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DNA Printing and Artificial Gene Synthesis: Unlocking the Secrets of Life

Introduction

In the realm of biotechnology, groundbreaking advancements are continually pushing the boundaries of what we thought was possible. One such innovation is DNA printing and artificial gene synthesis, which has the potential to revolutionize fields like medicine, agriculture, and biotechnology. These technologies enable scientists to manipulate the very building blocks of life, allowing for unprecedented control over genetic material. In this article, we will delve into the fascinating world of DNA printing and artificial gene synthesis, exploring their applications, challenges, and the ethical considerations that come with them.

Understanding DNA Printing

DNA printing is the process of synthesizing DNA molecules using chemical or enzymatic methods. This technology is based on the same principles as inkjet printing, but instead of ink, DNA nucleotides are used to create a pattern on a substrate.  Just like 3D printing creates physical objects layer by layer, DNA printing assembles genetic material base by base.  This technology enables the creation of custom-designed DNA strands with precise sequences and functionalities. DNA printing can be used to create synthetic genes, gene arrays, and even entire genomes.

The Evolution of DNA Printing

The first efforts to write DNA began in the 1980s using a phosphoramidite chemistry process, a breakthrough that expanded the horizons of genetic research and diagnostics. However, this method presented environmental and safety challenges, limiting its accessibility to many labs.

More recently, enzymatic DNA synthesis (EDS) has emerged as a safer and more efficient alternative. It doesn’t rely on toxic chemicals, offers improved precision, and simplifies the process, making it accessible even to inexperienced lab staff.

Applications of DNA Printing

  1. Biomedical Research: DNA printing is instrumental in studying genes and their functions. Researchers can create customized DNA sequences to investigate genetic disorders, develop targeted therapies, and gain insights into disease mechanisms.
  2. Vaccine Development: The rapid development of mRNA vaccines, such as the COVID-19 vaccines, relies on artificial gene synthesis. Scientists can design and synthesize DNA segments to produce specific antigens, leading to more effective and efficient vaccine production.
  3. Agriculture: DNA printing is used to engineer crops for improved resistance to pests, disease, and environmental conditions. This can enhance food security and reduce the need for harmful pesticides.
  4. Synthetic Biology: Synthetic biology leverages DNA printing to construct biological systems and organisms with novel functions. This has applications in biofuel production, bioremediation, and the creation of biodegradable materials.

Some scientists have even proposed storing information in DNA, much like digital data is stored today in computer hard drives, since a gram of DNA could theoretically store the equivalent of 50 million DVDs and should be stable for centuries. However, that would mean synthesizing immensely larger quantities of DNA strands than those used in the biotech industry today.

 

Challenges of DNA Printing

All of these applications require that the synthesis process faithfully produces the desired sequence of nucleotides or bases – the building blocks of DNA – in each of millions or even billions of copies of DNA molecules.

  1. Cost: DNA printing can be expensive due to the cost of reagents and equipment. As technology advances and economies of scale come into play, costs are expected to decrease.
  2. Accuracy: Ensuring the accuracy of synthesized DNA sequences is critical. Errors can lead to unintended consequences, especially when applied in living organisms.
  3. Ethical Concerns: The ability to create custom DNA sequences raises ethical questions. It opens the door to bioengineering humans and the potential misuse of biotechnology.

Understanding Artificial Gene Synthesis

Artificial gene synthesis, also known as gene synthesis, is a remarkable set of methods within synthetic biology that allows scientists to construct and assemble genes from nucleotides without the need for template DNA. In contrast to DNA synthesis within living cells, gene synthesis enables the creation of custom DNA sequences with precision. Artificial gene synthesis can be used to create genes that do not exist in nature or to modify genes to improve their function.

