Gene Synthesis Custom Order

Gene synthesis is the process of building artificial genes or modifying existing ones entirely from scratch. Unlike DNA replication in living cells, which uses a template strand, gene synthesis creates DNA molecules one nucleotide (the building block) at a time.

Usages of gene synthesis:

• Medical research: One can produce specific proteins for research on diseases, leading to new treatment discoveries.
• Vaccine development: Gene synthesis allows the creation of synthetic copies of viral or bacterial proteins to be used in vaccines.
• Genetically modified organisms (GMOs): This technique allows for the creation of organisms with desired traits, such as pest-resistant crops or those with enhanced nutritional value.
• Biofuels: One can design and synthesize genes for microbes that can more efficiently produce biofuels.

Nagoya Protocol is an international agreement on Access and Benefit-Sharing (ABS) of biological genetic resources, which has various implications for gene synthesis and cloning in synthetic biology related to genetic information.

1. The Nagoya Protocol and Digital Sequence Information(DSI)

• The Nagoya Protocol regulates the use of biological genetic resources and the fair sharing of benefits arising from them, but currently lacks clear provisions regarding Digital Sequence Information (DSI).
• However, some countries and organizations are advocating for DSI to be considered part of genetic resources and are showing movements to include it as a regulatory target.

2. Impact on Gene Synthesis and Cloning

• When synthesizing the genetic sequence of a specific organism or performing cloning through PCR or DNA manipulation, ABS compliance may be necessary if the original source organism is from a country that has joined the Nagoya Protocol.
• Particularly, if the genetic sequence is obtained from public databases (NCBI, EMBL-EBI, etc.), research and commercial activities using this information may be subject to the Nagoya Protocol.

3. Impact and Future Prospects on Synthetic Biology Research and Industry

• Research institutions and companies may need to comply with Prior Informed Consent(PIC) and Mutually Agreed Terms(MAT) of the country of origin when using genetic resources.
• Since the free use of DSI may be restricted, legal review and data source verification procedures for compliance with the Nagoya Protocol should be strengthened, and international regulatory trends should be continuously monitored.

The biggest difference between NGS-based low-error rate gene synthesis technology and traditional single colony-based gene synthesis lies in how the accuracy of the synthesized gene is verified and the final correct sequence is secured.

1. Single Colony-Based Gene Synthesis (Traditional Method)

• Principle: Oligonucleotides (short DNA fragments) are chemically synthesized and assembled to create the desired gene length. This initial pool of synthesized genes inevitably contains sequence errors (insertions, deletions, substitutions). This gene pool is inserted (cloned) into plasmid vectors and transformed into host cells like E. coli. The transformed bacteria are cultured on agar plates to obtain numerous single colonies. Each colony theoretically originates from a single plasmid molecule. Several colonies are selected, cultured individually, and plasmids are extracted. The sequence of the inserted gene within each extracted plasmid is individually analyzed, typically using methods like Sanger Sequencing. Finally, a colony containing the accurate, error-free gene sequence is selected from the screened colonies for use.

2. NGS-Based Low-Error Rate Gene Synthesis

• Principle: Attempts are made to lower the initial error rate from the synthesis step itself, using advanced synthesis chemistry or enzymatic synthesis methods. Next-Generation Sequencing (NGS) is applied to the synthesized gene pool or intermediate gene fragments. NGS can simultaneously read the sequences of millions of DNA fragments, allowing for an accurate assessment of the error distribution and characteristics of the entire synthesized pool. Based on this NGS data, molecules with very few errors are selected, or the synthesis process itself is optimized, ultimately yielding a gene pool with an extremely low error rate. In some cases, cloning and single colony confirmation might still follow NGS verification, but the success rate of final selection is much higher, and screening effort is reduced because a high-quality pool has already been secured. Some technologies might directly use the NGS-verified pool without cloning.

In conclusion, NGS-based technology leverages the powerful analytical capabilities of NGS to improve the overall quality throughout the synthesis process and dramatically reduce the error rate of the final product. In contrast, single colony-based technology relies on traditional cloning and individual sequencing to find the 100% correct sequence among clones that may contain errors. Bioneer provides 100% accurate DNA using its single colony-based gene synthesis method.

Codon optimization is a technique used in genetic engineering to improve the efficiency of gene expression. It involves modifying the DNA sequence of a gene without changing the amino acid sequence it codes for.

