DNA Replication, Part III: How It Is Done

In 1957, Arthur Kornberg made a really interesting discovery. He showed that DNA can be replicated outside of a cell, in a laboratory test tube. Kornberg wasn’t much interested in which model of replication was right. Instead, he was interested in specifically how replication occurred. Watson and Crick had suggested that the replication of DNA may not actually require an enzyme. If you could somehow unzip DNA, they thought that new DNA might just self-assemble, because the complimentary base-pairing would bring in all the appropriate nucleotides. Kornberg thought, though, that there must be some enzyme involved. He set out to figure out what that enzyme was.

What Kornberg did was some old-fashioned tedious work. He thought that there must be some enzyme, so he started looking at all the candidate proteins in bacteria cells, and seeing if any of these synthesize DNA. He would essentially create culture media where he would put three things: some single-stranded DNA that should serve as a template for making new DNA, some of the nucleotides that the DNA had to be made of, and some candidate enzymes from bacteria cells. He then would see if DNA is synthesized. He did this over and over, with all sorts of candidate enzymes.

He did find one, actually. He found an enzyme that he named DNA polymerase. When he put this enzyme into the mix, he would get the synthesis of a new complimentary strand on the old existing strand that he added.

This was really an important discovery. This really opened up the modern era of molecular biology. The discovery of DNA polymerase kick started a 50-year long (and still continuing today) study of how DNA replicates, and specifically how DNA polymerase does its job. This is often how science works. There is an initial discovery, and then generations of scientists come along and fill in the details.

The Mechanisms of Replication

What I want to do now is to step through the mechanisms we think are responsible for replicating DNA. The first thing we know that has to happen is that the two sides of the DNA double strand have to be separated. They are separated by an enzyme called helicase. You might by now note a pattern of how scientists name enzymes. They always end with “ase”, and their name tells you exactly what they do.

Once helicases have done its job, there are other sets of proteins that come along. These are generically called single-strand binding proteins. These proteins come and sit on the now open DNA and hold it open. This is like putting a chock in there, so that the thing can’t zip back.

Now is the turn of the major player, the enzyme Kornberg found, DNA polymerase. What this enzyme does, as it names implies, is to polymerize the new nucleotides on the growing new strand of DNA, as it is being complimentarily matched to the older template strand. The nucleotide monomers that are added on to the growing strand are in a slightly different form.

The bases that are being added on by DNA polymerase are not being chosen by DNA polymerase itself. Instead, they are being lined up through the complimentary base-pairing that’s inherent to the nucleotides. A with T, C with G. All DNA polymerase does is to go to the next nucleotide, and build a strong chemical bond between the growing strand and the next nucleotide that’s going to be added. It just finds what’s there, and what’s there is there because of the complimentary base-pairing of that nucleotide with the corresponding one on the old template strand.

Complimentary base-pairing is really the key to DNA replication. All else are just details. We could talk about all these details, but we’ve already seen the key issues. At the end we see that Watson and Crick not only had it right, but almost 50 years later, we’ve seen exactly how that mechanism works. Our understanding of these mechanisms of DNA replication has been central to sequencing human DNA and manipulating it to our whims. Also, it helps us understand one of the essential processes of life, which is reproduction, and, by extension, the evolution of life.