Artificial gene synthesis is a subset of DNA printing, focusing specifically on the creation of genes. Artificial gene synthesis is the process of creating new genes or modifying existing genes by assembling DNA nucleotides in a specific order. It involves piecing together the nucleotides (A, T, C, G) in a specific order to form functional genes. This process is carried out by automated DNA synthesizers, which are programmed based on the desired gene sequence. This technology is based on the same principles as PCR, but instead of amplifying existing DNA, new DNA sequences are created.

In 2003, gene synthesis achieved a significant milestone when the first entire viral genome (phiX174 bacteriophage) was successfully synthesized. This marked a turning point in the field.

Custom DNA Sequences: It allows for the generation of mutated, recombinant, or entirely novel DNA sequences, all without the need for a template. This flexibility is invaluable for research and application.

Versatility: Gene synthesis extends beyond DNA; it can also be used to create RNA sequences and oligos with modified bases and chimeric DNA-RNA backbones.

DNA synthesis methods

Early DNA synthesis methods emerged in the 1980s, revolutionizing genetic research, diagnostics, and vaccine development. However, these techniques had drawbacks, requiring precise environmental controls, toxic reagents, and generating hazardous waste, making in-house synthesis impractical for most laboratories.

The current DNA synthesis methods, dating back to 1981, are constrained to producing oligonucleotides of about 200 bases in length due to errors in the process, necessitating the piecemeal assembly of longer genes.

Gene synthesis involves two key steps, among them, the first step is solid phase DNA synthesis also known as ‘DNA printing’ that produces oligonucleotide fragments which are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.

The turnaround time for synthetic genes ordered from companies can be as long as two weeks at a considerable cost, limiting researchers’ flexibility and speed in genetic experiments and early-stage diagnostic or therapeutic development. In-house DNA printing resources can mitigate these challenges, providing efficiency gains and reducing time-to-market costs.

Enzymatic DNA synthesis (EDS)

In 2018, a groundbreaking advancement emerged in the realm of DNA synthesis, offering a more straightforward, rapid, and eco-friendly approach. This novel technique stemmed from the innovative minds at UC Berkeley and Lawrence Berkeley National Laboratory. What sets this method apart is its reliance on a DNA-synthesizing enzyme found in the cells of our immune system. This enzyme, known as terminal deoxynucleotidyl transferase (TdT), possesses a unique ability to add nucleotides to existing DNA strands in a water-based environment, where DNA is most stable. Notably, TdT demonstrates exceptional precision, potentially enabling the synthesis of DNA strands up to ten times longer, equivalent to the size of a medium-sized gene.

The use of TdT represents a paradigm shift in DNA synthesis. Unlike typical DNA replication processes that rely on numerous polymerase enzymes and existing DNA templates within cells, TdT operates independently. It introduces nucleotides randomly to genes responsible for creating antibodies, fostering variability in these genes, which enhances the immune system’s ability to combat previously unseen threats. The versatility of TdT extends to all four DNA nucleotides, and it operates with remarkable speed, extending DNA at a rate of approximately 200 bases per minute, as noted by Sebastian Palluk, a doctoral student at Technische Universität Darmstadt in Germany and a visiting student at Berkeley Lab. Harnessing this enzyme has been a long-standing challenge in the scientific community, primarily due to difficulties in controlling its behavior. However, Arlow’s ingenious approach has made it possible to securely tether an unblocked nucleotide to TdT. This ensures that after adding a nucleotide to a growing DNA strand, the enzyme remains attached and safeguards the chain’s end from further additions. Subsequently, cutting the linking tether releases the enzyme, re-exposing the end for subsequent nucleotide additions. The practicality of these enzymatic DNA synthesis (EDS) technologies has been further enhanced by the introduction of commercialized benchtop synthesizers that mimic the DNA-building processes seen in cells.

