Key Summary:  

• A promoter is a DNA sequence that controls gene expression. 
• The promoter tells the RNA polymerase where the begin and allows the enzyme to attach to the DNA.
• The strength of a promoter refers to its ability to efficiently initiate transcription. 

In genetics, a promoter is a specific region of DNA that serves as the initial binding site for RNA polymerase and transcription factors. This
region is located upstream (towards the 5' end) of the gene it controls. The primary function of a promoter is to initiate the process of transcription, where the information encoded in the DNA is transcribed into RNA.

Promoters are essential elements in the regulation of gene expression. Here are some important aspects to consider:

• Initiating transcription: Promoters contain sequences of nucleotides that are recognized by RNA polymerase, the enzyme responsible for synthesizing RNA from a DNA template. When RNA polymerase binds to the promoter, it marks the beginning of transcription.
• Transcription factors: Promoters also interact with transcription factors, which are proteins that regulate gene expression. These transcription factors bind to specific sequences within the promoter region and help recruit RNA polymerase to the correct
  gene.
• Conserved sequences: Promoters often contain conserved sequences, known as core promoter elements, that are recognized by RNA polymerase and transcription factors. These elements include the TATA box, initiator element (Inr), and others, depending
  on the specific gene and organism.
• Promoter strength: The strength of a promoter refers to its ability to efficiently initiate transcription. Strong promoters result in high levels of gene expression, while weak promoters lead to lower levels of expression.
• Promoter regulation: Promoters play a crucial role in gene regulation, as the activity of a promoter can be modulated by various factors such as environmental cues, signaling pathways, and the presence of specific transcription factors or regulatory
  proteins.

Promoters are fundamental elements of gene expression regulation, as they control when and to what extent a gene is transcribed into RNA, thereby influencing the production of proteins within a cell.

How are promoters used in genetics?

In genetics, promoters play a crucial role in regulating the start of transcription, which is the process
where the genetic information in DNA is transcribed into RNA. Promoters act as binding sites for RNA polymerase and transcription factors, allowing these molecules to come together and begin the transcription process. Here's how promoters are used
in genetics:

• Initiating transcription: The primary function of a promoter is to initiate the transcription of a specific gene. When RNA polymerase and transcription factors bind to the promoter region, they form a transcription initiation complex, which marks
  the starting point for transcription.
• Regulating gene expression: Promoters play a crucial role in regulating gene expression. The activity of a promoter can be influenced by various factors, including environmental signals, cellular conditions, and the presence of specific regulatory
  proteins. By modulating the accessibility or activity of the promoter, cells can control when and how much of a particular gene is transcribed.
• Studying gene function: Researchers use promoters to study the function of genes in experimental settings. By manipulating the activity of a gene's promoter, researchers can control the timing and level of gene expression, allowing them to investigate
  the gene's role in various biological processes. Promoter sequences can be modified or replaced with synthetic promoters to achieve specific experimental goals.
• Gene therapy: In gene therapy, promoters are used to drive the expression of therapeutic genes in target cells. By selecting appropriate promoters, researchers can ensure that the therapeutic gene is expressed at the desired level and in the appropriate
  cell type. Promoters that are active in specific tissues or under certain conditions can be used to achieve targeted gene expression while minimizing off-target effects.
• Biotechnology and genetic engineering: Promoters are also used in biotechnology and genetic engineering to produce recombinant proteins or modify organisms for various purposes. By coupling a gene of interest with a strong promoter, researchers can
  produce large quantities of the desired protein for research, medical, or industrial applications. Promoters can also be engineered to drive the expression of multiple genes simultaneously, allowing for the construction of complex genetic circuits
  and metabolic pathways.

What is transcription in genetics?

Transcription is a fundamental process in genetics where the genetic information encoded in DNA is copied into RNA molecules. This process is essential
for gene expression, as it serves as the first step in the central dogma of molecular biology, where genetic information flows from DNA to RNA to protein. Here's an overview of transcription in genetics:

Initiation: Transcription begins with the binding of RNA polymerase, along with other transcription factors, to a specific region of DNA called the promoter. The promoter contains sequences that signal the start site for transcription.
Once RNA polymerase is bound to the promoter, it unwinds the DNA double helix to expose the template strand.

Elongation: As RNA polymerase moves along the template strand of DNA, it synthesizes a complementary RNA molecule by adding nucleotides one at a time. The growing RNA molecule is elongated in the 5' to 3' direction, complementary to the
template DNA strand. The DNA double helix is reformed behind the polymerase as it progresses.

Termination: Transcription continues until the RNA polymerase reaches a termination signal in the DNA sequence. In prokaryotes, termination signals may include specific sequences that cause the RNA polymerase to dissociate from the DNA
and release the newly synthesized RNA molecule. In eukaryotes, termination is more complex and can involve different mechanisms.

RNA processing (in eukaryotes): In eukaryotic cells, the initial RNA transcript, called pre-mRNA, undergoes additional processing steps before it becomes mature mRNA. These processing steps include capping, splicing, and polyadenylation.
The 5' end of the pre-mRNA is modified with a 7-methylguanosine cap, introns (non-coding regions) are removed through splicing, and a polyadenine tail is added to the 3' end. The mature mRNA is then ready to be transported out of the nucleus and translated
into protein in the cytoplasm. This process takes place to ensure protection from degradation and accurate and efficient gene expression.

Gene expression regulation: Transcription is a highly regulated process that can be influenced by various factors, including environmental signals, cellular conditions, and the presence of specific regulatory proteins. Gene expression
can be regulated at initiation, elongation, or termination, allowing cells to control when and how much of a gene is transcribed into RNA.

Transcription is a crucial process in genetics that allows cells to convert the information stored in DNA into functional RNA molecules, which in turn play essential roles in protein synthesis, cellular function, and regulation of gene expression.

What role does IDT play in promoters?

The promoter is a fundamental element of gene expression regulation, making it crucial to use the correct sequence. Integrated DNA Technologies (IDT) can assist with this. For more information on various cloning techniques, sequence design, and codon
optimization, check out our DNA Cloning Guide. You can also use our Codon Optimization tool to help maximize your results.

Synthetic, double-stranded DNA fragments, such as eBlocks™ Gene Fragments or gBlocks™ or gBlocks HiFi Gene Fragments, are useful in cloning and gene assembly applications. While DNA sequences like the promoter region can be challenging to synthesize, IDT offers a variety of vectors that contain
all the necessary elements for transcription so check out your options here.

The Takeaway: Artificial intelligence and machine learning are changing our lives in huge ways, automating tasks such as data entry, customer service, and even driving cars. The next frontier? Using artificial intelligence and machine learning in protein and antibody design.

Artificial intelligence (AI) is a broad term that describes the use of machine learning (ML) and other cognitive technologies. AI is when computers mimic human understanding to learn, think, and make decisions. ML is an application of AI that allows machines to gather knowledge from data, then learn from it autonomously.

These two technologies are making inroads into healthcare.

How is AI used in healthcare?

