BioXp™ 3200 System

The BioXp™ System is the world’s first DNA printer, a machine which will allow any biotechnology company or academic laboratory to create genes, genetic elements and molecular tools on their benchtop hands-free, starting with electronically transmitted sequence data. SGI-DNA’s BioXp™ 3200 Instrument will dramatically improve the workflow for applications such as protein production, antibody library generation and cell engineering.

To learn more about the system, visit the BioXp™ 3200 System page.

BioXp™ Custom Cloning

Build and clone gene fragments directly into your vector in an overnight hands-free run

The BioXp™ System allows you to automate cloning 32 of your synthetic genes directly into your vector of up to 12 kb in a single hands-free overnight run. This capability allows much greater versatility for downstream applications. The BioXp™ System utilizes the Gibson Assembly® method to provide seamless, high efficiency cloning.

Custom Cloning on the BioXp™ System Allows:

  •  Direct cloning of synthetic fragments into your vector
  •  Clone using up to 4 vectors at once
  •  Automated multi-fragment cloning
  •  Combinatorial assemblies

Multiple Vector Cloning

BioXp™ Custom Cloning allows you to clone up to 4 different vectors in a single run. Once you determine the DNA fragment and vectors you’d like to clone, SGI-DNA will help you organize your sequences within your FASTA file following SGI-DNA’s guidelines. Our customer service team is available to assist you:email for assistance.

Please refer to Multi Vector Cloning Guidelines

BioXp™ Vector Preparation

Preparing your vector for the BioXp™ System is simple. Linearize your vector using unique restriction enzymes flanking your cloning region or by PCR using a high fidelity DNA polymerase. Once complete, you can store this vector for multiple BioXp™ custom cloning runs.

To prepare cloning vector:

  • Design your Gibson Assembly® cloning strategy
  • Linearize your vector using either unique restriction enzymes or PCR
  • Purify linearized vector
  • Check quality of vector on the benchtop to confirm design and successful preparation
  • Quantitate final linearized vector
  • Aliquot for use into provided 8-well strip

Please refer to the protocols for BioXp™ vector preparation.

BioXp™ Vector Preparation Guide

BioXp™ Post Run Analysis

BioXp™ Vector Preparation Service

SGI-DNA also offers services to prepare your BioXp™ vector for you. Our scientists will linearize your vector and provide you with multiple reactions of vector, ready for use on the BioXp™ system

Once your vector is prepared and received, order the BioXp™ Custom Cloning Kit with your desired sequences. To run the reaction, load your vector along with your BioXp™ reagents to produce synthetic DNA fragments to clone directly into your vector.

Contact for more information.

Other Available BioXp™ products:

BioXp™ Tiles

BioXp™ pUCGA 1.0 Cloning

How It Works

Custom cloning on the BioXp™ System is Simple:

  • Design sequences and vector for Gibson Assembly® cloning
  • Prepare and test vector
  • Order desired sequences for the BioXp™ Custom Cloning Kit
  • Load your vector together with BioXp™ Custom Cloning reagents
  • Run the instrument
  • Collect cloning reaction and proceed with transformation and downstream processing

Placing Your Order

  1. Log onto your SGI-DNA account
  2. Select Custom Cloning
  3. Upload sequences
  4. Submit order

Assembly is based upon specially designed oligonucleotide pools, specialized reagents and BioXp™ system protocols. You will receive a custom build BioXp™ kit to build your DNA fragments and clone them directly into your prepared vector.

Load the instrument and begin the run. The next day, collect your BioXp™ clones, analyze the fragments and proceed to transform into E. coli to select and screen colonies.

Cloning runs generally take 15 hours depending on your constructs and are ready for downstream processing.

Loading the BioXp™ machine is simple.

A loading map is included with each kit that provides step-by-step instruction for each of the components. These maps and the related manuals can also be found within the documentation

Key components include:

  • Oligo Vault™ Carrier
  • Reagent Plate
  • Cloning reagents
  • 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 cloned on the BioXp™ System. When the run is complete, collect your BioXp™ custom clones, analyze the fragments and proceed to transform your cloning reaction into E. coli to select and screen colonies.

High cloning efficiency from the BioXp™ 3200 system

Gibson Assembly® Cloning on the BioXp™ system is not only robust, but also dependent on many factors, such as design, vector preparation, sequence dynamic of the inserts and characteristics of the overall experiment.

As a reference, we include the cloning results of our BioXp™ pUCGA cloning module for comparison. The overall cloning efficiency of full-length pUCGA 1.0 clones is 83%. Additionally, 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 which can then be utilized in an automated BioXp™ cloning reaction. BioXp™ Tiles that 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 is reviewed 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 the 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, it is very important to first screen for full length clones prior to sequencing to find your error-free clone.

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.

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 for a sales representative to contact you. To order a BioXp™ 3200 System or to receive a quote, please contact for a sales representative to contact you.


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 to request a demonstration. You can also see a Virtual Demo by clicking on the button below.

See Virtual Demo

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 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 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™ Cloning kit includes:

  • Module A: BioXp™ Oligo Vault Kit
  • Module B: BioXp™ 1.8 kb Reagents
  • Module C: BioXp™ Cloning 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

pUCGA 1.0 Cloning

BioXp™ NGS Library Construction

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