BioXp Tiles | Synthesis of DNA Fragments | SGI-DNA

BioXp™ Tiles

Build high-quality genes and gene libraries, hands-free, on your benchtop

The BioXp™ System generates high-quality, linear DNA fragments in an overnight run on the benchtop. Standard BioXp™ Tile assembly incorporates an error-correction step to improve sequence fidelity and purification, ensuring that BioXp™ Tiles are high-quality DNA fragments.

BioXp™ Degenerate Library Tiles are also available. These Degenerate Library Tiles utilize IUPAC codes for a reliable and economical way to generate variants-of-interest quickly.

BioXp™ 3200 System benefits:

  • Fast — Builds DNA fragments faster than conventional methods
  • Efficient  — Generate custom DNA fragments in a hands-free overnight run
  • Robust — Delivers de novo DNA assembly across a wide section of the complexity continuum
  • Versatile — Works with multiple cloning and genomics workflows

The BioXp™ system reliably assembles DNA fragments ranging from 300 bp to 1800 bp with a wide range of GC content. The BioXp™ system provides the ability to precisely build constructs without cumbersome traditional methods or relying on outside service agencies and their off-target delivery schedules. This benchtop genomic workstation provides 1 to 32 custom DNA fragments in each run, allowing up to 155 DNA fragments or 279,000 bases to be built per week.

BioXp™ Tiles types

BioXp™ Tiles, True ends are DNA fragments that are built precisely to the sequence you provide. Design constructs for compatibility with your downstream application.

BioXp™ Degenerate Library Tilesare DNA fragments that utilize degenerate base providing a simple and efficient way to build libraries. Standard Degenerate Library Tiles are 300 – 800 bp in length and include up to 12 degenerate bases. Larger sizes or the inclusion of more degenerate bases are also available.

BioXp™ Tiles, GA ends are available to help standardize downstream applications. Tiles with GA ends enable direct cloning into SGI-DNA pUCGA cloning vectors using Gibson Assembly® Cloning. To submit BioXp™ Tiles, GA ends, simply submit your sequence of interest. These Tiles automatically include unique 30-bp ends at no additional cost to you.

Other Available BioXp™ products:

BioXp™ Libraries

pUCGA 1.0 Cloning

BioXp™ Custom Cloning

How It Works

Ordering BioXp™ reagents for building genes is simple.

After your BioXp™ System is installed in your laboratory or core facility, you may place an order to build Tiles on the instrument.

BioXp™ Tile Reagents with specially designed oligonucleotide pools unique for your DNA fragments are shipped to you in approximately 3–5 business days. You may load the instrument the same day you receive your order and have BioXp™ Tiles ready the following morning.

Loading the BioXp™ machine is simple.

Follow the instructions with each kit that provides step-by-step instruction for each of the components.

BioXp™ Kit Components include:

  • Customized Oligo vault
  • Reagent plate
  • Recovery plate
  • 50 and 200 µl tips
  • DNA purification strip
  • Fresh 70% ethanol

After loading the instrument, used the instrument touch screen to begin the run. DNA assembly runs generally take 14 – 17 hours for standard Tiles (up to 1.8 kb) or approximately 6 hours for Degenerate Library Tiles, depending on the number of reactions in your run.

The next day, collect your BioXp™ Tiles or Degenerate Library Tiles, which are provided in 45 µL of TE, analyze the fragments, and proceed to your downstream application, such as cloning, off-line sequencing, and further assembly into larger constructs.

See BioXp Tutorials
Deck of BioXp 3200 DNA synthesis machine
The BioXp™ instrument is easy to load for virtually hands-free genomic applications.

Cloning BioXp™ Tiles

BioXp™ Tiles can be cloned using the Gibson Assembly® method and other cloning methodologies. Fragment design is key to successfully cloning your DNA fragment. Simply design your BioXp™ Tiles to be compatible for your intended cloning method.

BioXp™ Tiles are purified using magnetic bead methods and are ready-to-use. We recommend performing gel electrophoresis of your BioXp™ Tiles to determine the overall success of each assembly run. Gel purification prior to downstream use is often helpful if your final product has multiple smaller assemblies in the final reaction.