Codon bias: Most organisms have a bias towards using certain codons (triplets of nucleotides) to specify a particular amino acid. This is called codon bias.

Foreign genes: When a gene from one organism (e.g., human) is introduced into another organism (e.g., bacteria) for protein production, the codon bias might be different. This difference can lead to problems with translation (the process of making proteins from mRNA).

How it works:

• Analyze codon usage: Scientists analyze the codon usage patterns of the host organism (where the gene will be expressed).
• Modify codons: The DNA sequence of the foreign gene is then modified to use codons that are more frequently used by the host organism. This is done while ensuring the amino acid sequence remains the same.
• Improved translation: By using preferred codons, the ribosomes (cellular machines responsible for translation) can translate the mRNA more efficiently, leading to higher protein production.

Benefits of codon optimization:

• Increased protein expression: By improving translation efficiency, codon optimization can significantly increase the amount of protein produced from a foreign gene.
• Enhanced cloning efficiency: Optimized genes may also improve the efficiency of cloning the gene into a vector for expression.
• Better mRNA stability: Codon optimization can sometimes improve the stability of the mRNA molecule, leading to longer protein production.
• It can remove/optimize of high/low GC content, Repeat and Homopolymer runs, eventually gene synthesis cost reduction and increased efficiency. It is considered essential in heterologous expression (mRNA, Protein).

Definition of hazardous gene sequence:

Hazardous sequences are DNA sequences that have the potential to cause harm to humans or the environment in genetic engineering experiments. These sequences may have the following characteristics:

• Pathogen genes: Genes derived from pathogens such as viruses or bacteria. These genes can cause disease or worsen its severity.
• Toxin genes: Genes that produce toxins. These toxins can cause harm to humans or the environment.
• Allergen genes: Genes that produce proteins that cause allergies. These genes can cause allergic reactions or, in severe cases, death.
• Out-of-control genes: Genes that can behave in unpredictable ways or cause unintended consequences. These genes can cause harm to humans or the environment.

Relationship between gene synthesis and hazardous gene sequence:

• Gene synthesis can be used to create hazardous genes. For example, one can develop new vaccines by synthesizing genes from a virus, or new treatments by synthesizing genes that produce toxins.
• However, gene synthesis must be performed in a safe and ethical manner. One must take strict safety precautions when handling hazardous gene sequences and ensure that results obtained using these sequences do not cause harm to humans or the environment.
• There are also ethical debates about the potential misuse of gene synthesis technology. For example, some people worry that gene synthesis technology could be used to develop biological weapons.
• Bioneer will request the signed consent form before the gene synthesis if customer’s sequences are analyzed as hazardous gene sequences by IGSC’s Harmonized Protocol.

Bioneer provides not only gene synthesis services but also a variety of additional linked services:

• Codon optimization service: If the gene sequence does not match the codon usage bias of the strain used for expression, further research, such as protein expression, may be affected. Bioneer has a codon optimization program jointly developed with KAIST and provides codon optimization services in connection with gene synthesis services.
• Cloning service: This is a cloning service that provides not only the vectors provided by the company but also a specific vector in plasmid form. If you have an insert, you can order the cloning service alone. If you do not have an insert, we will provide a vector containing the gene you want in conjunction with the gene synthesis service.
• Mutagenesis service: If you want to produce mutant genes that are essential for research on protein structure and function and enzyme function improvement, you can prepare easily and conveniently by using Mutagenesis service along with Bioneer's gene synthesis service. We provide site-specific mutation samples by specifying specific locations and sequences, and can be used in conjunction with gene synthesis services and cloning services.
• mRNA synthesis service: Bioneer's mRNA synthesis service provides a variety of mRNAs desired by customers. The DNA template used for mRNA synthesis can be provided, or it can be linked to our own gene synthesis service. We provide various types of mRNA such as 5' Capping and 3' poly A tailing. If you do not have the gene used for synthesis, you can use Gene & Standard mRNA Synthesis or Gene & Complete mRNA Synthesis.
• Gene to Protein Synthesis: If you want everything from gene synthesis to protein expression, you can use our Gene to Protein Synthesis service. Our Gene to Protein Service is an integrated service of “gene synthesis-protein synthesis service” and is a service that allows you to receive the desired protein and gene within at least 2 weeks at a reasonable price. The service is classified into Standard and Cloning-free services depending on the gene synthesis method, and the synthesis of various proteins is possible.

