Category: Codon Optimization

Synbio Technologies’ Codon Optimization Strategy

Translation is the last step in protein synthesis that results in stable proteins from DNA replication, mRNA transcription and modification in cells. Codon optimization aims to increase the yield of protein expression in different organisms by rebalancing usage of synonymous codons. High quality protein has a wide range of applications, including study of protein structure and function, biological research, clinical medicine.

Higher protein yield in turn can be a valuable feature in a wide range of applications, including…

  • Codon usage bias

There are 64 codons in total, 61 codons encode 20 amino acids and the remaining 3 are stop codons. Redundant codons exist for most amino acids; multiple different codons encode the same amino acid. In general, the expression of heterologous proteins is negatively correlated with the occurrences of rare codons. In simpler terms, when the codon usage of a target protein in its native organism differs significantly from the average codon usage of the expression host, this could cause problems during expression. Therefore, an effective solution is to replace rare codons in the original sequences with major codons that are preferred in the host.

  • The secondary structure of mRNA

Translation refers to the conversion of nucleic acid sequences into amino acid sequences, and is greatly affected by complex secondary structures in mRNA. The translation of codons in the non-structural part of the α-helix is the rate-determing step in the translational process. Identifying the hairpin structure in an mRNA can lead to significant optimizations of translational efficiency for that mRNA.

  • Changing regulatory elements and restriction sites

The process of optimizing protein expression is affected by many factors: not only basic DNA transcription and translation, but also a series of regulatory elements. By incorporating signal peptides, tags, other regulatory elements, or appropriate restriction sites during gene synthesis, expression of synthetic genes in heterologous host organisms can be significantly improved.

Synbio Technologies NGTM Codon Optimization software can intelligently optimize codon usage to effectively improve protein expression, in order to better meet the needs of scientific research and industrial production.

Synbio Technologies’ NGTMCodon Optimization Software

Synbio Technologies’ proprietary NGTMCodon optimization software provides customers with free codon optimization services bundled with gene synthesis. Our NGTM Codon optimization software optimizes gene sequences based on different expression systems to maximize protein expression.

NGTM Codon optimization software advantages:

  • Elimination of codon usage bias

Codon usage bias refers to the differences in frequency of synonymous codons in coding DNA, and exists in a wide variety of organisms. The most frequently used codon is called the optimal codon, and lower frequency codons are called rare codons. Synbio Technologies’ proprietary codon optimization software, NGTM Codon optimizes the usage of both the optimal codon and the rare codons to achieve superior protein expression.

  • Fine-tuning secondary structure of mRNA

The secondary structure of mRNAs play an active role in the translation process. The complexity and stability of mRNA secondary structure both greatly affect the smoothness of the translation process, in particular, secondary structure near the ribosome binding site (RBS) is crucial. NGTM Codon can effectively identify and minimize hairpin structures in mRNA, effectively optimize the original sequence, and generate significant improvements in protein expression.

  • Removal of negative cis-acting elements and restriction sites

NGTM Codon was designed to eliminate multiple obstacles during transcription and translation by minimizing negative cis-acting elements that interfere with transcription and translation.

Case study:Targeting protein was reproducibly expressed in E. coli after codon optimization by NGTM Codon.

codon-optimization

 

NGTM Codon improves codon usage efficiency

 