AI can diagnose patients, remotely treat them, and monitor their health. AI can also help detect and track infectious diseases, such as COVID-19, tuberculosis, and malaria. In addition, it helps with drug discovery, communication between patients and physicians, the transcription of medical documents, the analysis of radiographic data, and the identification of patterns and irregularities that may be overlooked by humans, resulting in the early detection of diseases like cancer.

How is ML used in healthcare?

ML uses systems and tools to sort and categorize patient data. ML algorithms can discover patterns in sets of data that allow medical professionals to identify new diseases and predict treatment outcomes. ML can also predict which patients are at risk of developing certain diseases, provide personalized recommendations for diet and exercise, improve the efficiency and speed of medical services, quickly scan electronic health records to manage patient records, schedule appointments, and automate processes.

What is protein engineering?

Protein design is an arm of synthetic biology that engineers custom proteins and peptides for specific applications. This process involves manipulating an amino acid sequence to create new proteins with specific properties. Protein design combines computational techniques and lab experiments, with the goal of creating proteins with functions that are not available naturally. There have been many useful proteins engineered for both bioproduction and biomedical applications, one example is an enzyme that can break down plastics. Protein design is challenging because it’s hard to model how a protein’s three-dimensional structure and function is encoded in its amino acid sequence.

What is antibody engineering?

Antibody design is the process of predicting then designing the structure of antibodies. The main goal of antibody engineering is to create antibodies that will bind strongly to a desired target at a desired site. Antibodies are host proteins produced by a body’s immune system as a reaction against foreign molecules that enter the body. These foreign molecules, also called antigens, are what elicit the immune responses that make you sick, while antibodies are how a body defends itself against the antigens.

How can AI and ML support protein and antibody design?

Designing antibodies and proteins can be challenging. When it comes to antibody design, challenges include:

• Functional limitations: Therapeutic antibodies may have inadequate pharmacokinetics, tissue accessibility, or impaired interactions with the immune system.
• Physical instabilities: The protein nature of monoclonal antibodies (mAbs) makes them highly sensitive to various physical and chemical conditions, which can lead to instabilities.
• Modeling of an antibody/antigen complex structure: Modeling of an antibody/antigen complex structure remains an unsolved problem.

Meanwhile, protein design has two main challenges:

• Lack of understanding the factors that contribute to the protein structure and functions within an amino acid sequence.
• A lack of structural prediction from folding.

AI and ML, however, offer many advantages and can help break through some of these challenges in protein and antibody design. AI has the potential to take an antibody and improve it using knowledge gained from investigating other similar antibodies. AI also has the ability to design an antibody from scratch by picking, choosing, and combining different attributes found in other antibodies.

When it comes to protein design, machine learning can generate protein designs that have valuable structural features that don’t exist naturally. These proteins can be used to make materials with mechanical properties that are similar to existing materials but that have a much smaller carbon footprint.

IDT’s role in protein and antibody design

Integrated DNA Technologies provides custom nucleic acids for research applications, and has a variety of tools for protein and antibody design, including:

• Codon Optimization Tool: Converts DNA or protein sequences from one organism to another for expression. The IDT algorithm screens and filters sequences to minimize complexity and secondary structures.
• eBlocks™ Gene Fragments: Can be used for protein design research and in antibody discovery workflows.
• Protein Engineering Booklet: A free booklet that explores how synthetic biology has benefited a wide variety of applications.
• Alt-R™ CRISPR Systems: A workflow for CRISPR-based gene disruption.
• Antibody discovery: Workflows for targets assessment, hit generation, and lead optimization.

In the rapidly evolving field of molecular pathology, the role of organizations like the Association for Molecular Pathology (AMP) are more crucial than ever. Laurie Menser, CAE, the CEO of AMP, provides a unique perspective on the challenges and advancements in this field, emphasizing the importance of education, speed of discovery, and the promising future of implementing artificial intelligence (AI). In this interview with IDT at the AMP 2024 Annual Meeting and Expo, Menser shares her journey, the mission of AMP, and how the organization is poised to support molecular pathologists and oncologists in optimizing patient care.

A journey of dedication and a rapidly evolving landscape

Menser’s journey with AMP began long before she assumed the role of CEO in January 2024. With a background in strategic development and marketing within AMP, Menser’s dedication to the organization is clear with her nearly 17-year commitment to the association, and her involvement is also deeply personal. Her mother’s battle with non-small cell lung cancer (NSCLC) highlighted the critical role of molecular testing in patient care and fueled her passion for AMP’s mission.

“Seeing the perspective of the patient and how testing can impact their journey, making sure it's covered, and getting the right test, I realized the importance of our work,” Laurie reflects. “It’s not just a job—it’s a mission I genuinely believe in.”

Menser notes the dynamic nature of molecular pathology, specifically how the field’s rapid advancements pose both opportunities and challenges. The speed of discovery often outpaces the existing infrastructure, creating a constant need for updated education, practice guidelines, and regulatory frameworks.

“Our biggest asset is also the hardest thing to face: our speed. We’re moving faster than the systems built to support us,” Menser explains. She also highlights how AMP works to face this challenge: “AMP tackles challenges from three directions: education, clinical practice improvement, and public policy and advocacy.”

Collaboration and education

Menser underscores the importance of collaboration between pathologists and oncologists to enhance patient care. AMP works closely with oncology societies to develop practice guidelines and educational programs, fostering integrated care teams.

“Education and practice guidelines should be developed together to ensure everyone is on the same page,” Menser asserts. “The more pathologists and oncologists collaborate the better care patients will receive.”

Navigating regulatory and reimbursement challenges

Although integrated care teams can make a significant impact on outcomes, regulatory and reimbursement issues remain significant hurdles in the field. Menser explains that without proper coverage, patients may not receive the necessary tests, which can impact treatment outcomes.
“Reimbursement and coverage are patient access issues. If people aren’t getting paid, patients aren’t getting tested,” Menser states. “We need to ensure that appropriate testing is covered to provide the best patient care.”

Global perspectives

While the educational efforts of AMP primarily focus on the U.S., Menser is keenly aware of the global landscape. She notes the importance of monitoring international regulatory frameworks and how different healthcare systems approach coverage and reimbursement.

“We closely follow European regulatory issues like In vitro Diagnostic Regulation (IVDR). It will be interesting to see if providing easy access to testing in other countries leads to better patient outcomes and economic benefits,” Menser says.

Menser is particularly interested in data emerging from countries that have made significant efforts to make comprehensive testing more accessible. For example, Germany's initiatives in whole exome sequencing (WES) could provide valuable insights into how widespread access to testing impacts patient outcomes and healthcare costs.

“Systems that provide comprehensive coverage might show that early access to testing leads to better patient outcomes and could be more economical in the long run. This kind of data can influence how testing is covered in the U.S.,” Menser explains.

Promise of AI and machine learning

One of the most exciting developments in molecular pathology is the integration of AI and machine learning. Menser discusses the potential of these technologies to revolutionize the field, particularly in managing the vast amounts of data generated by next generation sequencing (NGS).

