Biochemistry 101: DNA Charge and Gel Electrophoresis

At its most basic, biochemistry is one of the building blocks of life, and the study of biochemistry will unlock secrets about the chemical processes present in all living matter, from eradicating diseases through the genome to answering basic questions like what charge does DNA have and how do we find out.

But biochemistry isn’t just relegated to medicine: it can also be used and applied in all manner of sciences across different industries: biochemistry is one of the leading fields of study in the environmental conservation sector, where scientists are leveraging the process of photosynthesis to create crops that have enormous yields or using bioremediation to help heal contaminated soil. Biochemistry can also be used in conjuncture with industrial fields, like engineering, where energy-efficient engines are being created to take on biofuels as their main source of energy.

Medicine, however, is where biochemistry is the most prominent, considering that it encompasses a plenary majority of that particular field. The study of the biochemical processes happening within our cells has helped us grow our understanding of health itself, from learning about the origins of cancer to understanding the way genes dictate the proliferation of Alzheimer’s or arteriosclerosis. Biochemistry has allowed scientists and doctors to map out the very blueprint of biological existence: the human genome and its building blocks deoxyribonucleic acid and ribonucleic acid, or DNA and RNA.

Without biochemistry, medicine would grind to a halt; there is perhaps nothing more valuable to the field than biochemistry. In fact, every branch of medicine uses some form of biochemistry as its base. Physiology, which involves more physical movement than any other medical discipline, still uses biochemistry to help them understand how physical alterations to the body will create a chemical change.

In this article, however, we’ll be talking about the building blocks of biological life itself: the deoxyribonucleic acid, or DNA.

What is DNA?

Grouped DNA
Retrieved from Pixabay

DNA or deoxyribonucleic acid is a type of long molecule that has our unique genetic code encoded within its walls. It’s the building block of the genome. The genome is what makes each and every biological organism unique to each other, and is what determines everything about our physical makeup, from the bone structure and skin color to chemical imbalances and potential diseases.

Deoxyribonucleic Acid is made up of 4 different monomer nucleotide bases: Guanine, Adenine, Thymine, and Cytosine. These blocks are usually represented by their first letters: GATC. The sequence in which these bases are formed is what creates the genome and is what decides the uniqueness of the organism.

As a molecule, the DNA is composed of two strands of its bases shaped into a double helix. Each strand is then composed of a unique sequence of the bases GATC. Each base on opposite sides of the strands are paired with complementary bases on the other side, Guanine always pairs with C (G to C), and Adenine always pairs with Thymine (A to T). These pairs reach out to each other from their side of the strand, creating a connection; a ‘rung’ in the twisted ladder that is our DNA. During DNA replication, these strands are separated and then repaired with another strand that is an exact copy of each one.

The DNA’s double helix structure was discovered by Cambridge scientists James Watson and Francis Crick, who was inspired by the (incorrect) theories of Linus Pauling to create an accurate and working model for the DNA and were helped by fellow DNA researcher Rosalind Franklin. Together, these scientists were responsible for paving the way for genome studies, something that has helped shape our understanding of biochemistry and life itself.

DNA has so many different aspects to study, but for this article, we will be studying its charge.

What is the Charge of a DNA And Why is That Important?

DNA has a negative charge, and its charge is important to know because the processes and machinery of cells are adapted to a negative charge. DNA carries a negative charge thanks to the phosphate group pentose, nitrogenous base, and phosphate, which make up all the nucleotides in the genome.

Were DNA positively charged, the interactions between DNA and all possible biological processes would be so vastly and fundamentally different, we would have no idea how it would affect the genome. This negative charge is also what made DNA so easy to study: when denaturalized, DNA strands become straight because negatively charged things naturally repel themselves. However, if one wanted to go deeper into studying the individual parts of the DNA, they’ll need to use Gel Electrophoresis.

What is Gel Electrophoresis and What’s It For?

DNA forming human
Retrieved from Pixabay

In science, electrophoresis is a process that scientists use in order to separate differently charged molecules and arranging them according to size. In genetics, this is helpful in separating different monomer nucleotides of DNA using a special kind of electrophoresis called Gel Electrophoresis.

Gel electrophoresis is much like the regular electrophoresis, except it is used to separate different elements of the genome by size: DNA, RNA, and different types of proteins. A genome sequence is placed inside a gel, where its charged molecules are made to move using an electric current. These molecules move, called migration, towards one end of the gel to the other. Each end of the gel has an opposing charge to the other, with one end being positive and the other being negative.

The gel itself has a permeable matrix that allows molecular migration as the electric current is passed through and across it. As the molecules pass through the gel, the smaller molecules get farther because of how fast they are. Meanwhile, larger, slower molecules are slowed down in the gel and caught by the matrix like a sieve. In this way, scientists can separate the molecules by size and have a clearer look at each building block of the genome.

Using Gel electrophoresis, scientists can break down different fragments of DNA and help distinguish each part depending on the length of the fragments. Because DNA has a negative charge, it will migrate towards the positively charged side of the gel. As it migrates, shorter strands will make it all the way through gel while longer strands get left behind, thereby arranging the different monomer nucleotides by size.

After the strands are separated, scientists will use various types of labels in the form of radioactive or fluorescent dyes to tag individual strands for easier identification. These tags will appear as varying shades of grey bands on the gel.

Leave a Comment