Many would concede that the 20th century was the “century of technology.” Why? Because of the many breakthroughs that define the century, including atomic energy, computers, and the unending list of medical diagnostics. And that the dramatic effect of these discoveries has made evident and promised more possibilities for science and technology.
The 21st century is nothing short of a similar view. In any case, the century is exceeding prior science expectations, especially now that we are witnessing what we are very much likely to corroborate as the “century of DNA.”
What is Gene Synthesis?
Traditionally, DNA sequences could only be synthesized via single base mutations. Unfortunately, this form of DNA synthesis made it impossible to generate long strands of natural and unnatural nucleic acid sequences.
But thanks to gene synthesis, we now have efficient methods of generating long stretches of nucleic acids. Better yet, we can now routinely generate, from labs, DNA sequences that could not be isolated from natural sources before. This new synthesis capacity dictates a tremendous impact on biological possibilities.
Important Things to Know About Gene Synthesis Methods
Different methods and techniques of gene synthesis are of distinct niches depending on the requirements of each genetic project. This characterization makes it very important to have a foundational understanding of every method whenever involved in a genetic or related project. The rest of this post makes a quick rundown through most of the essential things you need to know about gene synthesis.
1. Oligonucleotide is the Primary Building Block for Gene Synthesis
Traditional or current, every method of gene synthesis depends on oligonucleotide synthesis. Only through this synthesis would you generate blocks for enzymatic assembly. And for someone needing longer strands of nucleic acids, a sufficient supply of these building blocks is no doubt necessary for your project.
Oligonucleotides have traditionally been synthesized via a four-step phosphoramidite synthesis method. The only problem is that this synthesis method is limited to 200 nucleotides in length of the generated DNA strand. The current synthesis methods offer ways to circumvent this limitation.
2. Methods for Synthesis Performance
The three major methods for gene synthesis include:
- Solid-phase synthesis
- Chip-based synthesis, and
- Polymerase chain reaction (PCR)-based enzyme synthesis
The solid-phase synthesis uses a solution from a column full of chemicals to attach a nucleotide residue at the end of the chain one after the other. As we noted, this process is accomplished through four steps: de-blocking, coupling, capping, and oxidation. Also, we noted that the process is limited to only 200 oligos. However, it boasts high accuracy, an advantage that counterbalances the challenge of low output.
Emerging technologies are embracing microchips to reduce the output limitation of solid-phase synthesizers. With these technologies, you only need spatial control, like light-directed illumination, to fuse different DNA strands on a single microchip. Unfortunately, this synthesis allows you a larger output at the expense of synthesis accuracy.
You can also grow the output DNA strand by assembling sequences of short oligonucleotides using PCR. Here, you achieve gene synthesis by assembling targeted genes, usually in a mixture of PCR products, through a single enzymatic reaction and multiple assembly steps. The final DNA strand comprises a full assembly of all the used gene products.
3. Gene Design Software
Gene design software? Yes. At times the technical considerations relating to a given synthesis process could be too overwhelming that the challenge is not just limited to the synthesis phase. Software packages such as GenoCAD are beneficial in navigating such a challenge. With GenoCAD, you don’t have to go through every step of the synthesis process physically. You could drag and drop database aspects of genetic elements from national databases, notably the Registry of Standard Biological Parts.
4. Gene Synthesis Fidelity
One problem with synthesizing longer nucleic acid strands is an increased likelihood of sequence errors. Remember, every addition of successive monomers comes with its probability of error. So the longer the strand, the greater the chance for errors. Also, gene synthesis generates DNA strands from unnatural sources. What is more likely in such a production process is a big mixture of correct and incorrect sequences. Worse, traditionally, separating and amplifying each strand would hardly isolate an incorrect sequence if the error only affected one sequence.
What does that tell you? That error correction is a necessity with gene synthesis. That could be via oligonucleotide purification since the building block forms the largest source of potential error. Or functional selection facilitated by prescreening and correcting mutation-deficient sequences.
5. The Future is Full of Innovative Technologies
One thing is for sure. Biotechnology and synthetic biology are currently among the most competitive industries. Such a competition level invites strategic adaptations best suited to innovative technologies. That’s why you shouldn’t be surprised by the on-chip gene synthesis technique and many other evolutions parallel to this innovation.
Brace yourself for more. That’s just the beginning, especially if the industry has to meet and even exceed the needs and expectations attributed to DNA complexities. Oh, and do you know one more good thing about this trend? That the prices for gene synthesis are braced to drop dramatically in the coming years. The beauty of technological innovations.
The Bottom Line
A lot of the 21st-century innovative projects demand the use of gene synthesis. Whether establishing a modular biological component or genetic circuits for metabolic improvements, gene synthesis is the roadmap for a successful project. The bottom line is that the success of your project would significantly benefit from seeking a foundational understanding of gene synthesis methods and techniques.
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