Polymerase Chain Reaction – Turning a Few Strands of DNA into Many

Prior to a process known as polymerase chain reaction, or PCR, studying DNA was a much more complicated process. With just a few drops of blood at a crime scene or dry brittle bones at an archaeological dig site, collecting a usable amount of DNA was nearly impossible. Then came a man named Kary Mullis who helped develop the innovative technique that is still used in laboratories worldwide today.

Kary Mullis is not your “stereotypical” scientist. As a local of California, he did a lot of his scientific thinking while surfing. He also often openly criticizes the way that scientists must apply for grants in this country and the system that this creates. Alongside this, he openly chronicled how he would develop and test his own psychedelic drugs, such as LSD. We could tell tales of his life behind the science.

Personal life aside, Kary Mullis will certainly go down in history for perfecting the polymerase chain reaction. PCR, while incredibly useful, is not a difficult procedure. To understand the process, we must go back to the basics of DNA. DNA is a double stranded molecule connected in the middle of the strands by bases known as adenine (A), thymine (T), cytosine(C), and guanine(G). In DNA, adenine always pairs with thymine (A-T), whereas cytosine always pairs with guanine (C-G). Attached to each of these bases is a sugar (deoxyribose) phosphate backbone. The molecule is weakest between the bases. This is because DNA is only held together between the bases by hydrogen bonds. There are two hydrogen bonds between adenine and thymine and three between cytosine and guanine. While these bonds are weak individually, together they hold the molecule into a stable, double-stranded form.

(Click Images to Enlarge – Images and Image Legends Found on Wikipedia articles “Base Pair” and “DNA”)

PCR works by manipulating temperature in a cyclic fashion. There are three steps to the procedure that occur over and over again.

  1. Denaturation
  2. Primer Annealing
  3. Elongation

Prior to the first step, you must add the DNA that you are attempting to amplify (AKA multiply), enzymes (proteins) to make the process work, free bases (nucleotides – the A’s, T’s, C’s, and G’s discussed above), and primers. Primers are simply sequences of nucleotides that bind to a segment of your target sequence in the DNA that you want to be amplified. One primer binds to the beginning and the other primer binds to the end of your particular sequence (forward and reverse primers). Once the primers attach, the proteins can go to work and add the rest of the bases.

The first step, denaturation, means that we simply raise the temperature to a point in which the DNA unwinds (since it is in a helix form) and all of the hydrogen bonds break between the bases in the DNA strands. This temperature must be hot enough to accomplish this, but not too hot as to denature the rest of the molecule. Generally, this is around 94 degrees Celsius.

Step two, primer annealing, simply involves the scientist lowering the temperature to a point in which the primers can bind to the DNA (generally around 56 degrees Celsius.) Once this has occurred, step three of the process can begin after the temperature is raised once more to approximately 72 degrees Celsius. One of the major enzymes needed for this process to run is known as DNA polymerase. Simply put, DNA polymerase actually goes through the newly single stranded molecules and adds the bases to make them double stranded once again. This process begins where the forward primer is attached.

One of the original problems with this process is that human DNA polymerase does not function at these high temperatures. The enzyme denatures, or breaks down. To remedy this situation, the polymerase of another organism is used. The Bacterium, Thermus aquaticus (Taq), lives and thrives in hot temperatures. Therefore, its DNA polymerase functions in these heated environments. This is why it can be used for this process. To reiterate, Taq Polymerase it does not denature in the heat the way that human polymerases do.

Once this process is complete, your DNA molecules should have duplicated. You then repeat this process approximately forty times. This causes an exponential increase. One molecule becomes two, two becomes four, four becomes eight, eight becomes sixteen, and so on and so forth until you are dealing with a usable amount of DNA.

With the correct ingredients and a cyclic change in temperature, we can prompt one of the most important molecules in the world to duplicate. Naturally, we do not change the temperatures manually. We have thermal cyclers to do this for us. Simply put the concoction together and add it to a PCR machine, apply the correct settings, close the lid and wait. We must thank the scientists who came before us for helping make our research a bit easier. Until next time, carry on with curiosity!

 

Works Cited

Base pair. (2016, May 28). In Wikipedia, The Free Encyclopedia. Retrieved 19:26, July 15, 2016, from https://en.wikipedia.org/w/index.php?title=Base_pair&oldid=722444608

DNA. (2016, July 24). In Wikipedia, The Free Encyclopedia. Retrieved 20:09, July 26, 2016, from https://en.wikipedia.org/w/index.php?title=DNA&oldid=731351649

Introgression from the Ancients

As stated in my previous blog, it appears that we were not the first “human-like” species to leave our mother-country of Africa. The Neanderthal and Denisovan people made this migration before our ancestors did. However, the Neanderthals and Denisovans may have played a role in our own ancestry. Unless your heritage comes solely from Africa, it is likely that you have a bit of Neanderthal DNA in you. This is partially because our ancestors mated with the Neanderthals in the Near and Middle East as they were leaving Africa. This caused major introgression events, meaning that the Neanderthals introduced non-human genetic material into the human population migrating out of Africa.