“AI and machine learning are coming hard and fast in molecular pathology. These technologies will support the field long-term, but they won’t replace the role of the pathologist or the laboratory,” Menser emphasizes. “You need someone who understands it well enough to say when it’s wrong.”

The application of AI and machine learning in molecular pathology can significantly enhance data analysis, making it possible to interpret the immense volumes of information generated by NGS more efficiently. These technologies can help identify patterns and insights that may not be immediately apparent to human analysts, thus expediting the discovery process and improving diagnostic accuracy.

Supporting innovation and collaboration in molecular pathology

AMP celebrated its 30th year as an association at the 2024 annual meeting in Vancouver. As the organization continues to navigate the complexities of the molecular pathology field, Menser’s leadership and vision will be instrumental in driving the organization forward. By addressing challenges from multiple angles and embracing new technologies, AMP is well-positioned to support molecular pathologists and laboratory professionals in the ever-changing landscape of this field.

To learn more about how IDT supports researchers in molecular pathology with NGS research solutions, visit idtdna.com/CancerResearchSolutions. 

The Takeaway: By using expression vectors, researchers can introduce genes of interest into cells and study their function or produce specific proteins for various purposes, such as medical research, biotechnology, or pharmaceutical development. Different types of expression vectors are used depending on the host organism and the specific goals of the experiment or application.

What is an expression vector?

An expression vector is a type of DNA plasmid or other DNA molecule used to shuttle or introduce a specific gene into a target cell, typically a bacterium or a eukaryotic cell such as yeast or mammalian cells. These vectors are designed to facilitate the expression of the gene, meaning they contain regulatory sequences that allow the gene to be transcribed into messenger RNA (mRNA) and translated into protein within the host cell.

Expression vectors usually contain several key components:

• Promoter: This is a DNA sequence that initiates transcription of the gene. It's usually a strong promoter that ensures efficient transcription of the inserted gene.
• Selectable marker: This is a gene that confers a selectable phenotype to cells that have taken up the vector. For example, it might provide resistance to an antibiotic, allowing only cells that have successfully incorporated the vector to survive when grown in a medium containing that antibiotic.
• Reporter gene: Sometimes, an expression vector will include a reporter gene. This is a gene whose expression can be easily detected and quantified, allowing researchers to monitor the activity of the promoter or the efficiency of gene expression.
• Polyadenylation signal: This is a DNA sequence that signals the end of transcription. It's typically located downstream of the gene of interest and ensures that the mRNA produced is properly processed and stabilized.
• Origin of replication: This is a DNA sequence that allows the vector to replicate within the host cell. In bacterial cells, this might be the origin of replication for the plasmid, while in eukaryotic cells, it might be a sequence that allows the vector to integrate into the host cell's genome.

How do you clone a gene into an expression vector?

Cloning a gene into an expression vector involves several steps. Here's a general overview of the process:

1. Select an appropriate expression vector
2. Prepare the gene of interest
3. Design compatible restriction sites
4. Digest the expression vector
5. Digest the gene of interest
6. Ligate the gene into the vector
7. Transform the recombinant vector into host cells
8. Screen for transformed cells
9. Verify the presence of the gene
10. Express the gene

For a more in depth look at various cloning techniques get the handbook.

Explaining recombinant protein production

Recombinant protein production is the process of generating proteins using genetic engineering techniques to introduce a gene encoding the protein of interest into a host organism or cell line, which then produces the protein. This method allows for the production of proteins that are not naturally abundant or available in large quantities from their native sources. Recombinant protein production is widely used in various fields, including biotechnology, pharmaceutical development, and basic research.

Here's an overview of the typical steps involved in recombinant protein production:

Gene cloning: The first step is to isolate the gene encoding the protein of interest. This gene is then cloned into a suitable expression vector. The vector contains regulatory elements such as promoters and enhancers to drive gene expression, as well as other necessary sequences like those described above.

Vector transformation: The recombinant expression vector is introduced into a host organism or cell line. The choice of host organism depends on factors such as the protein's complexity, post-translational modifications required, and the scale of production needed. Common hosts include bacteria (e.g., Escherichia coli), yeast (e.g., Saccharomyces cerevisiae), insect cells (e.g., baculovirus-infected insect cells), and mammalian cells (e.g., Chinese hamster ovary cells).

Expression: Once inside the host cell, the recombinant expression vector replicates, and the gene of interest is transcribed into messenger RNA (mRNA) by the host cell's machinery. The mRNA is then translated into the protein of interest by ribosomes.

Protein purification: After expression, the recombinant protein needs to be purified from the host cell lysate or culture medium. Various purification methods can be employed, including affinity chromatography, ion exchange chromatography, size-exclusion chromatography, and others. The choice of purification method depends on the properties of the protein and the desired purity level.

Quality control: The purified recombinant protein undergoes quality control measures to ensure its integrity, purity, and functionality. This may include techniques such as SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis), Western blotting, mass spectrometry, and functional assays.

Storage and distribution: Once the recombinant protein passes quality control, it is typically stored under appropriate conditions to maintain its stability and functionality. Depending on its intended use, the protein may be distributed to researchers, used in biopharmaceutical manufacturing, or stored for future experiments.

What is protein expression and purification in E. coli?

Protein expression and purification in Escherichia coli (E. coli) is a common method used to produce recombinant proteins for various research, biotechnological, and industrial applications. E. coli is a popular host organism for protein expression due to its rapid growth, well-characterized genetics, and ease of genetic manipulation. Here's an overview of the protein expression and purification process in E. coli:

Gene cloning: The gene encoding the protein of interest is first isolated and cloned into an expression vector suitable for E. coli. The vector typically contains regulatory elements such as a strong promoter (e.g., the T7 promoter) to drive gene expression, as well as a selectable marker for identifying transformed cells.

Transformation: The recombinant expression vector is introduced into E. coli cells by a process called transformation. This can be achieved using various methods such as chemical transformation, electroporation, or conjugation.

Expression: Once inside the E. coli host cells, the recombinant expression vector replicates, and the gene of interest is transcribed into messenger RNA (mRNA) under the control of the promoter. The mRNA is then translated into the protein of interest by the host cell's ribosomes.

Induction: In many cases, protein expression in E. coli is induced by adding an inducer molecule to the growth medium. For example, if the expression vector contains the T7 promoter, protein expression can be induced by adding isopropyl β-D-1-thiogalactopyranoside (IPTG), which triggers transcription.

Cell harvesting: After a period of growth and induction, the E. coli cells are harvested by centrifugation. The cells are then lysed to release the intracellular contents, including the recombinant protein.

Protein purification: The recombinant protein is purified from the cell lysate using various chromatography and purification techniques. Common purification methods include affinity chromatography (e.g., using His-tag or GST-tag), ion exchange chromatography, size-exclusion chromatography, and hydrophobic interaction chromatography.

Quality control: The purified recombinant protein undergoes quality control assays to assess its purity, integrity, and functionality. This may include SDS-PAGE analysis, Western blotting, mass spectrometry, and functional assays specific to the protein's activity.