Assembling Larger DNA Fragments

BioXp™ Tiles can be assembled to build larger constructs that have been designed accordingly using the Gibson Assembly® HiFi Kit or the Gibson Assembly® Ultra kit. It is important to design the DNA fragments appropriately for efficient downstream Hierarchical assembly. We recommend BioXp™ Tiles with true ends for assembling into larger fragments, learn more by reading this application note titled "Build Custom Designed Synthetic Genes in Your Lab Quickly and Efficiently."

Other Applications of BioXp™ Products

The BioXp™ System provides a unique way to utilize synthetic genomic tools, such as the following:

  • Library construction
  • Site-Directed Mutagenesis
  • Building larger DNA constructs
  • Gene construction and modification
  • Build templates for use in multiplex PCR

Performance

The BioXp™ System has the capacity to build up to 32 DNA fragments in a single run. DNA fragments are provided in 45 µl of TE and are ready for cloning, off-line sequencing, and further assembly into larger constructs.

Reliable Results Across a Range of DNA Fragments

The BioXp™ system provides consistent results across a range of DNA sequences. BioXp™ Tiles from 400 bp to 1.8 kb and consisting of 40 – 60% GC content were assembled on the BioXp™ System. Following the overnight run, an aliquot of each BioXp™ Tile was analyzed by gel electrophoresis. The image shows consistent results across a wide size and GC content range.

Construct Results

Construct Size (bp)
Control 1476
1 430
2 660
3 890
4 1120
5 1350
6 1580
7 1810
ladder 2-log
BioXp 3200 GC Panel gel

BioXp™ Compatibilities

Building DNA fragments successfully depends on the overall characteristics of the DNA sequence and the protocol. Two factors that influence successful de novo assembly are the length and average GC content of the sequence. In addition, dynamics such as tandem repeats and other internal complexities can make assembly challenging.

Each sequence submitted for building on the BioXp™ System is reviewed upon submission to ensure it has a high probability of success. If a sequence is outside the current capabilities adding the sequence to your Tile order is at your discretion. You may also request a quote to have complex Tiles built for you in the SGI-DNA Custom Synthesis lab.

BioXp™ Degenerate Library Tiles are also analyzed in their wild type sequence to check for overall complexity. Variants are then analyzed for successful build when using degenerate bases. Guidelines for building BioXp™ Degenerate Library Tiles include:

  • No degenerate bases within 60 bases of the terminal ends
  • No more than 9 degenerate bases in a row

BioXp™ Degenerate Libraries will ideally be between 300 and 800 base pairs long and will typically realize >85% accuracy in conserved regions of the library. Degenerate libraries larger than 800 – 1000 bp may begin to lose accuracy in the conserved regions of the DNA. This dynamic could potentially impact your results/project.

BioXp™ Tile Compatibilities

Size Ranges 400 bp to 1800 bp DNA Fragments, larger tiles are allowed
Composition A, T, C or G residues only
Ave GC% 20 – 70% GC for 400 bp – 1 kb; 40 – 60% GC for 1 kb – 1.8 kb
Sequence Complexity Sequence analysis will determine best approach for construction and assembly. Custom DNA synthesis performed in our services laboratory is available for DNA is outside the region of compatibility.
Amount Approximate yield: 200 ng of purified, linear dsDNA PCR product.
Format 96 well plate format in final volume of 45 µl in TE.

BioXp™ Degenerate Library Tile Guidelines

Size Ranges 300 bp to 800 bp are ideal, larger libraries are allowed
Composition Any IUPAC code designation
Ave GC% 20 – 70% GC for 400 bp – 1 kb; 40 – 60% GC for 1 kb – 1.8 kb
Sequence Complexity Sequence analysis will determine best approach for construction and assembly. Custom Services is available to discuss optimization if DNA is outside of desired compatibility.
Amount Approximate yield: 200 ng of purified, linear dsDNA PCR product.
Format 96 well plate format in final volume of 45 µl in TE.

BioXp™ Tiles Analysis

It is important to run the BioXp™ Tiles on a gel to evaluate the success of the assembly. Gel examples are shown below. The image on the left shows the assembled fragment (BioXp™ Tile) clearly distinguishable without the presence of secondary bands. If you observe similar results, proceed directly to downstream applications of your choice. The gel on the right shows multiple bands. In this case, we recommend gel-purifying the Tile band to remove byproducts before proceeding.