    Gene Synthesis Plasmid Preparation

    At Synbio Technologies we pride ourselves in being one of the premier companies within not only the gene synthesis industry, but the biotechnology industry as a whole. This confidence is relying upon our tested and proven methods of gene synthesis. Gene synthesis can be defined as the method in synthetic biology used to engineer an artificial gene of interest in a laboratory setting. Ever since gene synthesis was first successfully conducted in the early 1970s it has become a highly sought mechanism in various fields of genetics research. For this reason many companies, like Synbio Technologies, have been attempting to optimize their gene synthesis products; but none of them have done this with quite success like Synbio Technologies. Our Syno Platform allows us to generate any sequence of interest up to and including 150 Kb in length. Another aspect of gene synthesis that Synbio Technologies has to offer is our gene synthesis plasmid preparation. Using this technology we are capable of generating any sequence and inserting it into any plasmid of interest. For gene synthesis plasmid preparation there are typically two forms of final product: transfection grade and research grade. Both differ slightly in their mechanism of being generated, as well as research application. Through use of Synbio Technology’s Syno® Platform, as well as our gene synthesis plasmid preparation we are ready to supply our customers with whichever plasmid product is necessary.

    The differences between the transfection grade and research grade generated plasmids lies mainly in the applications each particular plasmid is used for. First, the research grade is used more in a laboratory setting to conduct various types of genetics research. These topics include: molecular cloning, mutagenesis, southern blotting, etc. All of these methods are used in order to conduct various types of genetics research with use of gene synthesis. Where gene synthesis comes in is through the insertion of the requested sequence into the plasmid. This insertion, and subsequent amplification, allows our customers to conduct any type of research necessary that requires a research grade plasmid construction. Second, the transfection grade plasmid is used mainly for protein manufacturing, antibody production and other forms of gene therapy. The link between this plasmid and gene synthesis is again the insertion of the sequence of interest into the particular plasmid. This can be extremely useful when conducting different types of gene therapy. The requested sequence can be loaded into the plasmid with the hopes of reversing the endogenous mutated gene of interest. This powerful technology has the ability to further our understanding of genetics and it is all thanks to gene synthesis.

    Gene synthesis is something that Synbio Technologies does extremely well, mainly relying upon our Syno® Gene Synthesis Platform. This platform is used to generate the customer requested sequence with one hundred percent accuracy. The resulting gene synthesis product can then be used in order to prepare a plasmid of interest. This process is normally quite daunting, but Synbio Technologies is more than confident in our ability to generate the requested gene synthesis product and resulting gene synthesis plasmid. This process is all done within a quick turnaround time and competitive prices. For this reason, Synbio Technologies has risen to the top of not only the gene synthesis industry, but the resulting biotechnology industry as well. We offer a one stop shop for our customer’s gene synthesis plasmid preparation, with competitive prices, high quality output, and an efficient turnaround time. With this combination, our customers will be conducting research in no time with confidence in the product that we supply them.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Synbio Tenchologies can also design sequencing with codon optimization software -NGTMCodon Optimization Technology at no cost.

    Gene Synthesis Definition

    The traditional method of studying a gene’s function is to extract the gene of interest, amplify it and put the resulting sequence through various molecular assessments. These assessments can vary from generating a frameshift mutation within the sequence, to upregulating the expression of the sequence in order to observe the resulting phenotypes the mutated sequence has induced on the organism. All of these methods are particularly important within the field of genetics research, but the methods of extracting these sequences to then mutate and study is becoming laborious and cumbersome. One, relatively recent and groundbreaking method, gene synthesis , has taken this traditional method of studying genetics and introduced some interest alterations. Gene synthesis is defined as the synthetic biology method used to engineer artificial genes within a laboratory setting. This method has allowed us, at Synbio Technologies, to go from a sequence in text format to physical copy of the genetic sequence itself with ease and extreme accuracy. Ever since gene synthesis was successfully conducted in 1972, by Hard Gobind Khorana and associates, this technology has been growing not only in popularity but in effectiveness and efficiency. One of the main reasons this technology has increased in popularity is that it allows for the creation of long, up to 150 Kb, sequences to be synthesized with extremely high accuracy. With the capability of generating sequences this large, gene synthesis gives a powerful approach to studying various topics such as complex pathways and generating synthetic DNA libraries. This high accuracy and relatively long length have promoted gene synthesis to be applied to various fields of genetics and biological research topics.