Storage and distribution: Once purified and characterized, the recombinant protein is typically stored under appropriate conditions to maintain its stability and functionality. Depending on its intended use, the protein may be distributed to researchers, used in biotechnological processes, or stored for future experiments.

What are mammalian cell lines for protein expression?

Mammalian cell lines are widely used for protein expression due to their ability to perform complex post-translational modifications, produce correctly folded proteins, and maintain protein stability. Several mammalian cell lines are commonly utilized for protein expression, each with its own advantages and disadvantages. Here are some of the most popular mammalian cell lines for protein expression:

Chinese hamster ovary (CHO) cells: CHO cells are one of the most widely used mammalian cell lines for protein expression in biopharmaceutical manufacturing. They offer high protein yields, efficient post-translational modifications (such as glycosylation), and scalability for large-scale production.

Human embryonic kidney (HEK) 293 cells: HEK293 cells are derived from human embryonic kidney cells and are frequently used for transient protein expression. They offer high transfection efficiency and can produce high levels of recombinant proteins. HEK293 cells are commonly used for producing proteins for structural studies, functional assays, and biochemical characterization.

NS0 and SP2/0 mouse myeloma cells: These mouse myeloma cell lines are commonly used for stable protein expression and generation of monoclonal antibodies. They are particularly useful for applications requiring high protein expression levels and clonal selection of recombinant cell lines.

Yeast cells (e.g., Pichia pastoris, Saccharomyces cerevisiae): Although not mammalian, yeast cells are worth mentioning for their utility in protein expression. They offer advantages such as rapid growth, high protein yield, and ease of genetic manipulation. While they do not perform mammalian-like post-translational modifications, they are suitable for producing certain types of proteins, including antibodies and enzymes.

Insect cells (e.g., Sf9, Sf21): Insect cell lines such as Spodoptera frugiperda (Sf) cells are commonly used with the baculovirus expression system for producing recombinant proteins. They offer advantages such as efficient protein folding, secretion, and the ability to perform certain post-translational modifications.

IDT’s role in protein expression

IDT has numerous products for researchers using expression vectors. They include:

• eBlocks™ Gene Fragments: High-quality gene fragments designed for fast turnaround times
• gBlocks™ and gBlocks HiFi Gene Fragments: Double-stranded DNA fragments up to 3000 bp in length, designed for affordable and easy gene construction or modification
• Gene Synthesis: Easy-to-use solution for researchers who want to skip in-house cloning steps and move quickly to functional studies
• qPCR Gene Expression: Multiple solutions including probe assays, master mixes, primer assays, and more

 

The Takeaway: Biosecurity is a hot topic in the nucleic acid industry, and IDT plays a leading role in ensuring appropriate screening for our products and our customers. Recent federal legislation has many researchers wondering how their work could be impacted. Read more about what biosecurity is, why it matters, and the role IDT plays in giving scientists peace of mind that their work can go on unimpeded.

What is biosecurity?

Biosecurity is a set of preventive measures that are designed to reduce the risk of misuse of synthetic nucleic acid sequences of concern related to infectious diseases, pests, and other harmful biological agents. In the oligo manufacturing industry, biosecurity ensures measures that prevent the misuse of dangerous biological materials and ensures that those agents do not escape into the environment or fall into the wrong hands.

Key elements of biosecurity include:

• Quarantine protocols
• Access controls
• Monitoring and surveillance
• And more

Why is biosecurity important?

Biosecurity is important because it helps protect public health, agriculture, ecosystems, and entire economies from the risks posed by misuse of synthetic nucleic acid sequences of concern related to infectious diseases, pests, and harmful biological agents. Strong biosecurity measures can:

1. Prevent disease outbreaks
2. Protect public health
3. Prevent bioterrorism and biological warfare
4. Safeguard food supplies
5. Protect biodiversity and ecosystems
6.  Promote and protect ethical responsibility and scientific integrity

How does pending U.S. federal legislation impact biosecurity?

The BIOSECURE Act (H.R. 7085), introduced in Congress in early 2024, is a proposed law that would restrict U.S. federal agencies from contracting with some biotech companies that have connections to People’s Republic of China military companies. In essence, the bill would prevent taxpayer money from funding the biotech efforts of what some consider to be foreign adversaries and prevent American genomic data from being sent to the Chinese government.

This bill also prohibits entities that receive federal funds from using biotechnology that is from a company associated with a “foreign adversary.”

Specifically, federal agencies and groups that receive federal funds may not procure or use any biotech equipment or service that is from a biotechnology company of concern and may not contract with any entities that do so. The bill defines “biotechnology company of concern” as an entity under the control of a foreign adversary and that poses a risk to national security based on its research or multiomic data collection.

As currently envisioned, the law would work like this: Federal agencies would develop a list of prohibited companies, including several listed specifically in the bill, and also solicit and consider restriction waivers. Agencies must then also report on the national security risks posed by multiomic data collection by foreign adversaries in connection with biotechnology equipment or services, and biotechnology companies that have those data.

What are the potential issues at hand and how does it impact the research community?

The BIOSECURE Act, which is attempting to enhance the security of pharmaceutical and life science manufacturing in the U.S., could significantly impact the research community by restricting access to biotech services and equipment from the targeted foreign companies. In some research settings, consistency is critical, and researchers must use the same products throughout every step of their work to ensure efficacy, safety, and confidence in the results.

What could happen if a team had to change the products they use because their supplier is deemed to have connections to an adversary? In many cases, they would have to start over from the beginning, which would hinder research progress, increase costs, and cause delays. In particular, it could lead to:

• Limited collaboration: Researchers may be forced to avoid collaborations with some companies.
• Disrupted supply chains: Researchers who rely on specific equipment or services from blacklisted companies may face challenges in obtaining necessary materials for their research.
• Increased costs: Seeking alternative sources for research needs may lead to higher costs for researchers who have to scramble to find replacements.
• Potential for research slowdown: Restrictions on collaborations and access to technology could slow research progress.

How IDT helps

IDT is uniquely positioned to support researchers for the continuum of their projects. IDT’s vertically integrated supply chain was designed to prevent interruptions to work. In the specific case of the BIOSECURE Act, IDT has a global manufacturing footprint, with manufacturing operations located across the U.S. and in Belgium and Singapore.

In addition to this, IDT is a leader in developing and adhering to biosecurity protocols, which include:

• Screening DNA orders and carefully vetting clients
• Limiting access to sensitive genetic materials, databases, and production facilities
• Adhering to national and international regulations governing the production, handling, and export of synthetic DNA
• Comprehensive employee training, physical security, data security, and incident response and containment

Since 2016, IDT has collaborated with BBN/Raytheon Technologies to support initiatives from the Intelligence Advanced Research Projects Activity (IARPA, a government agency). This led to the development of Raytheon’s FAST-NA software, which IDT uses to screen all double-stranded nucleic acid products longer than 200 base pairs. This process complies with the Bureau of Industry and Security, the Federal Select Agent Program, and the International Gene Sequencing Consortium (IGSC) Harmonized Screening Protocol.

