pUCGA 1.0 Cloning

Build high-quality genes and clone into a vector, hands-free, on your benchtop

The pUCGA 1.0 Cloning module for the BioXp™ System has been developed to generate up to 32 unique, high-quality, linear DNA clones from custom-designed oligonucleotide pools and reagents in an overnight run on a personal laboratory benchtop.

BioXp™ 3200 System Cloning is:

  • Fast — Operating with a quicker turnaround time than conventional methods
  • Efficient  — Generates up to 32 custom DNA clones in an overnight run
  • Robust — Delivers de novo DNA fragment into vectors across a wide section of sequences
  • Automated — After loading the instrument deck, the process is completely hands-free

Other Available BioXp™ products:

How It Works

Ordering BioXp™ reagents for building genes or cloning is simple.

Log onto your SGI-DNA account and submit your sequences. Assembly is based upon specially designed oligonucleotide pools, specialized reagents and BioXp™ system protocols. You will receive a custom built BioXp™ kit to build your DNA fragments. Load the instrument and begin the run. The next day, collect your BioXp™ Tiles or clones, analyze the fragments and proceed to your downstream application.

DNA assembly runs generally take 14 – 17 hours depending on your constructs and are ready for downstream processing.

Loading the BioXp™ machine is simple.

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

Key components of the BioXp™ Tiles include:

  • Oligo vault carrier
  • Reagent plate
  • Recovery plate
  • 50 and 200 µl tips
  • DNA purification strip
  • Fresh 70% ethanol
See BioXp Tutorials
Deck of BioXp 3200 DNA synthesis machine
The BioXp™ instrument is easy to load for virtually hands-free genomic applications.


A capacity of up to 32 custom genes of 400 bp to 1.8 kb can be assembled on the BioXp™ System. DNA fragments provided in 45 µl of TE and are ready for cloning, off-line sequencing  and further assembly into larger constructs. Additional genomic applications are in development and will work with the existing hardware on the system.

High cloning efficiency from the BioXp™ 3200 system

The overall cloning efficiency of full-length pUCGA 1.0 clones is 83%. Additionally, as expected, highest cloning efficiencies (>90%) are observed for the smallest DNA fragments (<900 bp). The total cloning efficiency (CE) for full-length inserts was calculated using the following formula:

CE (%) = (Number of white colonies/Total number of colonies) × (Number of full insert colonies/Total number of colonies) × 100.

Reliable Results Across a Range of DNA Fragments

The BioXp™ system provides consistent results across a range of DNA sequences. In this data, BioXp™ Tiles were assembled across a wide size range and %GC content of approximately 400 bp to 1.8 kb. and 40 – 60% GC.

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 and Cloning

Cloning DNA on the BioXp™ system begins with assembling the DNA successfully prior to cloning. Success depends on the overall characteristics of the DNA sequence and the protocol. Two factors that influence successful de novo assembly is 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 assure it has a high probability of success. If a sequence is outside the current capabilities, you may submit for BioXp™ assembly or request a quote to build the Tile in the SGI-DNA Custom Synthesis lab.

BioXp™ 3200 DNA Fragment and Cloning Compatibilities

Size Ranges 400 bp to 1800 bp DNA Fragments
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 Services is available if DNA is outside of compatibility.
Amount Approximate yield: 200 ng of purified, linear dsDNA PCR product. DNA may need to be gel purified prior to downstream applications.
Format 96 well plate format in final volume of 45 µl in TE.

BioXp™ Tiles Analysis

To evaluate the success of the assembly it is important to run the BioXp™ Tiles on a gel. 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.

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 a 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 your error free clone.

We recommend the following as a guideline to determine how many full- length clones to pick to find your error free clone.

Number of Full Length Clones Recommended 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 a BioXp™ System

To order a BioXp™ System, please contact info@sgidna.com for a sales representative to contact you. To order a BioXp™ 3200 System or to receive a quote, please contact info@sgidna.com for a sales representative to contact you. You can also See a Virtual Demo by clicking on the button below.

See Virtual Demo


You may also request a demonstration of the instrument. We host Demos at our corporate headquarters in La Jolla. CA and may also have an instrument in your area that you can visit. Please contact info@sgidna.com to request a demonstration.

Pilot Program

Our pilot program allows you to order sequences that are built in our in house BioXp™ system. We ship you the resulting product. 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. 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 Kit
  • Module B: BioXp™ 1.8 kb Reagents

Additional materials required include (provided by customer):

  • Freshly made 70% Ethanol (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 on the BioXp™ PreCheck (link) web site 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.

Those sequences that PASS BioXp™ compatibility standards have a very high likelihood of successful assembly on the instrument (>85%). Those that do not PASS have a lower chance of successful assembly. Successful assembly on is dependent on the overall complexity of the sequences.

Those 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%). You are welcome to order any sequence you like, compatible or not, to test the instrument for your needs.

Other Available BioXp™ products:

BioXp™ Tiles

BioXp™ Custom Cloning

BioXp™ NGS Library Construction

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