    The fields of biological research that gene synthesis has been applied to vary from targeted mutagenesis in order to study a gene’s function to agriculture through increasing crop production. One of the main advantages that gene synthesis offers it the ability for a customer to request a specific sequence of DNA in text format up to 150 Kb in length. This text format is then converted into a physical copy with relative ease and high accuracy. The resulting sequence is then amplified an adequate amount of times in order to comply with the customer’s request. The accuracy allows the customer to generate a mutation anywhere within a gene of interest specific to their research topics. Not only can the mutation be generated anywhere, but any type of mutation can be used: frameshift, deamination, deletion, insertion, or nonsense mutation. In addition to this, gene synthesis can also be used to upregulate a gene of interest in order to cause an overexpression of the resulting phenotype. All of these mutations can be requested and inserted or applied the sequence of interest in order to obtain a better understanding of different types of genetics research such as evolution, or antibiotic resistance. In addition to these applications, gene synthesis has also been applied to agriculture through use of genetic engineering. Gene synthesis is the basis of genetic engineering, allowing for the creation of a resistance gene to a particular bacteria for example. The advantage that gene synthesis has to offer here is the ability to generate mutations within the synthesized gene to keep up with the constantly evolving bacteria. Gene synthesis through genetic engineering, have helped grow the agriculture industry, as well as develop a better understanding on how to improve crop survivability in varying climates as well as exposure to certain harmful bacteria. These applications have large impacts on not only the field of genetics, but the world. This is the main reason as to why Synbio Technologies is proud to be one of the premier companies within the gene synthesis industry.

    At Synbio Technologies, we try to keep our gene synthesis process as simple as its definition. Gene synthesis is carried out with ease and extremely high accuracy through our Syno® Gene Synthesis Platform. This three phase platform allows us to generate the physical genetic sequence of the customer specified request. This generated sequences is guaranteed to be one hundred percent identical to the customer requested sequence. The guarantee is backed by Sanger sequencing at multiple phases of the three platforms. The resulting gene synthesis product will then be shipped to the customer specific location within an efficient timeframe. This entire process allows Synbio Technologies to offer the highest quality product, with an efficient turnaround time. These two aspects, combined with competitive prices and respectable reputation, it is clear that Synbio Technologies is one of the premier companies within the gene synthesis industry.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Large Gene Synthesis

    An interesting and important aspect of genetic research that has grown drastically in popularity over the last ten to fifteen years is gene synthesis . Gene synthesis can be defined as the construction of a physical genetic sequence from a requested sequence in text format. Gene synthesis allows us, at Synbio Technologies, to manufacture genetic sequences that may not already exist within nature. In addition to the de novo sequences generated, sequences can also vary greatly in length, from short sequences to large sequences up to 150 Kb. This process is carried out with Synbio Technology’s, patent pending, Syno® Platform. This three stage platform makes going from requested costumer specific sequence to physical copy of the sequence with ease. One aspect in particular that the Syno® Platform is known for is large gene synthesis. The Syno® platform has the ability to synthesize large genes up to and including 150 Kb in length. The wide range of possibilities makes Synbio Technology’s Syno® Platform attractive and sought out by researchers all over the world especially when it refers to large gene synthesis. This has led Synbio Technologies to become one of the premier companies within the realm of not only large gene synthesis, but any length gene synthesis. This confidence in our large gene synthesis relies upon one of the two most popular methods of gene synthesis, proven time and time again.

