Your colleagues submitted interesting questions during the webinar, “GeneArt® Elements™ Vector Construction and Combinatorial Parts,” so we’ve collected and answered them here.
Find the answer quickly by clicking your desired question.
Q-Are vector construction orders synthesized from scratch, or do you re-use certain GeneArt® Elements™ DNA parts?
A- We give our customers maximal flexibility in terms of their vector design, and in most cases this requires the complete synthesis of the DNA parts/vector. For many GeneArt® Elements™ parts it would not make sense to have them pre-synthesized because they are too short (for example, ribosomal binding sequence), and it would be challenging to have them fused to longer DNA parts.
Q- Are there any design restrictions?
A- No, all DNA parts can be combined in all possible ways. However, vector functionality requires that you include at least one resistance marker and an origin of replication from the offered GeneArt® Elements™ collection. For more information, please refer to our vector construction and ordering information.
A- Currently there isn’t optimization functionality within the vector construction application. However, ORFs can be optimized online within the gene synthesis application of the GeneArt® portal and then copied into the respective custom part.
Q- What exactly are your stuffer sequences in the vectors? How do you know how long the stuffer sequence has to be at one specific location?
A- There isn't currently a good technique to predict the length that is required for stuffer sequences. It has been our experience that between some DNA parts stuffer sequences are not required (e.g., between ori and resistance markers). To facilitate the vector construction process, we have included vector templates that include stuffer sequences that work between the relevant parts. You can make use of the templates within the online GeneArt® portal by simply replacing the DNA parts that you want to omit with parts from the repository or your own custom parts. More information can be found in the GeneArt® Portal Tutorial.
Q- Why is 12 kb the limit for vector construction services?
A- The limit for the GeneArt® Elements™ Vector Construction is based on technical reasons within our standardized production unit. We are able to produce much longer vectors, but these are custom services instead of GeneArt® Elements™ Vector Construction applications.
Q- Can you export your construct in FASTA format?
A- Yes, construct sequences can be exported as .gb files.
Q- What is the price to construct a custom vector?
A-The price is 0.59 USD per bp.
Q- Can Combinatorial Parts Assembly also be ordered via the GeneArt® portal?
A- No. Currently, orders for GeneArt® Elements™ Combinatorial Parts Assembly can only be fulfilled by completing the questionnaire and sending it to firstname.lastname@example.org
Q- How many different combinations of DNA parts can you provide?
A- Pooled libraries provide up to 1x 106 different constructs. Learn more about Combinatorial Parts Assembly.
Q- Is there any limit to the insert size for Combinatorial Parts Assembly?
A- No. There is basically no limit to the insert size. However, feasibility will be checked on a case by case basis.
Q- What is the delivery time for a Combinatorial Parts Assembly project?
A- The delivery time for GeneArt® Elements™ Combinatorial Parts Assembly is project-specific. It depends on the complexity of the project; for example, the number of variants being requested or how many building blocks need to be created.
Q- What is the price for a Combinatorial Parts Assembly?
A- Pricing is project-specific and depends on the setup of the project. It is affected by the number and length of de novo synthesized building blocks, how often those can be re-used, and which assembly technology is required within production.
Q- How do you quality control the libraries?
A- Quality control methods depend on the nature of the deliverable. If you request separate constructs, they will be completely sequence verified. However, if the diversity of the library is very high (for example, greater than 1 x 104) and a pool of clones will be delivered, then a peer-group of library specimens will be sequenced in order to verify the library quality.
Q- Have you used next-generation sequencing to verify combinatorial libraries?A- Yes, Ion Torrent™ next-generation sequencing technology is part of the quality control process when necessary.
Q- Do you provide Combinatorial Parts Assembly in formats other than E. coli plasmids or cells ?
A- No, we are currently using only E. coli in our standard production process for GeneArt® Elements™ Combinatorial Parts Assembly. This means that the plasmids we are using need to be at least shuttle vectors that allow for propagation in E. coli.
Q- Do you have binary vector (plant transformation) components in your library? Will this system work for plants? Do you have any positive controls to use in plants?
A- Currently, we do not have any GeneArt® Elements™ available for plants. However, you could insert those as custom DNA parts.
Q- Will we have access to a set of today's presentation's slides?
A- Yes, access the recorded version of the presentation here.