BioXp™ Cloning is also available

Build high-quality genes and clone directly into a vector in a hands-free overnight run

The Cloning module for the BioXp™ System generates up to 32 unique, high-quality clones from custom-designed oligonucleotide pools and reagents in an overnight run on a personal laboratory benchtop.

Sequencing to Identify Error Free Clone

Cloning Full Length Fragments

BioXp™ Tiles are often cloned and colonies are picked for sequence verification of an error-free-clone. The number of clones to pick for sequencing is dependent on the size and characteristics of the DNA insert. After DNA assembly is complete, we recommend performing gel analysis to determine the success of assembly and to confirm the presence of full-length BioXp™ Tile.

If your DNA fragment is NOT a single product of the expected size as determined by gel analysis, we recommend gel purifying the fragment migrating at the expected size prior to cloning. You may also choose to clone directly without gel purification, but you will need to sequence additional clones to find an error-free clone.

We recommend the following as a guideline to determine how many full- length clones to pick to find an error-free clone within a 95% likelihood.

Full-Length Clones to Sequence to Identify an Error-Free-Clone

DNA fragment size # Clones to pick (full length)
< 1000 bp 2 to 3
1000 – 1500 bp 3 to 5
1501 – 1800 bp 4 to 6

Ordering

Ordering a BioXp™ System

To order a BioXp™ System, please email us at info@sgidna.com. You can also See a Virtual Demo by clicking on the button below.

See Virtual Demo

Demos

Please contact info@sgidna.com to request a demonstration.

Pilot Program

Our pilot program allows you to order sequences that are built on SGI-DNAs in house BioXp™ system. We ship you the resulting product for analysis. These sequences are available to you for a special price. SGI-DNA ships you the resulting product for you to analyze when considering a BioXp™ purchase. Please contact info@sgidna.com to make your request to participate in our pilot program.

Ordering BioXp™ Reagents

BioXp™ System reagents are custom built to your sequence specification.
The ordering process begins by entering the desired sequences into the BioXp™ ordering portal located on sgidna.com or following the link below.

To Place an Order for BioXp™ Reagents:

  • Log into your SGI-DNA account
  • Click on BioXp™ Reagents
  • Complete required information
  • Submit FASTA file or text file containing your sequences
  • Review the sequences for BioXp™ compatibility
  • Select/Confirm sequences to order
  • Provide payment information
  • Submit order

BioXp™ Reagents are shipped to you in approximately 3 – 5 business days in the US. You may load the instrument the same day you receive your order and have BioXp™ Tiles ready the following morning.

BioXp™ Tile kit includes:

  • Module A: BioXp™ Oligo Vault
  • Module B: BioXp™ DNA Assembly Kit

Additional materials required include (provided by customer):

  • Freshly made 70% Ethanol (minimum 12 ml)
  • BioXp™ Tips; 3 ea of 50 µl and 1 ea of 200 µl Tips
    Order tips by logging into your SGI-DNA account, click to order BioXp™ Tips and Accessories. You can also follow the links provided at the final pages of ordering BioXp™ reagents.
BioXp™ Oligo Vault Kit
BioXp™ Oligo Vault and +4C Reagents
BioXp™ 1.8 kb DNA Assembly Reagents
BioXp™ -20C Reagents

BioXp™ PreChecker (Optional)

You can check your sequences for compatibility with the BioXp™ System using the PreCheck prior to placing your order. This PreCheck tool provides you quick results regarding BioXp™ compatibilities for your sequences. It also provides detailed information for sequences that are deemed outside the BioXp™ compatibility.

Sequences that PASS BioXp™ compatibility standards (GREEN) have a high likelihood of successful assembly on the instrument (>85%). Those that do NOT PASS (RED) have a lower success rate (~50%). Sequences that do not pass may be included in your BioXp™ order at your discretion.

Other Available BioXp™ products:

pUCGA 1.0 Cloning

BioXp™ Custom Cloning

BioXp™ NGS Library Construction

Fill out my online form.