    There are two common methods of large gene synthesis: Gibson Assembly Method and Yeast homologous recombination technology. The Gibson Assembly Method now the most common method of achieving directed cloning and in vitro multiple-segment assembly. The Gibson Assembly Method is commonly used by various companies to conduct gene synthesis for varying lengths. It is an effective method for gene synthesis, but the one major restriction that comes along with this method is the inability to easily synthesize fragments over 20kb in length. This is an acceptable method for small gene synthesis, but a different method is needed for large gene synthesis. The yeast homologous recombination technology has the ability to assemble fragments up to 1.08Mb in length. This length is larger than the average prokaryotic genome, making yeast homologous recombination technology a reliable method to use for both large and small gene synthesis. It is yeast homologous recombination that is utilized for Synbio Technology’s Syno® 2.0 and Syno® 3.0 platforms, the foundation of gene synthesis at Synbio Technologies. It is this technology that allows us to provide one-stop services which includes: basic gene synthesis, gene cluster, and large gene synthesis. With this technology, the Syno® Platforms not only makes it possible to synthesize large genes, but small genomes as well. In addition to the large gene synthesis, Synbio Technology also offers the ability to guarantee 100% sequence verification. This is carried out using Sanger sequencing at multiple steps of the Syno® Platform stages in order to verify the sequence accuracy. The sequencing verification is necessary when dealing with large gene synthesis. The accuracy of sequences of this length is not always guaranteed to be one hundred percent to the identical sequence with other companies, but with our Syno® Platform it is.

    At Synbio Technologies we are more than confident in our abilities to generate your requested genetic sequence, up to and including 150 Kb in length. The possibility of synthesizing a gene this large has opened up a vast amount of new opportunities and approaches to various topics within genetics research. Large gene synthesis is not a task that is easily accomplished, but at Synbio Technologies we are capable of generating the requested sequence with one hundred percent accuracy in an efficient timeframe. This confidence is relying upon the efficiency and accuracy of our Syno® Platform and how it has been proved its ability to generate genetic sequences up to 150 Kb. In addition to this, our prices are at an all-time low, starting at $0.19 per base pair through our gene synthesis promotions. With this confidence in our large gene synthesis protocol and low prices we are more than ready to offer you the highest quality product for an extremely competitive price.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Synbio Tenchologies can also design sequencing with codon optimization software -NGTMCodon Optimization Technology at no cost.

    Gene Synthesis Vectors

    A relatively recent discovery, dating back to the early 1970s, in biology has revolutionized the field of genetics research. This discovery is known as gene synthesis , which allows for the manufacturing of a physical genetic sequence from a string of base pairs in text format. Gene synthesis allows for the creation of a genetic sequence that may not be preexisting within nature. Previously, a sequence of interest was required to be present within an organism in order to be extracted and later amplified to study its function. Gene synthesis allows us, at Synbio Technologies, to bypass this requirement entirely. This is accomplished through our, patent pending, Syno® Platform, which allows us to move from a sequence in text format to a physical copy with ease and accuracy. One common advantage that gene synthesis offers is the construction of gene synthesis vectors. Gene synthesis vectors vary widely in structure, function, length, and physical sequence characteristics. With the use of Synbio Technology’s Syno® Platform we are capable of not only synthesizing any gene of interest, up to 150 Kb in length, but constructing any gene synthesis vector specified by the customer. The generated gene synthesis vector can then be used in a wide range of applications, specific to each type of gene synthesis vector.

    There are three main types of gene synthesis vectors that Synbio Technologies prides itself in its ability to generate with high accuracy in order to better suite the customer’s particular request. The three vectors are: short hairpin RNA (shRNA), transcription activator-line effector nuclease (TALEN), and CRISPR-Cas9. All three have similar functions, gene knockout also known as gene silencing, but have various methods in order to accomplish this. shRNA use RNA interference in order to block the transcription and translation of the gene/sequence of interest, rending it inactive. TALEN and CRISP-Cas9 use genome editing in order to render the gene/sequence of interest inactive. All three have been tested and proven as effective methods of gene silencing and inhibiting the resulting protein expression. Gene silencing is a common method within genetics research in order to determine the function of a gene. Once the gene is rendered inactive, researchers can study the resulting phenotype and infer on the function of gene of interest. Where gene synthesis comes into play is through our Syno® 2.0 and Syno® 3.0 Platforms Synbio Technologies is capable of constructing the requested sequence within any of these vectors, in addition to other popular vectors. This technology allows the customer to design a sequence, in text format, which allows Synbio Technologies to generate the requested gene synthesis vector. Once generated, the sequence and resulting vector will work to inhibit the endogenous gene, lowering protein expression and essentially silencing the gene of interest. As mentioned before, this silencing is achieved through the various methods of gene silencing utilized by each vector.