In response to President Biden's 2023 Executive Order on the Safe, Secure, and Trustworthy Development and Use of Artificial Intelligence, IDT is committed to meeting guidelines in the Framework for Nucleic Acid Synthesis Screening. These include:

1. Expanded screening requirements to include biofoundries, cloud labs, and contract research organizations
2. Federal purchase restrictions for compliant companies
3. Enhanced screening protocols to include nucleic acid sequences of concern in non-threat species and reduce the minimum sequencing length from 200 bases to 50 bases

IDT is proactively enhancing our nucleic acid screening processes by:

• Identifying and addressing weaknesses in current screening methods
• Collaborating with other nucleic acid providers to establish standards for testing and verifying screening methodologies
• Actively participating in the IGSC as a founding and voting member

IDT’s commitment to our customers

We focus on critical details so you can have confidence in your research:

• IDT has a global footprint and continuity plan in place
• 15 years ago, IDT helped to form the International Gene Synthesis Consortium (IGSC) to promote the secure and safe synthesis of DNA. Since then, we’ve supported the adoption of the Screening Framework Guidance and follow this guidance in our application of the Harmonized Screening Protocol.
• We are actively working with Microsoft on the use of AI screening for biosecurity.

Learn more about IDT here.

How to resuspend eBlocks and gBlocks Gene Fragments

Standard gBlocks Gene Fragments  and gBlocks HiFi Gene Fragments are dried down and shipped in tubes (unless otherwise requested to ship in plates or ship wet). Plate products, including gBlocks and eBlocks Gene Fragments, are shipped on dry ice, if wet and ambient, if dry. Once you receive your DNA fragments, it’s recommended to perform IDT’s resuspension protocol. gBlocks Gene Fragments are stable for up to two years while dried and stored at −20C.

Follow the steps below when resuspending your DNA fragments:

1. Prepare your DNA fragment: Once you receive your DNA fragments, spin down the tube in a microcentrifuge for 5 seconds. This ensures that the DNA pellet is at the bottom.  Since the pellet can be statically charged or lodged in the cap during shipping, doing this step prevents the pellet from flying out of the tube or remaining in the cap thus losing yield.

2. Add molecular grade water or buffer:  After centrifugation, resuspend the pellet in molecular-grade water or TE buffer (pH 7.5–8)  the required concentration. We recommend you use either a molecular grade water or a buffer such as IDTE, pH 8, to achieve a final concentration of 10 ng/µL. Please note that concentrations <1 ng/µL can result in material loss due to adherence to the plastic tube.

3. Vortex briefly: Mix the solution briefly using a vortex.

4. Heat the tube: Incubate at approximately 50°C for 15–20 minutes. Heating ensures the solvent contacts the entire pellet, even if it is stuck to the side of the tube, thereby increasing the likelihood of complete resuspension.

5. Vortex and centrifuge: After heating, briefly vortex again and then centrifuge.

6. Measure final concentration: Verify that the concentration of the resuspended gBlocks Gene Fragments to ensure that the full product has gone into solution. Use Nanodrop quantification to verify the final concentration. This method is preferred for short gBlocks Gene Fragments, as the Qubit™ system may give artificially low readings[1].

How to store eBlocks and gBlocks Gene Fragments

IDT Gene Fragments are stable for up to two years under proper storage conditions.

Here are some recommendations for improving the preservation of your gBlocks Gene Fragments:

• After resuspending in a high-quality, molecular-grade water or buffer, pH 7.5–8.0, you should store the DNA at −20°C and if necessary, aliquot to avoid more than 2 or 3 freeze-thaw cycles. Adding a carrier to your resuspension and dilution buffers can help prevent any potential decrease in product concentration.
• If stored dry at ambient temperature, IDT Gene Fragments remain stable for approximately three months due to inherent moisture causing DNA damage over time.

• It’s recommended that you generate aliquots at concentrations >1 ng/µL and reduce repetitive freeze-thaw cycles of the stock. Avoid more than 3 freeze-thaw cycles. If necessary, aliquot your IDT Gene Fragments before freezing to minimize degradation.

How to stabilize eBlocks and gBlocks Gene Fragments

If storing the DNA fragments at a concentration less than 1 ng/µL, you might experience a decrease in your final concentration over time. We have observed a decrease in DNA fragment concentrations in solutions with a starting concentration of less than 1 ng/µL, even when stored in low-bind tubes. This may be related to the very high purity of DNA fragments. Synthetic DNA lacks normal cellular debris found in DNA isolated from natural sources. In the absence of these natural carriers, synthetic DNA will bind irreversibly to plastic, resulting in DNA loss. Hence, small amounts of carrier can prevent this loss.

To prevent concentration loss, consider adding natural carriers like tRNA or poly A (0.1–1.0 mg/mL) to prevent product loss over time. You can add tRNA or poly A at concentrations of 0.1–1.0 mg/mL to the dilution buffers. Both tRNA (55714-250MG) and Poly A (P9403-25MG) can be sourced from Sigma. Without these natural carriers, the gBlocks Gene Fragments bind irreversibly to the tube plastic over time, leading to the observed decrease in concentration. Adding a carrier to your resuspension and dilution buffers can help prevent this loss of product.

By following these guidelines, you can ensure the integrity and longevity of your gBlocks Gene Fragments. Ready to use your gBlocks Gene Fragments for your experiment?  Read more about how to clone with your IDT Gene Fragments by downloading our free cloning guide.

The Takeaway: The latest iteration of the avian flu is grabbing headlines and prompting caution in the United States and around the world. H5 bird flu is common in wild birds globally but is currently causing outbreaks in poultry and dairy cows, and now cases are spreading to dairy workers in the U.S. IDT has responded quickly to this outbreak, offering a primer and probe set for the identification of Type A (H5) Clade 2.3.4.4b. Read on to learn more.

What is avian flu?

Avian influenza, also known as bird flu, is an infectious disease caused by viruses that mostly target wild birds. Wild aquatic birds like ducks, geese, and storks are most likely to catch this flu, though domestic poultry like chickens and turkeys can get it too. Symptoms include sudden death, low energy, swelling, reduced egg production, and nasal discharge, coughing or sneezing. Avian flu can also infect domestic and wild mammals such as dogs, cats, cows, bears, raccoons, and foxes. Symptoms in these animals can include fever, difficulty breathing, and death.

Can avian flu spread to humans?

Yes. While bird flu is mostly spread between birds, and from birds to other animals, there are cases of it spreading to humans. As of May 30, there have been four total reported human cases in the U.S., including three that occurred after exposure to dairy cows and one that occurred after exposure to poultry.

While bird flu is rare in humans, it’s a disease you want to avoid getting. Avian flu does not usually infect people, but there have been rare cases of human infection. Infections range in severity from unnoticeable to death.