By relying on biological principles, EDS sidesteps the need for toxic reagents and simplifies the DNA synthesis process. It empowers even inexperienced laboratory personnel to initiate synthesis runs in approximately 15 minutes, yielding custom oligos within a few hours. These enzymatic synthesis methods hold great promise, potentially enabling the assembly of entire chromosomes and genomes. Notably, this technology may pave the way for the use of novel nucleobase pairs, expanding the horizons of artificial gene synthesis. This remarkable progress has the potential to revolutionize the field of genetics and synthetic biology, offering more accessible and environmentally friendly DNA synthesis techniques.

Applications of Artificial Gene Synthesis

This technology is opening doors to a multitude of applications in fields such as medicine, agriculture, and biotechnology. Synthesizing DNA is a growing business as companies order custom-made genes so they can produce biologic drugs, industrial enzymes or useful chemicals in vats of microbes. Researchers purchase synthetic genes to insert into plants or animals or try out new CRISPR-based disease therapies.

  1. Synthetic Biology: Scientists construct biological systems and organisms with novel functions, with applications in biofuel production, bioremediation, and the creation of biodegradable materials.
  2. Gene Therapy: Gene synthesis allows for the creation of therapeutic genes that can treat genetic diseases. By replacing or repairing faulty genes, gene therapy offers hope for previously untreatable conditions.
  3. Biomedical Research: Researchers harness gene synthesis to explore genes and their functions, particularly in the context of genetic disorders and targeted therapies.
  4. Biological Engineering: Scientists can design genes that produce proteins with specific functions. This is valuable in the production of enzymes, biofuels, and pharmaceuticals.
  5. Pharmaceuticals: Artificial gene synthesis accelerates drug development by enabling the efficient production of proteins and antibodies used in the pharmaceutical industry.
  6. Vaccine Production: The development of vaccines against emerging diseases often relies on the quick synthesis of genes encoding viral antigens. The rapid development of mRNA vaccines, like the COVID-19 vaccines, relies on gene synthesis to produce specific antigens.
  7. Agriculture: Genes can be engineered to enhance crop resistance to pests, and diseases, and changing environmental conditions, promoting food security and sustainable farming.

Latest Developments

  • Development of benchtop DNA printers: Benchtop DNA printers are small, affordable devices that can be used to synthesize DNA in a laboratory setting. This makes it possible for researchers to produce their own DNA constructs without having to rely on outsourcing.
  • Development of unnatural base pairs: Unnatural base pairs are synthetic nucleotides that can be incorporated into DNA molecules. This allows scientists to create DNA with new and unique properties. For example, unnatural base pairs can be used to create DNA that is more resistant to heat or radiation.
  • Assembly of entire genomes: DNA printing and artificial gene synthesis can now be used to assemble entire genomes. This has been achieved for several bacterial species, and scientists are working on assembling the genomes of more complex organisms, such as yeast and even humans.

These breakthroughs are opening up new possibilities for research and development in a wide range of fields, including medicine, agriculture, and materials science. For example, DNA printing and artificial gene synthesis could be used to develop new drugs and treatments for diseases, create crops that are more resistant to pests and diseases, and produce new materials with unique properties. Here are some specific examples of how these latest breakthroughs are being used today:

  • Researchers at the University of California, Berkeley have developed a benchtop DNA printer that can synthesize DNA oligonucleotides up to 120 nucleotides in length. This printer is small enough to fit on a desktop and is relatively inexpensive, making it a practical tool for use in research laboratories.
  • Scientists at the University of Washington have developed a new enzymatic DNA synthesis method that is capable of synthesizing DNA oligonucleotides up to 1,000 nucleotides in length with high accuracy. This method is more efficient than traditional chemical methods and could be used to produce large quantities of DNA for a variety of applications.
  • Researchers at the Massachusetts Institute of Technology have developed a new type of unnatural base pair that can be incorporated into DNA molecules. This unnatural base pair is more resistant to heat and radiation than natural base pairs, making it possible to create DNA that is more durable.
  • Scientists at the Craig Venter Institute have assembled the genomes of several bacterial species using DNA printing and artificial gene synthesis. They have also used these technologies to create a synthetic yeast chromosome. This work is paving the way for the assembly of more complex genomes, such as the human genome.