    At Synbio Technologies we are extremely confident in our ability to construct these gene synthesis vectors to the customer’s exact specifications. We guarantee with one hundred percent accuracy within our generated sequences in order to produce the highest quality output. With this accuracy we can guarantee the best possible method of achieving a gene knockout through the use of our gene synthesis vectors. At Synbio Technologies we don’t only offer the highest quality product, but extremely fast turnaround times and competitive prices as well. Within as few as 10 days the customer’s gene synthesis vector will be constructed and be shipped to the customer specified location. With this confidence, high quality output, fast turnaround time, and competitive prices it is clear the Synbio Technologies is one of the leading companies within the gene synthesis industry.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Gene Synthesis Mutagenesis

    One of the fundamental ways to study the function of a gene is to void, knockout, its function and observe the resulting phenotype. This void of function, commonly known as mutagenesis, has been practice within the field of genetics for many years and has been proven effective countless times. A more commonly utilized method of mutagenesis, site-directed mutagenesis, is one of the most traditional methods of generating a knockout gene. The process of gene synthesis mutagenesis begins with the selection of a short primer. The primer must meet two important characteristics: it must be complementary to the sequence of interest, and it must contain a debilitating mutation that will leave the gene of interest incapacitated. The complementary nature of the primer is necessary for the primer to hybridize with the sequence of interest. The debilitating mutation is necessary in order to generate a knockout in the gene of interest. The single stranded primer is then replicated by DNA polymerase, allowing the amplification of the gene of interest which now includes the mutation specific to the primer. The mutated sequence is then inserted into a bacteria host cell via a viral vector and cloned. After amplification, the resulting sequence is then verified for accuracy. This process is laborious and may also not yield a high quality of resulting sequences. This inefficiency is due to the reliance of multiple different biological methods that are not easy to control. Over the past thirty years there have been multiple additional methods to generate mutated sequences but few with high efficiency. A new method, gene synthesis mutagenesis, has the recently become more popular as a result of its effective results and efficiency. Gene synthesis mutagenesis offers a unique approach to generating a genetic knockout within an organism. Instead of the normal site-directed mutagenesis, and somewhat hoping that the induced mutations will render the gene inactive, gene synthesis mutagenesis has the ability to generate any type of mutation within a gene. This gene synthesis is carried out by our Syno® Platform, which guarantees one hundred percent accuracy of the generated sequence. This guaranteed sequence will now contain a debilitating mutation, resulting in the creation of a knockout with little effect and high probability of success.

    Gene synthesis itself has revolutionized the field of genetics. This unique technology offers the ability to synthetically engineer a gene of interest in order to be studied. Since this is possible, it is also possible to generate a gene of interest and insert mutations. This is the basic background of gene synthesis mutagenesis. Gene synthesis is the process of requested genetic sequenced in text format to the engineering of a physical copy of the requested sequence. This process has multiple steps of verification of the sequence of interest. These verifications and overall process can be altered in order to generate a sequence of interest that renders the previously functional gene inactive. Multiple different types mutations can be synthetically engineered, ranging from a frameshift mutation to a large deletion of an entire codon, both of which result in a gene damaged beyond repair. This gene can then be amplified, be either use of polymerase chain reaction or traditional subcloning, and then studied for the effects the knocked out gene has on the organism. The process of gene synthesis mutagenesis completely bypasses the reliance of DNA polymerase replicating the primer necessary in site directed mutagenesis. It relies solely on the ability to generate a mutation in text format, which can easily be done.