Human infections with avian flu usually happen when the virus gets into your eye, nose, or mouth, or is inhaled. Guidelines for humans who might come into contact with the virus include:

• Wear personal protective equipment (PPE) when in direct or close contact (less than about 6 feet) with sick or dead animals like poultry or wild birds, or with other animals, litter, feces, or material potentially contaminated with the virus
• Those who come into contact with suspect animals, including those who were wearing PPE, should be monitored for new respiratory illness symptoms, including conjunctivitis, for 10 days after their last exposure
• Poultry farmers, poultry workers, livestock farmers and workers, veterinarians and vet staff, backyard bird flock owners, and emergency responders should avoid unprotecrted direct physical contact or close exposure with sick birds, livestock, or other animals; the carcasses of birds, livestock, or other animals; feces or litter; raw milk; and surfaces and water that might be contaminated with animal excretions
• Clinicians should keep in mind that there is a chance that there could be virus infection in people with signs or symptoms of acute respiratory illness who have relevant exposure history
• State health departments should be on alert and ready to notify the CDC if there’s a case under investigation
• There are also detailed recommendations for surveillance and testing

There is currently no evidence of human-to-human spread and the current public health risk, as assessed by the Centers for Disease Control and Prevention, is low. No human vaccines for avian flu exist in the U.S., and normal flu vaccines won’t work to protect you against avian flu.

Why is testing for avian flu important?

According to the CDC, there are currently nine states with outbreaks in cows, 48 states with poultry outbreaks, and bird flu is present in wild birds basically everywhere. To protect both human and animal health, testing is important.

There are two testing methods, depending on who or what is being tested—humans or poultry.

Bird flu tests for humans: A healthcare worker collects a nose or throat swab and sends it to a testing lab, which uses a polymerase chain reaction (PCR) test to get results in a few hours.

Bird flu tests for poultry: A bunch of tests can be used on poultry, including virus isolation, direct RNA detection, and an antigen capture immunoassay. Which test to use depends on different circumstances—for example, the immunoassay test is available commercially and can be good for screening flocks but is less sensitive than a molecular assay. Identified early enough, avian flu can be treated with antiviral meds.

What is avian flu clade 2.3.4.4b?

Avian influenza virus H5N1 has evolved over time into 10 clades and multiple subclades. These clades are defined based on their phylogenetic characterization and the sequence homology of the hemagglutinin gene.

The current clade in circulation is H5N1 clade 2.3.4.4b. CDC has termed this clade “highly pathogenic” in dairy cattle and cats. This clade showed up in the U.S. in late 2021 and has been blamed for human disease in Ecuador and Chile. It made a resurgence in dairy cattle in the U.S. in the winter of 2024, affecting herds in Kansas, Texas, and New Mexico, as well as domestic cats that were fed raw milk from sick cows. More recent testing showed that “dairy cattle are susceptible to infection with HPAI H5N1 virus and can shed virus in milk and, therefore, might potentially transmit infection to other mammals via unpasteurized milk.”

What role does IDT play?

IDT recently launched the Avian Influenza Type A (H5) Primers and Probe Set, which specifically targets clade 2.3.4.4b. Manufactured in a certified template-free environment, this product is available to labs for research on the virus. The primers and probe set helps researchers involved in 2.3.4.5b identification and surveillance, research and understanding, vaccine development, and public health preparedness.

Click here learn more about IDT’s Avian Influenza Type A (H5) Primers and Probe Set.

 

The Takeaway: iGEM 2024 is here—the Grand Jamboree takes place in Paris again, where students from around the world give a glimpse into the future of synthetic biology. Teams from more than 50 countries presented projects that were rated by a panel of 400 judges, with past work leading to future research, thesis projects, and even the launch of new companies. As a long-time platinum iGEM sponsor, IDT helps teams create innovative projects through access to IDT products as well as expert support. Here’s what some teams had to say about this year’s projects.

Cornell iGEM

Project: Oncurex

What inspired you to participate this year?

Every year, the Grand Jamboree has so many wonderful events. The people who attend are always incredibly welcoming and provide so much information about the world of synthetic biology that we wouldn’t be able to get at our university. Last year, we met teams such as iGEM Latvia-Riga, reconnected with old friends at iGEM Rochester, and networked with like-minded individuals. Being part of that vast world inspired us to compete this year and continue expanding our world of synthetic biology.

What problem are you trying to solve?

The current method of obtaining ursolic acid (UA) requires extraction from fruits, such as apples and loquats, which is generally environmentally taxing [Yu, et al., 2018], time consuming, and not standardized across scientists. Although UA has high promise in oncology studies, it also has low bioavailability, which limits its use. We can improve the speed, efficiency, and standardization of UA production by switching to our biosynthesis method in Oncurex and designing a high-specificity carrier system to assist with the low bioavailability.

What is the most surprising thing you uncovered?

The lack of general education on drug development and medical advances. Using Oncurex as a platform, we can not only educate about ursolic acid's benefits but also how medicines are created. We can also take a policy approach to provide insight into the process and requirements of drug development.

What IDT products did you use?

We used IDT's gBlock™ HiFi Gene Fragments and custom DNA oligos!

What has been the most memorable part of your iGEM experience so far?

The most memorable part of our iGEM experience was our summer session. With classes out, we got together for a few months to focus on taking our project from an idea to a tangible product. We were given the time to educate about Oncurex, and synbio in general, to communities throughout the U.S. and bond with our members through weekly social events like our annual Iron Chef competition.

MSP-Maastricht

Project: Natronaut

What inspired you to participate this year? 

We believe that, through synthetic biology, we can create meaningful and sustainable impacts, and iGEM provides the ideal platform for us to pursue these goals collaboratively and effectively. We see iGEM as a platform to push the boundaries of biotechnology, innovate, and create solutions that can have a tangible impact on society.

What problem are you trying to solve? 

Rapid population growth has led to a reliance on synthetic fertilizers, causing nitrogen imbalance and environmental issues like eutrophication and marine dead zones, particularly in agricultural regions like the Netherlands. Inspired by severe local algal blooms, we aim to develop innovative solutions to manage coastal eutrophication, protect marine biodiversity and human health while producing value-added products such as single-cell proteins.

What is the most surprising thing you uncovered?

The challenge of developing a truly unique and innovative idea. We initially assumed that it would be relatively straightforward to come up with a distinctive concept. However, we quickly realized that many ideas have already been explored. We spent a considerable amount brainstorming, researching, and refining our project to ensure it stands out. Our goal has been to create a project that not only addresses a significant problem but also introduces novel approaches or techniques that push the boundaries of what has been done before in iGEM.

What IDT products did you use?

We are incredibly grateful to IDT for their partnership with iGEM, which provided us with up to 20kb of free gene fragments. This support has been crucial for our project, as it involves long fragments, making our work much easier. Additionally, it gave us the opportunity to consult with experts about our fragments. IDT's support has been integral in bringing our iGEM vision to life.

What has been the most memorable part of your iGEM experience so far?

When we first delved deeply into V. natriegens. This exploration completely transformed our project, helping us refine its focus and establish a distinct identity. Before this, we had a broad concept, but the unique properties and potential of V. natriegens allowed us to make crucial adjustments and tailor our approach in a way that set our project apart.

UMaryland iGEM

Project: CetviCare

What problem are you trying to solve?