In gene synthesis, difficult genes are those that pose challenges to the process due to their inherent characteristics. These characteristics can make it harder or less efficient to synthesize the gene using standard methods. Here are some factors that can make a gene difficult to synthesize:

• GC content:
• GC refers to guanine and cytosine, two of the four building blocks of DNA.
• Genes with an extremely high (>80%) or low (<20%) GC content can be difficult to synthesize.
• This is because the process relies on the preferential pairing of these nucleotides during assembly.
• Secondary structures:
• Some DNA sequences can fold back onto themselves and form complex structures.
• These structures can interfere with the chemical synthesis process.
• Repetitive sequences:
• Genes with long stretches of identical or similar nucleotides (repeats) can be challenging.
• The repetition can lead to errors during synthesis.
• Homopolymer runs:
• These are stretches of the same nucleotide repeated consecutively.
• Long homopolymer runs can be problematic during synthesis.

Bioneer will offer gene synthesis services that typically have methods to address some of these difficulties:

• Gene fragmentation: Long genes can be broken down into smaller pieces, synthesized individually, and then assembled later.
• Codon optimization: This technique can be used to modify the gene sequence to make it more compatible with the host organism's machinery for protein production, although it's not directly related to difficulty in synthesis itself.

It is possible to synthesize sequences with high GC content or repeated sequences, but it can be challenging.

High GC Content:

• Standard methods for gene synthesis might struggle with very high GC content (greater than 80%).
• The reason is the preferential pairing of guanine (G) with cytosine (C) during assembly. This can lead to difficulties in incorporating other nucleotides (adenine (A) and thymine (T)).

Overcoming Challenges:

• Specialized techniques: Gene synthesis companies might use phosphoramidite chemistry, which is better suited for GC-rich sequences.
• Optimizations: Optimizing reaction conditions like temperature and salt concentration can also help.

Repeated Sequences:

• Long stretches of identical or similar nucleotides (repeats) can be tricky.
• Repetition can lead to errors during synthesis, as the machinery might struggle to differentiate between repeated units.

Possible Solutions:

• Shorter fragments: Breaking down the gene into smaller pieces, synthesizing them individually, and then assembling them later can help.
• Codon Optimization: If the gene is for mRNA or Protein, codon optimization can be utilized to remove high/low GC, repeat sequences and homopolymer runs.

Gibson Assembly and Golden Gate Assembly are two efficient methods used for long gene synthesis.

1. Gibson Assembly:

• Overview: Gibson Assembly is an enzyme-based method for joining multiple DNA fragments simultaneously. This is simpler and more efficient than PCR-based approaches, the traditional method used to assemble short genetic fragments.
• Key Principle: Gibson Assembly uses three enzymes.
  • Taq DNA polymerase: Performs DNA synthesis.
  • Phusion DNA polymerase: Joins DNA fragments by adding 3' base pair overhangs.
  • T5 exonuclease: Removes 5' base pair overhangs.
• Advantages:
  • Simple: Multiple DNA fragments can be linked simultaneously without a PCR step.
  • Efficiency: It has a high success rate and can efficiently synthesize long genes.
  • Accuracy: Low chance of incorrect connections.
• Disadvantage:
  • Cost: Gibson Assembly enzymes are relatively expensive.
  • Design complexity: DNA fragments must be designed carefully to effectively join them.
• Used for long gene synthesis: Gibson Assembly is a very effective method for long gene synthesis. This can be done by dividing a long gene into several smaller pieces and connecting each piece using Gibson Assembly. This method has a high success rate and accuracy, and is relatively simple to perform.