    The connection between Synbio Technologies and gene synthesis mutagenesis is a simple one, we pride ourselves as being one the leading companies in the gene synthesis industry. On average we synthesize over 10 million base pairs a month. This process is carried out by individuals who on average have been working in this field for 10 years or longer. With this experience and constant business we have been able to perfect the pipeline from original text format to engineered product through our Syno Platform. This format is then slightly altered to accomplish gene synthesis mutagenesis requested by the customer. Instead of using the Syno Platform to synthetically engineer a functioning gene of interest, we engineer a gene of interest with a debilitating mutation. Since Synbio Technologies is one the premier companies in the gene synthesis industry, we can also be considered to be one of the leading companies in the gene synthesis mutagenesis industry.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Synbio Tenchologies can also design sequencing with codon optimization software -NGTMCodon Optimization Technology at no cost.

    Gene Synthesis Cost

    Moore’s Law has been applied and shown in various industries ranging from the tech industry to the biotech industry. Moore’s Law has most notably shown within the field of genetics when analyzing the cost of sequencing the human genome. The first whole genome sequencing was conducted on a human in the early 2000s, and costed approximately $100 million dollars. Over the past ten to fifteen years the technology used to sequence the human genome has expanded rapidly, allowing the cost of sequencing to drop significantly as well. The current cost of sequencing a whole human genome is approximately $1,000 dollars, less than 1% of the original cost ten to fifteen years ago. This rapid decline of cost clearly demonstrated a variation of Moore’s Law. Another aspect of genetics that follows Moore’s Law is gene synthesis cost per base pair. Gene synthesis is the engineering of a physical sequence of DNA in a laboratory setting. It has been applied and used in various fields of research with much success. Gene synthesis has had long lasting impacts on the field of genetics due to its unique ability to generate physical copies of genes with ease, efficiency, and accuracy. Similar to the drastic decline in the cost of sequencing a human genome, gene synthesis cost per base pair has dropped from approximately $10 a base pair to approximately $0.10 a base pair over the past 10 years. Similar to the decrease in cost for whole genome synthesis, gene synthesis cost has been driven down by an increase in technology and a large number of companies supplying this technology. At Synbio Technologies we pride ourselves as being one of the leading companies for gene synthesis with some of the lowest prices in the business with the highest quality output.

    Although there has been a decrease in gene synthesis cost, there has been an opposite effect on the quality of the output. As cost has fallen, quality and potential gene lengths have risen. At Synbio Technologies we offer the ability to synthesize genes up to and including 150 Kb in length with one hundred percent accuracy. This is accomplished by our Syno Platform which offers sequence verification multiple times throughout each of the three phases. This process is carried out by use of Sanger sequencing to verify that the generated sequence is identical to the sequence requested by the customer. In addition to the quality, the applications of gene synthesis have increased drastically, causing it to increase in popularity. Gene synthesis is a popular method of research to develop more effective vaccinations as well as genetically modified organisms. All three of these aspects: decreased gene synthesis cost, increased applications, and quality are intertwined. Gene synthesis is a technology that is extremely effective and commonly used in many pipelines by many different researchers. It is a reliable, well tested and trusted technology that has changed genetics research for the better. Pair these advantages with the low gene synthesis cost and it is clear why this method has drastically risen in popularity throughout the genetics community.

    The decrease in gene synthesis costs has also caused us at Synbio Technologies to offer some of the lowest prices per base pair with the highest quality output. At Synbio Technologies, we are confident and ready to provide the costumer with the highest quality sequence for the lowest price. The confidence is relying upon our, patent pending, Syno Platform which guarantees one hundred percent accuracy within the synthesized genetic sequenced. This is accomplished with the constant verification of sequence quality for accuracy. This platform in place we can effectively engineering your gene of interest with low cost to you. With the low gene synthesis cost you and your team will be better suited to conduct various types of genetic research specific to your interests.

