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Gene Synthesis vs. Traditional Cloning: Which is Right For You?

Dec 19th 2023

Gene Synthesis vs. Traditional Cloning: Which is Right For You?

Many consider the twentieth century the "century of the atom" due to the many innovations made possible by new understandings of the elements' physical and chemical properties. These included, but are not limited to, the development of atomic energy (and weapons), diagnostics for medicine, computers, and the microchip, among others.

These breakthroughs shaped the potential and future of science and technology and profoundly impacted our daily lives. But we're living through what may be dubbed the "century of DNA." DNA is like the soundtrack to life's complex symphony; it serves as a template that dictates how cells work. Recent decades have seen tremendous progress in reading and synthesizing DNA sequences, greatly enhancing our capacity to understand and manipulate biological systems.

In today's post, we will consider two major branches of biological engineering: gene synthesis and traditional cloning. This blog will review the main benefits and drawbacks of each method to assist you in choosing the appropriate media for your project.

Let's begin with a closer look at the two camps.

What is Gene synthesis?

gene synthesis, traditional cloning

Photo by Sangharsh Lohakare on Unsplash

Gene synthesis is the in vitro method of producing a gene without requiring a preliminary template.

Alternatively, if you would want a more in-depth explanation, synthetic gene creation is a technique that involves a series of steps for producing a gene and other gene derivatives without the need for a DNA template. As a result, it eases the process of making various genes, notably custom genes with unique base pairs and sequences.

Har Gobind Khrona and colleagues performed the first effective gene synthesis using a yeast tRNA in 1972. Since 1972, advances in gene assembly andmolecular biology techniques have allowed the successful extraction of genetic sequences unique to a broad range of scientific issues.

Steps Involved in Gene Synthesis

A general overview of the steps towards a successful gene synthesis include:

  • Oligonucleotide synthesis
  • Oligonucleotide annealing
  • The cloning of gene sequences
  • Screening for clones
  • Analyzing sequences and fixing mistakes

A couple of decades ago, the idea of using gene synthesis for targeted gene therapy or other intriguing subjects would have appeared entirely out of reach. Gene synthesis opens up a world of possibilities beyond what has been explored so far, with applications spanning from gene regulation to a greater understanding of evolutionary development and antibiotic resistance, among many others.

Thanks togenetic engineering, we can now construct custom antibodies, variant libraries, custom peptides, operons, and enhanced protein functions.

Now, let's turn our gaze to the more traditional method of doing things.

What is Traditional Cloning?

gene synthesis vs. traditional cloning

Photo by National Cancer Institute on Unsplash

Traditional cloning is a type of DNA manipulation that typically involves employing restriction endonucleases to produce DNA fragments possessingparticular complementary termini, which are subsequently ligated together with a DNA ligase before undergoing transformation.

To do this, you usually need to cut the DNA sequence in two places so that there are two restriction enzymes on either side of the DNA sequence. These enzymes also reside at the best place for the vector to insert itself, sometimes called the multiple cloning site (MCS).

By applying two separate REs, incompatible ends are produced, leading to the directional cloning of the insert and reducing the transformation background of the re-ligated vector only.

Pros and Cons of Traditional Cloning


  • Low costs
  • Flexible
  • A wide variety of vector options
  • Performing directional replication is easy and stress-free


  • A restriction site's existence and translation may impose sequence limitations.

The first step in conventional cloning using recombinant DNA technology is to use restriction enzymes to prepare a vector to accept an insert DNA. Following digestion, the fragments are joined by the enzyme ligase, a procedure known as ligation, creating a new vector that can express a desired gene.

This is the most basic and old-fashioned method of genetic material production, and it served as the basis for the development of novel cloning techniques that capitalize on the unique properties of other modifying enzymes, including:

  • TA cloning
  • TOPO cloning
  • PCR cloning,
  • Ligation-independent cloning, and
  • gene assembly.

You can simplify the steps described above for typical traditional cloning as:

  • Vector preparation
  • Insert preparation
  • Ligation Transformation
  • Colony screening

Given this information, let's contrast the two (gene synthesis vs traditional cloning) to better understand their differences.

Traditional Cloning vs. Gene Synthesis: Major Differences

When compared to molecular cloning and polymerase chain reaction (PCR), two of the more conventional approaches to gene cloning, gene synthesis has numerous significant benefits. There are two main limitations to these two traditional approaches. First, they can only amplify and clone genes; they cannot synthesize them.

Another limitation of restriction molecular cloning and polymerase chain reaction is that the genetic code of interest must first be acquired and then amplified. This is a prerequisite for both techniques. With gene synthesis technology, the desired genetic sequence can be amplified without physically obtaining it, which is a significant upside.

Current gene expression technologies enable the synthesis of "de novo" sequences. This allows for synthesizing sequences of interest even without physical copies of genes, such as viral DNA or cancer cell mutations in particular genes. The lack of a physical replica of the target gene considerably reduces the financial and time investments required in contrast to conventional approaches such as cloning, amplification, gene target knockouts, and targeted mutagenesis.

Owing to this benefit, gene synthesis has grown in popularity across several scientific domains.

Therefore, gene synthesis has been utilized extensively in numerous scientific domains due to its user-friendliness and cost-effective procedure.

Suffice it to say both techniques have unique applications based on the requirements of a given project.

Continue reading to learn some essential applications of these two approaches.

Applications of Gene Synthesis and Traditional Cloning