Z. Genome-Linked Application for Metabolic Maps. Lehvaslaiho, H. BioBrick vectors from BioBrick parts.

Genome Res. Marillonnet, S. PLoS One 6, e Methods Enzymol.

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Jay D Keasling Research Article pubs. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar- less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. KEYWORDS: DNA assembly, design automation, BioCAD, combinatorial library D eveloping the ability to construct large and functionally complex DNA sequences, such as those encoding biosynthetic pathways, genetic circuits, partially synthetic however, designing optimized protocols for scar-less multipart DNA assembly methods is often tedious, laborious, and error- prone.

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j5 DNA Assembly Design Automation

ACS Synth Biol. Epub Dec Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.

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