    Gene Synthesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Synbio Tenchologies can also design sequencing with codon optimization software -NGTMCodon Optimization Technology at no cost.

    Gene Synthesis by PCR

    Prior to the 1970s traditional cloning was used in order to amplify a gene of interest. This process of gene synthesis by PCR is still used today, but relies on a laborious process of achieving the final amplified product. Traditional cloning relies on recombinant DNA being integrated into a bacteria host’s genome. Once the DNA is integrated into the bacteria host’s genome, the DNA is then amplified and later extracted. Unfortunately, this process allows for many variables to be interfered with resulting in a tarnished and lower quality product. In the early 1980s, Kary Mullis discovered and developed a much more efficient method of amplifying genes of interest. This method is called polymerase chain reaction (PCR). The basic process that PCR follows starts with the addition of two primers and a heat-stable Taq polymerase to the targeted gene. The mixture is then heated, allowing the hydrogen bonds between strands to denature. The mixture is then cooled, allowing the primers to hybridize to the complementary sequences of target DNA. Heat is then applied again to allow for the Taq polymerase to extend complementary strands from the primers. This process is then repeated hundreds or thousands of times, allowing for a large amount of amplification with ease. PCR has revolutionized the genetics research community, allowing millions of copies of DNA to be synthesized within hours. It is this efficiency that has made PCR become increasingly popular over the past thirty years. Another aspect of genetics that has revolutionized genetics research is gene synthesis. Gene synthesis is the process by which a physical sequence of DNA is constructed from a desired sequence in text format. Gene synthesis is carried out here, at Synbio Technologies, by our Syno® Platform. This allows us, at Synbio Technologies, to synthetically engineer genes up to 150 Kb in length. The sequence can then be amplified as many times as necessary by PCR. It is this connection between gene synthesis and PCR that has caused a large impact and various applications on the field of genetics.

    The connection that these two technologies have is that gene synthesis uses PCR to amplify the gene of interest. The reliance is shown when PCR is used to amplify the synthetically engineered gene to the requested amount of copies. The gene of interest starts in text format, specified by the costumer, and put through our Syno Platform in order to generate the physical copy of the sequence. Throughout this process the possibility for errors within the sequence being generated can be quite high. For this reason, the Syno Platform includes multiple quality assessments to verify that the sequence of interest is identical to the one generated by Synbio Technologies. We offer one hundred percent sequence verification, analyzed with Sanger sequencing. After the sequenced is verified to be one hundred percent accurate, PCR is used to amplify the synthetically engineered gene. The resulting amount of product, specified by the customer, will then be shipped to your location, within as few as five days. The high quality product that the costumer receives from Synbio Technologies can then be put to use in various fields of genetics research that gene synthesis and PCR are commonly associated with. Gene synthesis itself offers a wide range of applications. It has been used to generate more effective vaccinations, as well as to study and improve the delivery of viral vectors used in gene therapy. Gene synthesis is the creation of the sequence of interest, but it is PCR that does the hard work to generate a sufficient amount of the sequence necessary to conduct these types of research. PCR offers the most efficient process to amplify the gene synthesis product in order to obtain a sufficient amount of product. Gene synthesis is a technology that is constantly utilized and relied upon, and few companies offer the efficiency and high quality product that Synbio Technologies offers.

    This process, from costumer requested sequence to the final physical product, has been in use by Synbio Technologies for many years and we pride ourselves on our efficiency as well as high quality output. In addition to the efficiency and high quality output, we offer competitive prices and fast turnaround time. For gene synthesis, our prices starts at approximately $0.10 per base pair, which is near the lowest price in the gene synthesis industry. We offer the ability to synthesize a wide range of gene lengths, ranging from 100 base pairs to 150 Kb base pairs in length with one hundred percent accuracy. In addition to the range of lengths, using our Syno® 2.0 Platform, we are capable of generating many different structure of DNA. These structures include: repeated sequences, hairpin structures, high GC percentage, etc. These structures are of course then amplified by PCR in order to fulfill as many copies as the customer may need. After amplification by PCR and before shipping, the engineered sequences are then verified again in order to assure the quality of the product and the conservation of the requested product. This allows us to correct for any errors that may have occurred during the gene synthesis process or amplification by PCR. With the ability to generate large and complicated structures with this high of accuracy it is clear the Synbio Technologies is one of the leading companies in the gene synthesis industry.