CReATiNG (Cloning Reprogramming and Assembling Tiled Natural Genomic DNA)

Researchers at the USC Dornsife College of Letters, Arts and Sciences have developed a groundbreaking technique called CReATiNG (Cloning Reprogramming and Assembling Tiled Natural Genomic DNA), which has the potential to revolutionize synthetic biology. This innovative method simplifies and reduces the cost of constructing synthetic chromosomes, offering significant advancements in genetic engineering across various fields such as medicine, biotechnology, biofuel production, and even space exploration.

CReATiNG functions by cloning and reassembling natural DNA segments from yeast, allowing scientists to create synthetic chromosomes that can replace their native counterparts within cells. This technique enables the combination of chromosomes from different yeast strains and species, alteration of chromosome structures, and simultaneous deletion of multiple genes, previously deemed challenging.

Published in Nature Communications on Dec. 20, CReATiNG addresses the challenges of synthetic genomics research, which typically involves synthesizing whole chromosomes or genomes using chemically synthesized DNA pieces, a labor-intensive and costly process. CReATiNG offers an alternative by utilizing natural DNA segments to assemble chromosomes, significantly reducing costs and technical barriers.

The potential applications of CReATiNG in biotechnology and medicine are vast. It could lead to more efficient production of pharmaceuticals and biofuels, aid in the development of cell therapies for diseases like cancer, and contribute to environmental bioremediation efforts. Furthermore, CReATiNG may have implications for space exploration, potentially enabling the development of microorganisms or plants capable of thriving in space or harsh environments.

One notable discovery from the study is the significant impact of rearranging chromosome segments in yeast on their growth rates. Certain modifications resulted in up to a 68% increase or decrease in growth, highlighting the profound influence of genetic structure on biological function. This finding opens new avenues for research to explore these relationships further.

These are just a few examples of the latest breakthroughs in DNA printing and artificial gene synthesis. As these technologies continue to develop, we can expect to see even more innovative applications in the years to come.

Challenges and Advances

While gene synthesis opens doors to unprecedented possibilities, it also presents challenges:

  • Cost: The expense of gene synthesis, including reagents and equipment, remains a hurdle. However, as technology advances, costs are expected to decrease.
  • Accuracy: Ensuring the precision of synthesized DNA sequences is crucial, as errors can lead to unintended consequences.
  • Ethical Considerations: The ability to create custom DNA sequences raises ethical questions, particularly concerning the potential misuse of biotechnology.

Market

Global Gene Synthesis Market size is expected to be worth around USD 8.3 Billion by 2032 from USD 1.7 Billion in 2022, growing at a CAGR of 17.7 % during the forecast period from 2023 to 2032.

The rise in the global geriatric population, the rising prevalence of different chronic diseases, and increasing investments in synthetic biology are major factors that are likely to propel the growth of the market during the estimated time period. Moreover, increasing global demand for personalized medicine, rising research and development in the field of genomics, and the launch of new advanced products are expected to positively contribute to the overall market growth over the projected time period.

Rising technological advancements

Blockchain technology is being explored to enhance transparency, security, and traceability in the gene synthesis process. By leveraging blockchain, stakeholders can track and verify the origin, authenticity, and integrity of synthesized gene sequences, ensuring confidence in the data and materials used in research and development. These technological advancements are expected to stimulate the growth of the market in the upcoming time period.

  • By method, the solid-phase synthesis segment dominated the market with the highest revenue share of 38%.
  • By application, the gene & cell therapy development segment is likely to grow at the highest rate, with a revenue share of 39%.
  • By end-user, academic & government research institutes dominate the segment with a revenue share of 51% in the account.
  • North America held a significant revenue share of 42% in 2022.
  • Asia Pacific market is projected to increase at a high CAGR during the forecast period.