Cervical cancer is the fourth most common cancer in women globally; our project aims to improve early-stage screening capabilities in lower- to middle-income countries, where death rates remain disproportionately high. We are developing a paper-based screening device, similar to a pregnancy test, that targets urine biomarkers found in a vast majority of cervical precancer patients. Additionally, our cell-free, synthetic RNA device-based system is centered around easy deployment in low-resource areas.

What is the most surprising thing you uncovered?

It has been surprisingly difficult to find clinically relevant miRNA concentrations in urine. Though this biomarker has been used in a variety of screening and diagnostic tools, this has been an obstacle for us.

What IDT products did you use?

We used gBlocks Gene Fragments for multiple design and testing iterations of our biological parts. We were extremely well-supported throughout this process, and we even met with an iGEM-specific IDT representative to troubleshoot some of our designs.

What has been the most memorable part of your iGEM experience so far?

We were ecstatic to get preliminary data from in vivo testing that guided our project development. We were also honored to be able to share our work at multiple university-wide presentations and conferences.

CCU_Taiwan

Project: SERENE

What problem are you trying to solve?

Unchecked negative emotions can potentially lead to more serious issues, like depression. SERENE aims to offer a comprehensive approach to help people manage and alleviate these emotions.

What is the most surprising thing you uncovered?

In our mission to help people alleviate negative emotions, we discovered that many are not fully aware of their emotional state. To address this, we developed a stress detection and management app and promoted emotional education to foster self-awareness.

What has been the most memorable part of your iGEM experience so far?

The most memorable part of our iGEM experience so far has been holding free hug events at a local night market to promote emotional well-being through human interaction. We were fortunate to have a reporter who interviewed us, and our efforts were featured on the news. It was incredibly rewarding to see our project making a real impact and gaining community recognition.

iGEM Aachen

Project: OncoBiotica

What problem are you trying to solve?

Cancer remains a formidable healthcare challenge globally. A primary objective in cancer research is the development of innovative precision oncology strategies. OncoBiotica seeks to explore a novel approach for precision cancer therapy by targeting tumor-associated microbes through both wet lab experimentation and computational modeling.

What is the most surprising thing you uncovered?

Non-industrialized countries have limited access to both advanced cancer treatments and the ability to test drug efficacy on individual tumors. To address this global health disparity, our hardware team developed a microfluidic chip designed as a rapid efficacy assay.

What has been the most memorable part of your iGEM experience so far?

Our iGEM experience included participating in public events, and our most impactful conversations were those with individuals who had personal experiences with cancer, either directly or through family members.

We understand how frustrating it is to not obtain any colonies when cloning or not obtain the correct construct while screening. Although IDT Gene Fragments are synthesized using the highest fidelity synthesis methods it is important to acknowledge that
mutations can occur at various steps during the cloning process. Design considerations for your gBlocks™ Gene Fragments should be weighed when using a specific cloning method. Although cloning experiments can be complex, here are a couple of
troubleshooting steps to consider: 

• Check the design of your IDT Gene Fragment: The gBlocks Order Entry page
  has a built-in complexity screener that will help you identify potentially troublesome elements, such as repeats, hairpins, and GC fluctuations. You can use the information provided by the tool to help design and remove complexities to facilitate
  a higher chance of synthesis success.

• Confirm the concentration of your insert and the ratio of insert to vector: Ensure that the concentration of your IDT Gene Fragment is within the optimal range. If the concentration is too low, it may result in a lack of visible colonies.
  Also ensure that the ratio of insert to vector is correct.

• Sequence more colonies. It’s advisable to pick 3 or 4 colonies to screen. This provides the highest probability of ensuring that the recombinant vector is present in the cell and the DNA fragment was inserted in the correct
  location and orientation within the vector. See Table 1 for an estimated number of colonies to screen. 

Table 1. The approximate number of colonies to screen for a 90% chance of getting a correct clone.

Sequence length (bp)	eBlocks Gene Fragments	gBlocks Gene Fragments	gBlocks HiFI Gene Fragments
500	2	2	N/A
900	3	3
1500			2
2000	N/A	4
2500

See this DECODED article, Tips for working with IDT Gene Fragments, for how to resuspend,
quantify, and calculate copy number.

Why do mutations occur when cloning?  

The cloning process involves multiple steps, ranging from generating recombinant DNA and vector constructs to introducing them into host cells [1]. While cloning experiments can be complex, here a
couple of considerations:

Mutations are not dependent on PCR amplification of the IDT Gene Fragment. It’s worth noting that mutations can be observed even without amplifying the insert. PCR amplification of gene
fragments prior to cloning should be avoided due to the possibility of introducing point mutations, base insertions, or deletions, which can lead to non-functional or altered gene sequences. Moreover, there are various DNA and cellular mechanisms
that can introduce errors 
[2]:

• DNA replication can lead to mutations. DNA polymerases are responsible for synthesizing new DNA strands and are not infallible. This can lead to incorrect nucleotides being incorporated into the new DNA strand.
• DNA repair mechanisms are not perfect. The host cells possess DNA repair mechanisms that fix errors and can also damage the IDT Gene Fragment by introducing mutations during the repair process.
• Altered recombination events between the IDT Gene Fragment (or DNA insert) and host genome. Additional elements such as plasmids, integrons, transposons, or short DNA sequences can alter recombination events thus leading to mutations 
  [3].

• Bacterial replication is not perfect and can introduce errors and DNA damage due to various endogenous or exogenous factors:
  • The replication speed of host cells. Bacterial replication occurs rapidly to ensure efficient cell division and proliferation [3]. This can increase the likelihood of errors.
    The faster the replication process, the less time there is for accurate proofreading and correction of errors.
  • Environmental stressors affecting replication mechanisms or leading to DNA damage. Bacteria (host cells) can encounter various environmental stressors, such as exposure to oxidative damage, mutagens, chemical or physical stressors,
    base analogs, flat aromatic compounds, alkylating or deaminating agents [3]. These factors can compromise the replication process or increase the likelihood of errors causing damage to
    the DNA.

• Sequence complexity and toxicity can contribute to errors.
  • Sequence complexity: When designing your IDT Gene Fragments, keep in mind that complex sequences, repetitive elements, secondary structures, or regions with extremely high or low GC content can pose challenges for accurate
    replication. IDT developed the SciTools™ suite of web tools which can help
    you assess your DNA sequences for complexities and optimize codon usage based on a host organism. See this DECODED article, Codon optimization tool makes synthetic gene design easy, for IDT’s free online Codon Optimization Tool to simplify designing your IDT Gene Fragments.
  • Toxicity: Some gene sequences or inserts can be toxic to the host cells, which can interfere with the normal cellular processes or cause DNA damage. If the DNA insert is toxic, the host cell may exhibit cellular stress responses
    or undergo genetic changes to cope with the toxicity [2]. These changes can include mutations that occur because of the cellular response to the toxic insert.