    Gene Synhtesis Related Services

    • Codon Optimization
    • Vector Construction
    • Small Genome Synthesis
    • Pathway Synthesis

    Synbio Tenchologies can also design sequencing with codon optimization software -NGTMCodon Optimization Technology at no cost.

    Gene Synthesis Codon Optimization

    Gene synthesis refers to the technology of artificially synthesizing double-stranded DNA molecules in vitro through reverse transcription of mRNA of a known template gene. Intelligent synthetic gene design is critical to gene engineering and the efficient production of recombinant protein through heterologous hosts.

    Unfortunately, not all genes can be successfully and effectively expressed in heterologous expression systems. The intrinsic sequence characteristics of genes including stability, codon bias, GC content, and mRNA secondary structure play unexpected roles in regulating translation. The genetic code consists of 64 different tri-nucleotide codons which correspond to only 20 amino acids. This degeneracy allows multiple synonymous codons to encode the same protein. Codon optimization , described as altering codons within the gene to improve recombinant protein expression, is an important part of efficient synthetic gene design.

    The Origins of Codon Usage Bias

    Codon bias arises from the observed uneven usage of codons across different organisms. In Escherichia coli and Saccharomyces cerevisiae (yeast), certain synonymous codons are optimal and preferred to match the most abundant tRNAs in the cell or bind to those tRNAs with best binding strength. The preferred codons might tend to be read by abundant tRNA molecules while low-usage codons might tend to be read by scarce tRNA. The reason why some highly expressed genes possess preferentially selected codons is still unknown. One conventional perspective is optimal codons would be translated faster than rare codons, enhancing the efficiency of translation. Another alternative assumption is that using preferred codons may increase translation accuracy.

    The Functional Impact of Codon Optimization

    Codon usage bias is correlated with gene expression levels. In heterologous protein expression, the gene of interest can be overexpressed. Their products can take up to 30% of the cell’s total proteins. The attempt to generate more protein by changing codon assignments led to broad use of codon-optimized mRNAs. Originally, codons within the gene were altered by replacing rare codons with synonymous counterparts, which were more preferable and more frequently used by hosts. It was found that optimized codons led to an increase in corresponding protein expression in both plants and mammalian cells. Surprisingly, expression of viral proteins has also been found to decrease after substitution of synonymous codons or adjacent codons. The many unanswered questions related to codon optimization may have profound significance in exploring novel methods of vaccine design.

    Strategies of Codon Optimization

    A variety of approaches and programs can design and produce various codon-optimized mRNA sequences. The quantification of codon usage as well as the completion of codon changes must be considered. Synthetic codon optimization tends to substitute rare codons with synonymous counterparts used at a higher frequency. Another variation referred to as codon harmonization alters codons within gene sequences to correlate with the codon usage bias of the host organism.

    Admittedly, for protein expression, optimizing codon usage alone is not sufficient to perfect the design of synthetic genes. Many other factors can potentially interfere; for example, mRNA secondary structure can affect gene transcription. Additionally, cryptic splice sites, polyadenylation signals, and other regulatory elements ought to be avoided, as they can lead to undesirable processing of mRNA. GC content has a direct impact on the binding stability and annealing temperature of DNA sequences. Translation initiation and termination efficiency also influence protein output and solubility. Only by taking all of above factors into consideration can gene synthesis codon optimization achieve maximum value.