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DNA Modification Explained

What is DNA Modification?

DNA modification, also referred to as genetic modification or genetic engineering, is defined as the alteration of the genetic makeup or original genome of organisms that wouldn’t occur by natural means. 

DNA is the central information storage system for all organisms, excluding some viruses that only have RNA as their genetic material. It was first discovered in the late 1860s by Swiss chemist Frederich Miescher.

However, decades passed and several notable discoveries were made before DNA’s importance was realized and appreciated. Among these discoveries was the unearthing of it’s helical structure in 1953 by Watson and Crick, using Rosalind Franklin’s clear x-ray patterns. (Although they got the exact structure slightly wrong.) 

Genetic modification wouldn’t come about until 1973, when American biochemists Stanley N. Cohen and Herbert W. Boyer invented recombinant-DNA technology and subsequently revolutionized the way scientists look at DNA.

Genetic modification has allowed researchers to edit (adding, deleting, or changing the nucleotides from the DNA sequence) the genomic DNA of organisms by using different biotechnology methods, including recombinant DNA, gene targeting, or genome editing.

The terms “engineering” and “modification” are interchangeable. Both are used in the context of labeling genetically modified, or “GMO”, food. Broadly, genetic engineering denotes selective breeding, cloning, or stem cell research. 

A popular method of DNA modification includes the making of a recombinant plasmid, the steps of which are listed below:

  • Step 1: Selecting the desired gene and isolating it using restriction enzymes.
  • Step 2: Amplify it using Polymerase Chain Reaction (PCR).
  • Step 3: Insert the desired gene into bacterial plasmids using restriction enzymes and DNA ligase.
  • Step 4: Plasmids are transfected into competent bacteria, selected, and allowed to multiply. Once cloned, the gene can be easily isolated and analyzed/modified.
  • Step 5: Cloned or modified DNA can be introduced back into the donor organism.

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DNA Modification Due to Epigenetic Changes

The process of DNA modification also involves epigenetic changes that have heritable effects (especially when the modification occurs in germline cells) on gene expression without changes in DNA sequences. 

These changes in organisms are regulated by DNA modifications, histone modifications, and non-histone chromosomal protein modifications that control several gene functions.

The most common chemical modifications of histones include enzymatic methylation, acetylation, phosphorylation, ubiquitination, and sumoylation. They play essential biological roles in epigenetic regulations. Most of them indicate DNA damages and are involved in DNA repair pathways.

DNA Modification Due to Methylation of DNA

The methylation or demethylation of histones is one of the most extensively studied epigenetic mechanisms. Depending on the position or base modification, it can cause the activation or silencing of the transcription. 

For example, in vivo, histone H3 trimethylation at lysine 4 (H3K4me3) activates the transcriptional process that recruits DNA repair enzymes. However, DNA methylation at the fifth position of cytosine (5mC) in CpG dinucleotides (cytosine nucleotide followed by a guanine nucleotide), causes gene silencing. These methylations are carried out by DNA methyltransferases.

Cytosine Methylation at CpG sites is the most common genetic modification that has a crucial role in epigenomics, gene expression, or other essential functions of organisms. Some non-CpG methylation where guanine is replaced by adenine, cytosine, and thymine has also been observed in undifferentiated human embryonic stem cells (hESCs). 

The methylation patterns at different sites are executed by the enzyme DNA methyltransferase (DNMT), encoded by DNMT mRNA after the replication process. The enzyme catalyzes the transfer of a methyl group from S-adenosyl methionine to DNA. 

5-hydroxymethylcytosine (5hmC), a product of the ten-eleven translocation (TET) in the demethylation of 5mC, is another in vivo DNA modification. The molecule further undergoes the oxidation process, leading to the formation of 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC). 

5hmC is considered an essential epigenetic factor in many fields, including stem cell renewal, cancer development and progression, and neurological disorders. 

There are different available techniques to detect nucleic acid modifications. The copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), coupled with click DNA labeling, enables genome-wide profiling of any DNA modification at single-base resolutions or locus-specific resolutions. 

Further, copper-free approaches, such as Tet1-associated bisulfite sequencing, are also effective in profiling modified bases at single-nucleotides resolutions.

What is the Purpose of DNA Modification? 

Modification or engineering tools are used to add desired properties to living organisms, including plants, animals, or microorganisms. It has several applications in a range of areas, including medicine, research, industry, and agriculture, that are briefly discussed below:

  • Medicine: The three major applications of DNA modification in medicine are: (1) drug manufacturing, (2) creating transgenic model animals that mimic human conditions, and (3) gene therapy. For example, mouse hybridomas have been adapted through genetic engineering to create human monoclonal antibodies.

Further, gene therapy, developed by editing the human genome, is used in several clinical applications, including X-linked SCID, Parkinson’s disease, and cancer.

  • Research: Genetic modifications are popular for engineering biochemical pathways, studying the function of specific genes, and discovering the location of specific gene expression. Moreover, in labs, the technique is used extensively on animals for its efficacy in treating human diseases.
  • Industrial: The process involves the transformation of organisms’ cells with a gene involved in the synthesis of a useful protein. Then, the transformed cell or organism (that can involve any bacteria, yeast, insect cell, or mammalian cells) is placed inside a bioreactor for the mass production of the specific protein.
  • Agriculture: DNA modification is an essential technique to create genetically modified crops or livestock. It’s a solution to make crops and livestock resistant to several diseases and pests while also enhancing their productivity.

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How Does DNA Modification Work?

DNA/Genetic Modifications Methods for Crops

Genetic modifications have been useful in creating valuable solutions for agricultural problems. Several transgenic crops have been developed to increase the production of crops, increase tolerance to abiotic stresses, alter the composition of the food, and produce novel products.

The types of genetic modification methods for crops include: 

Traditional crop modification: This technique has been in use for more than 10,000 years. It involves the modification of plants through selective breeding and crossbreeding.

Image: An illustration of traditional crop modification.

Genetic engineering: This method allows scientists to copy a gene with a desired trait from one organism and put it into another. The transgenic plants developed by this technique have the potential to grow in conditions where they might not flourish otherwise.

Image: An illustration of genetic engineering to improve crop health and quality.

Genome editing: A technique that enables scientists to use a more targeted approach for crop improvement. It’s much easier and quicker than previous methods. The use of nucleases like TALENs and CRISPR-Cas9, which have more specificity towards the target gene, allows scientists to get the desired results with less variability.

Image: An illustration of gene editing to replace unwanted genes with the desired gene.

Lab Equipment Simplified with Excedr 

DNA/genetic modification is a process that involves base modifications or alterations in the microbial, mammalian, or human genome to achieve targeted goals. It is done by using traditional methods, genetic engineering, and gene editing techniques. 

DNA modification has several applications, ranging from the synthesis of specific proteins and hormones, developing targeted therapies for several human diseases, and crop improvement. However, this multi-step process of genetic modification requires several high-tech equipment and machines, and procuring them can be financially challenging.

Our customized lease program helps labs working in the fields of genetic modification procure the necessary, cutting-edge equipment it needs to establish an efficient workflow, all at a reasonable cost. You can lease PCR systems, imaging systems, spectrometers, and other biological equipment without hamstringing your operational budget or shortening your cash runway.