Amazingly, thousands of pairs match in one second… “Shocking common sense” by DNA polymerase (Masaharu Takemura) |. Kodansha (1/3)

Solve “life's greatest mystery” hidden in the beautiful double spiral structure!

DNA is said to be one of the so-called biological blueprints that is unique to living organisms and some viruses (DNA viruses). The information in DNA is called “genes,” and this information is used to create the proteins and RNA necessary to sustain life. Therefore, DNA is said to be the “main body of genes.”

However, is it really just a blueprint for living organisms? How did DNA come into existence on this Earth in the first place?

Although DNA is the most important material for connecting generations, it exhibits dynamic behavior inside and outside cells. The ultimate life science puzzle that explores the essenceWhat is DNA?“, we will introduce you to topics that will completely change the way you look at DNA. This time we will provide an explanation of the function of DNA polymerase responsible for DNA replication.

*This article was published by Kodansha/BluePaxWhat is DNA? An intelligent mechanism that copies genetic information almost completely'', the content has been reorganized, re-edited and delivered to you.

How does DNA polymerase work?

Let's take a somewhat chemical look at how DNA polymerase works.

DNA polymerase catalyzes the distal end (3' end) of a growing (newly synthesized) polynucleotide chain, and the 3'-OH group (hydroxyl group) attached to the third carbon of the deoxyribonucleotide) reacts with the phosphate group of the next nucleotide to form a phosphodiester bond and extend the DNA by a nucleotide One (one base).

By causing this reaction one by one, nucleotides are “polymerized” one by one to form a polynucleotide chain, and DNA is synthesized and elongated. By the way, the “PCR” that everyone knows now, is short for “polymerase chain reaction,” which makes us realize that DNA polymerases are found in everyday places like this.

From the time I was in graduate school until I was an undergraduate assistant, I conducted experiments to purify DNA polymerase and measure its activity. When testing the activity of purified DNA polymerase, it is necessary to add magnesium chloride to the reaction system, and if you forget to add it, no activity at all will be obtained, and all of that day's experiments will be spoiled.

The reason for adding magnesium chloride is that the active center (the central part of the DNA polymerase function) of DNA polymerase needs a positive charge possessed by magnesium ions, and the magnesium ion absorbs the accumulated electrons (negative charges) in the hydroxyl group at the end of the polynucleotide chain, because by attracting Phosphoric acid (which has a negative charge) in the next nucleotide (the oxygen atom has an extra electron), it bonds with the hydroxyl group, facilitating the formation of a phosphodiester. Association (Figure “Function of magnesium ions in the active center of DNA polymerase”).

Function of magnesium ions in the active center of DNA polymerase. Magnesium ions attract electrons, promoting the attachment of the 3′ hydroxyl group of the primer to the nucleotide (Adapted from A. Kornberg, T. A. Baker, “DNA Replication, Second Edition”, University Science Books, 2005, p135)

I fondly remember that I was replicating experiments as a graduate student without knowing it.