  In addition to the factors mentioned earlier, there are several other common mistakes that can contribute to poor results or failed cloning experiments. Here are some suggestions to follow when performing your experiments:

  • Avoid contamination. Here are common contaminants that can affect your cloning experiments: 

  • Foreign DNA contamination: This form of contamination can occur when DNA from unintended sources, such as other plasmid DNA, genomic DNA, or residual DNA are inadvertently introduced into the cloning experiment [3].
  • Microbial contamination: Bacterial or fungal contamination can occur during the cultivation of host cells or the handling of plasmids or other DNA constructs. Microbial contaminants can affect the growth of the transformed
    cells or alter the integrity of the cloned DNA [3].

  • Contaminated reagents: Errors can occur if the reagents used in the cloning protocol such as restriction enzymes, ligases, polymerases, or buffers are contaminated with DNA or other impurities [4].

   

• Minimize freeze-thaw cycles. This can cause physical stress to the DNA which can potentially lead to DNA strand breaks or structural alteration [2]. Follow best practices for storing your IDT Gene
  Fragments, enzymes, and critical reagents, used in your cloning protocol. 

  If there are few or no colonies after transformation, here are some factors to consider: 

  • Low or inefficient transformation. To validate the experimental conditions and ensure that the transformation step is working properly, include a positive control. This involves using a known, well-characterized DNA sample
    that is expected to yield colonies. This will help to rule out any issues with competent cells and antibiotic selection. If the positive control fails to yield colonies, it indicates a problem with the experimental setup or transformation
    process that needs to be addressed.
  • The gene product is toxic to bacterial cells. If the gene product is toxic to bacterial cells, the sequence may spontaneously mutate to allow survival of the cells. An alternative solution would be to check
    if the gene encoded in the DNA sequence is toxic to the competent cells. If so, use a different competent cell line. If the gene encoded in the fragment is toxic to the host cells, try a different competent cell line or a low copy plasmid.
    Low copies of the plasmid will undergo fewer replication cycles, generating less protein and lower toxicity in the process.

  • If the same mutation is across all clones. Even with a median error rate of 1:5000, gBlocks and eBlocks are not sequence-verified; therefore, observing the same mutations across all clones may indicate an error during
    fragment synthesis. For sequence confirmation, you may want to consider ordering your insert as gBlocks HiFi Gene Fragments, which are NGS-verified, have a median error rate of less than 1:12000, and are manufactured with the same industry-leading, high fidelity synthesis chemistries developed for our
    Ultramer™ DNA oligos.

  Download our free Cloning Guide, to read more about common methods and important sequence design consideration when designing your experiments.

 

The Takeaway: Oligos are short strands of synthetic DNA. First used in the 1950s, oligos have since helped revolutionize many areas of modern medicine, and they continue to impact our world in many ways.

Oligos, or oligonucleotides, are short nucleic acid polymers used in various scientific and medical applications. Read on to learn about ten notable ways oligonucleotides are revolutionizing life and medicine. First, though, a little background.

What are oligos?

Oligos, short for oligonucleotides, are short sequences of nucleic acids that are the building blocks of DNA and RNA. IDT sequences typically consist of 10 to 100 nucleotides and are synthesized in our labs for research applications.

There are two primary types of oligonucleotides:

DNA oligonucleotides: These are short sequences of DNA nucleotides, typically synthesized using chemical methods. DNA oligos are widely used in techniques such as polymerase chain reaction (PCR), DNA sequencing, gene synthesis, gene editing, and molecular cloning.

RNA oligonucleotides: These are short sequences of RNA nucleotides. RNA oligos have diverse applications, including gene silencing through techniques like RNA interference (RNAi) and antisense therapy, as well as in research areas such as RNA structure analysis and RNA-protein interactions.

How are oligos making life better?

Oligos are versatile tools in molecular biology and biotechnology due to their ability to hybridize specifically with complementary nucleic acid sequences. This property is exploited in various techniques for gene manipulation, detection, and analysis. Additionally, oligos can be chemically modified to enhance their stability, specificity, and other properties, expanding their utility in research and therapeutic applications. IDT’s oligos are strictly used for research use only.

Genetic engineering: Oligos are crucial tools in genetic engineering, enabling scientists to manipulate DNA sequences for various purposes such as gene editing and recombinant DNA technology.

PCR primer design: Polymerase chain reaction (PCR) relies on oligonucleotide primers to amplify specific DNA sequences, facilitating numerous applications in research, diagnostics, and forensics.

Gene synthesis: Oligos are used in gene synthesis to assemble artificial genes for research and to advance our understanding of genetics and molecular biology. Note that IDT manufactures oligos for strictly RUO purposes. 

Gene silencing: Oligonucleotides such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) are employed to silence or modulate gene expression, providing insights into gene function and offering new potential research for treating genetic disorders and diseases.

Antisense therapy: Antisense oligonucleotides can bind to specific mRNA sequences, preventing translation or promoting degradation of the target mRNA, leading to additional research into the development of antisense therapy for various diseases, including cancer and genetic disorders.

Diagnostic tools: Oligos are utilized in various diagnostic techniques such as qPCR and DNA microarrays and sequencing, enabling the detection and analysis of genetic variations associated with diseases, pathogens, and other biological phenomena.

Drug development: Oligonucleotides serve as the basis for developing nucleic acid-based therapeutics, including RNA-based vaccines, gene therapies, and aptamer-based drugs, offering promising approaches for treating a wide range of diseases.

Biotechnology: Oligos are integral components in biotechnological applications such as in vitro mutagenesis, site-directed mutagenesis, and protein engineering, facilitating the study and manipulation of proteins and enzymes for research and industrial purposes.

Forensic analysis: Oligos are used in forensic DNA analysis for identifying individuals, determining paternity, and solving crimes by analyzing DNA samples collected from crime scenes or other sources.

Research tools: Oligonucleotides serve as versatile tools in molecular biology research, including qPCR, DNA sequencing, cloning, site-directed mutagenesis, and in vitro gene expression studies, contributing to advancements in various fields of science and medicine.

These accomplishments highlight the diverse and impactful roles that oligonucleotides play in advancing scientific knowledge, technology, and medicine.

IDT oligos

IDT has been a leading manufacturer of oligos for more than 35 years, with customers consistently receiving high-quality oligos thanks to improvements in traditional synthesis chemistries and advances in our proprietary synthesis platform. This means IDT can synthesize longer oligos, with better sequence fidelity and at a higher percentage of full-product length, than competitors.

• Proprietary synthesis platform: Nearly everything IDT uses to produce an oligo is made in-house. IDT formulates all its own key synthesis reagents in-house, and designs, manufactures, and calibrates its own DNA synthesizers and manufacturing software.
• Highly streamlined synthesis process: All IDT synthesis platforms use solid-state synthesis to produce oligos, meaning they are tethered to a solid surface while they are made.
• Phosphoramidite approach: The synthesis process adds nucleotides one by one, using a repeated 4-step cycle of deblocking, coupling, capping, and oxidation for each A, C, T, or G addition, with repeated cycling, final processing, and desalting.
• Oligo purification: IDT uses PAGE and HPLC purification methods
• Quality control: IDT uses electrospray ionization mass spectrometry and capillary electrophoresis.

Ready to learn more? Simply head here!