2. Golden Gate Assembly:

• Overview: Golden Gate Assembly is a method of joining DNA fragments using Type II restriction enzymes and T4 DNA ligase. It is similar to the Gibson Assembly, but uses different enzymes and works differently.
• Core Principles: Golden Gate Assembly goes through the following steps:
  1. Prepare DNA fragments: Add specific Type II restriction enzyme cut sites to both ends of each DNA fragment.
  2. DNA cutting: Type II restriction enzymes are used to cut DNA fragments.
  3. DNA ligation: T4 DNA ligase is used to join the cut DNA fragments.
• Advantages:
  • Cheaper: Golden Gate Assembly enzymes are less expensive than Gibson Assembly enzymes.
  • Ease of design: Simple design is required to effectively join DNA fragments.
  • Adaptability: Can be used to join different types of DNA fragments.
• Disadvantage:
  • Complexity: A somewhat more complex process than Gibson Assembly.
  • Efficiency: Does not have as high a success rate as the Gibson Assembly.
  • Accuracy: Higher chance of incorrect connections.
• Used for long gene synthesis: Golden Gate Assembly can be used for long gene synthesis, but is not as effective as Gibson Assembly. This can be done by dividing a long gene into several smaller pieces and connecting each piece using Golden Gate Assembly. However, it may have a lower success rate and be more prone to error than the Gibson Assembly.

3. Bioneer’s Fragment Assembly:

• Overview: Bioneer has maximized the efficiency of Gibson Assembly for <3kb gene synthesis, and has developed a technology to connect >20 evenly synthesized fragments at once using its own Fragment Assembly technology for gene synthesis of 3kb to 15kb.
• Advantages: By applying it to <15kb gene synthesis, we have overcome the existing Golden Gate Assembly's 5kb ~ 8kb limitation in general. >15kb (up to 100kb) gene synthesis is performed using in vivo assembly.

Bioneer provides Rapid Gene Synthesis Service and AccuGeneBlock Service under our own standards so that you can receive gene synthesis products more quickly. For the services below, you can select the service on the gene synthesis service order page.

1. Rapid Gene Synthesis Service

This is a gene synthesis service that allows you to receive Gene Synthesis Service in as little as 7 days. We synthesize genes ranging in size from 1 to 1000 bp, and the final product is provided in the form of plasmid DNA.

2. AccuGeneBlock

This is a service that allows you to receive DNA fragments of 1 kb or less in as little as 5 days. We synthesize genes of 100 to 1000 bp in size, and the final product is provided in the form of a DNA Fragment (PCR product).

Gene synthesis service are basically provided in 1-2 μg lyophilized form. If you want a larger amount of gene synthesis product, you can select the Plasmid Increase Service on the order page. If you need more than 500 μg, you can also order additional service offline.

When requesting Bioneer's Gene Synthesis or Cloning service, you can select a vector (Bioneer_Vector information link). There is no need to purchase a commercial vector separately, so you can reduce costs and easily obtain the plasmid in the desired form. In particular, by using the pBT7-N-His vector and pBT7-C-His vector suitable for the Cell Free Protein Expression System, you can use ExiProgen™, Bioneer's fully automated protein synthesis and purification equipment, or AccuRapid™ Protein, a manually provided protein synthesis and purification kit. Protein expression and purification are possible quickly and easily using the Synthesis Kit product.

If you use the gene synthesis service in conjunction with cloning, cloning is possible in various types of vectors (Bioneer_vector information) provided by our company. Additionally, if you wish to clone genes into a vector you already own, you can use the cloning service alone. If you are using the cloning service alone, please send us your vector and we will provide a customized cloning service.

Bioneer performs QC through Sanger sequencing, a base sequence analysis method based on the Sanger method, and provides analyzed data with a report by applying strict QC standards.

Sanger sequencing is one of the common methods used to determine DNA sequence and is a technical process to determine the order of bases within a DNA molecule. It is a DNA sequencing method that includes electrophoresis and random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during DNA replication. It is based on Sanger sequencing is a highly accurate QC method that can generate DNA sequence reads of more than 500 nucleotides and maintains a very low error rate with an accuracy of approximately 99.99%.

In addition, Bioneer uses Sanger sequencing analysis software with a low error rate to evaluate the quality of each peak and remove low-quality basic peaks to confirm only more accurate sequence data, and uses a data program developed in-house. This minimizes human error and cross contamination, providing more accurate products.

Order Information and Instruction for an Order, link as below:

Gene Synthesis Order Manual

• Gene Synthesis Service
  Gene Length (bp)	Synthetic price (Normal sequence)	Synthesis Time
  ~ 400	$77	Average 5~10 working days
  401 ~ 1,200	$0.19/bp	Average 5~10 working days
  1,201 ~ 2,000	$0.19/bp	Average 10~17 working days
  2,001 ~ 3,000	$0.19/bp	Average 15~25 working days
  3,001 ~ 15,000	$0.19/bp	Average 25~30 working days
  15,001 ~ 100,000	$0.23/bp	Inquire
  100,001 ~	$0.27/bp ~	Inquire

  Price and delivery period are raised for gene segments containing complex structures such as high or low GC content, repeat sequences or homopolymeric runs.