Regional Analysis

North America region leads the market by accounting for a significant revenue share of 42%. The presence of a strong biopharmaceutical sector and increasing focus on research and development are key factors that are expected to stimulate the growth of the market in the region during the projection period. Moreover, new advancements in precision medicine, genetic research, synthetic biology, drug discovery, industrial biotechnology etc., are expected to positively impact the market growth during the estimated time period. The Asia-Pacific region is expected to grow at a high growth rate over the forecast period. Rising genetic research and genomics initiatives are likely to drive the growth of the market in the region during the forecast period.

 

Some of the Gene Synthesis Companies are Thermo Genewiz, Eurofins Scientific, Quintara Biosciences, ATD Bio Ltd.,Fisher Scientific, Inc., OriGene Technologies, Inc., Bioneer Corporation, Atum, Integrated DNA Technologies, Inc., BioCat GmbH, GenScript, Eurogentec,
Twist Bioscience, LGC Biosearch Technologies, Eton Bioscience, Inc., Bio Basic Inc., SBS Genetech Co., Ltd., Merck KGaA and others.

 

Industry News

French Biotech Raises $200 Million Series C for DNA Printing Platform in Jan 2022. The proceeds will enable DNA Script to advance the first EDS-powered benchtop DNA printer, the SYNTAX Platform, and accelerate the commercialization of the enzymatic DNA-printing platform.

 

DNA Script’s technology holds a promise to transform research processes across multiple industries where synthetic biology is involved by offering to print longer DNA sequences than before and deliver them within a matter of hours.

 

The SYNTAX System empowers scientists by allowing rapid, on-site DNA production. It accelerates lab workflows and helps scientists find answers faster as on-demand printing allows labs to iterate without waiting days or weeks to receive genetic material from third-party service providers.

Ethical Considerations

The power to create custom genes and DNA sequences raises ethical dilemmas. It opens the door to designer babies, where parents could potentially select specific genetic traits for their children. Furthermore, the accidental release of synthetic organisms into the environment could have unforeseeable consequences.

Gene synthesis has the potential to create controversial or potentially dangerous DNA sequences. The ability to synthesize genes raises ethical concerns, including the potential for bioterrorism, the creation of harmful pathogens, or the misuse of synthesized DNA for illegal activities. Ensuring responsible use and oversight of gene synthesis technology is crucial. Therefore, regulatory issues involved in the approval of gene synthesis may limit the market growth during the projected time period. Also, the market’s growth is anticipated to be negatively impacted by the high cost of gene synthesis.

Conclusion

DNA printing and artificial gene synthesis are advancing biotechnology to new heights. These two technologies have the potential to unlock the secrets of life and revolutionize the way we treat and cure diseases.

With applications ranging from medical breakthroughs to environmental solutions, these technologies hold immense promise.  For example, DNA printing could be used to create personalized cancer vaccines or to produce new drugs that target specific genes. Artificial gene synthesis could be used to create new crops that are resistant to pests and diseases or to develop new therapies for genetic disorders.

However, their responsible use and ethical considerations are paramount. As we continue to unlock the secrets of life through DNA printing, we must tread carefully, ensuring that the benefits far outweigh the risks. The future of biotechnology has arrived, and it’s up to us to harness its potential for the greater good.

 

 

References and Resources also include:

https://www.globenewswire.com/news-release/2023/09/12/2741787/0/en/Gene-Synthesis-Market-to-Hit-USD-8-3-Billion-by-2032-Academic-Government-Research-Segment-Revenue-Share-of-51.html

 

 

 

 

 

 

 

References and Resources also include:

https://www.forbes.com/sites/forbestechcouncil/2021/12/06/mind-the-gap-on-demand-dna-printing-and-synthetic-biologys-promise/?sh=6fa5c389769a

https://news.berkeley.edu/2018/06/18/new-dna-synthesis-technique-promises-rapid-high-fidelity-dna-printing/

About Rajesh Uppal

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