  Genes that produce toxic substances or inhibits growth in E.coli cell system will be delivered in the form of PCR products or plasmid DNA, even during the sequence check during the synthesis process.

• How much does it cost if the sequence is changed or canceled during synthesis?

  • Sequence change policy

  Sequence Change Length	Price
  Both ends (5` / 3`) 9bp or less	$50.00/end
  Within gene 20bp or less	$200.00(point mutation price applied)

  • Cancellation policy

  Order cancellation period	Cancel Price
  Within 5 days after ordering	50% of the total price
  After 5 days of order	80% of total price
  After guarantee period (Guarantee period: Date for finalized synthesis except for delivery time)	free

• 1) How do I use the Gene synthesis service?

  You can access the Gene synthesis service page on the Bioneer website (eng.bioneer.com), log in, check the quote, and place an order. For orders placed before 16:00 KST, synthesis will begin on the same day, and for orders placed after 16:00 KST, synthesis will begin the next day.

• 2) What is the maximum length when ordering gene synthesis?

  There is no limit to the length, but if the length is over 15 Kb, it may take a long time to synthesize. Additionally, when ordering more than 15 kb, please download the order form, fill it out, and send it to geneorder@bioneer.co.kr. We will assign a person in charge and provide services for quotation and ordering.

• 3) What type of product is provided by gene synthesis service?

  The requested gene is provided in the form of plasmid DNA cloned into a basic vector (pBHA vector), dried in an amount of 1 to 2 ug.

• 4) How do I use the final product?

  First of all, please refer to the user guide provided with the product when it is shipped. Add 20 μl (Final 250 ng/μl) of DW or TE buffer to the delivered DNA. After adding DW or TE buffer to the tube, it is recommended to store it at 4°C for 10 minutes before use. For long-term storage, be sure to store frozen at -20°C. It can be stored at room temperature in a dried state.

• 5) How are final products stored, and how long is the information and product stored for?

  Genetic information and products you request are stored safely for 6 months. If you wish to discard the information and finished product immediately after completing gene synthesis, you can do so.

AccuGeneBlock is a service that allows you to receive dsDNA fragments of 100 to 1000 bp in as little as 5 days. Due to the nature of dsDNA fragments, fragments that do not 100% match the reference sequence may be mixed.

• 1. Access the Gene synthesis service page on the Bioneer website (eng.bioneer.com).
• 2. Log in.
• 3. Enter the required information and check the quote.
• 4. Click Add to Cart and place your final order. For orders placed before 16:00 KST, synthesis will begin on the same day, and for orders placed after 16:00 KST, synthesis will begin the next day. (Closed on Korean holidays.)

Mixed bases can be added. For further details, please contact geneorder@bioneer.co.kr.

Only sequences of up to 1 kb or less can be synthesized.

The size of the synthetic gene is confirmed through agarose gel electrophoresis.

Add 10μl (Final 50ng/μl, 500ng Scale) of DW or TE buffer to the delivered DNA. (It is recommended to add DW or TE buffer to the tube and store it at 4°C for 10 minutes before use.) For long-term storage, be sure to keep it frozen at -20°C. It can be stored at room temperature in a dried state.

It is possible to synthesize the desired sequence at a relatively low cost, can be used quickly and easily for synthetic biology research, and can be cloned directly into the desired vector by the user.

Only sizes from 1 to 1000 bp are possible. If the sequence contains many high or low GC, repeat sequences, homo-polymeric runs, etc., synthesis is not possible. (General Gene synthesis service available)

For sequences for which Rapid Gene Synthesis is not possible, please order through the gene synthesis service.

In 2024, Bioneer completed the development of its proprietary Megabase Synthesizer, achieving a monthly oligo pool production capacity exceeding 20Mb (Megabases) with this equipment.
The Megabase Synthesizer drastically reduces raw material costs, enabling Bioneer to offer synthetic genes to customers at affordable prices.
Furthermore, Bioneer's proprietary oligo design technology enhances the success rate of fragment synthesis, and its efficient fragment assembly technology allows the company to provide synthetic genes up to 100kb (Kilobases) in length.