(Click Image to Enlarge – Image taken from Wikipedia article “History of human migration”
The numbers on this map represent how many years ago the human migrations occurred.
Homo erectus* – A hominin species whose DNA has not yet been sequenced)

Remnants of these introgression events (as well as others that took place at different points in time when the two groups came in contact with one another) can be spotted in our genomes. In fact, over half of the Neanderthal genome can be recreated using the DNA of today’s modern humans. This high percentage is due to an additive effect from the fact that each person with a heritage from outside of Africa gets approximately 1-3% of their DNA from Neanderthals. Keep in mind, your 1-3% might not be the same as my 1-3%. It simply depends on what part of one’s genome the Neanderthal bits survived in until today.

A similar story can be told with the Denisovan people. Introgression events granting Denisovan DNA to our ancestors occurred as our people spread southeast throughout Asia. Nowadays, it is generally the Melanesians, Papuans, and Australians that have the largest segments of DNA that come from the Denisovan genome. Approximately 3-6% of their ancestry comes from the Denisovans.

You may now be wondering why our genomes still contain segments of Neanderthal/Denisovan DNA. Some scientists will attribute the majority of this to genetic drift, meaning that it is entirely due to chance (**see previous blog post – “Survival of the Fittest? Not Always…”***). However, certain fragments may still be in our genome due to a process known as adaptive introgression. According to Racimo et al., “As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments.” This states that some of these segments from Neanderthals/Denisovans may be in our genomes because they were beneficial enough to help our ancestors thrive and reproduce successfully.

For my next blog post, I will be changing gears to talk about a scientific procedure known as Polymerase Chain Reaction, or PCR for short. The discovery of this simple technique allowed for DNA studies to blossom and allow for an array of studies. These range from the study of ancient DNA, such as that of the Neanderthals and Denisovans, all the way to the forensic analyses used so frequently in America’s judicial system. Until next time, carry on with curiosity.

 

Works Cited

Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015). Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics16(6), 359-371.

History of human migration. (2016, June 24). In Wikipedia, The Free Encyclopedia. Retrieved 20:47, July 13, 2016, from https://en.wikipedia.org/w/index.php?title=History_of_human_migration&oldid=726769187

The Men and Woman Who Walked Beside our Ancestors

As discussed briefly in my last blog post, there were populations of organisms from our own genus, Homo, that were so different from our ancestors that most scientists consider them their own species. These “people” lived long ago. However, the idea that they are their own species should be taken with a certain degree of criticism because of science’s loose interpretation as to what exactly constitutes a “species.” When discussing Neanderthals (Homo neanderthalensis), nobody can argue against the fact that they were fairly distinct from our ancestors (Homo sapiens). However, the extent of this distinction is worth discussing. For example, ancient Homo sapiens diverged from the Neanderthals at around the same approximate point in history in which western chimpanzees diverged from eastern chimpanzees (Prado-Martinez, et al. 2013). Despite this fact, we consider humans and Neanderthals different species, yet we consider eastern and western chimpanzees simply different subspecies.

(Click on image to expand. “Homo neanderthalensis, adult male. Reconstruction based on Shanidar 1 by John Gurche.” Image taken from:
http://humanorigins.si.edu/evidence/human-fossils/species/homo-neanderthalensis)

As we know, all human life began in Africa. All scientific evidence points to this fact. Our people eventually migrated out of Africa, but it appears as though the Neanderthals did this before our ancestors did. In fact, the majority of skeletal remains found from the Neanderthals were located in Europe. When they split off from the ancient group that contained both our ancestors and their ancestors, they likely migrated out of Africa through the North Eastern regions of the continent. They then traveled to Europe where they were able to continue evolving and developing the traits that made them unique from our own species. The discovery of Neanderthals was a grand one in scientific history, but it appears as though they were not the only group of “Homo” in the world other than our own species.

In 2010, a discovery was made in the Altai Mountains of Siberia. Specifically, it was made in a cave known as the Denisova Cave. The remains consisted mainly of a finger bone and a few molars (teeth). Despite the fragmented remains coming from different individuals, scientists were able to discover that they came from a new species that lived approximately 41,000 years ago! This species is now aptly named the Denisovans.

One might now be wondering how it is possible to tell that this was another species with nothing more than a few teeth and a finger bone from 41,000 years ago. The process is not a simple one, but it involves the isolation and amplification of ancient DNA from these sample. The isolation is necessary because there is so much “other” DNA that mixes with the ancient DNA. For example, countless bacteria exist, live, and thrive in the Denisova Cave, just as they do on the rest of our planet. Luckily, we are able to differentiate Hominin and bacterial DNA through bioinformatic analyses fairly simply because the two differ greatly. Then you run into the issue of “human contamination,” so you also need to separate the ancient DNA out from the highly similar human DNA that comes from the excavators and scientists working with the samples. Lastly, amplification is needed because only an extremely small amount of ancient DNA exists after 41,000 years. Amplification is done through a process known as polymerase chain reactions, AKA PCR, which takes a small amount of DNA and replicates it over and over again until you have enough to study. I will discuss this process further in a future blog post.

It is important to note that since these findings, there has also been evidence of other “ghost” hominin species similar to these ones. However, most of these were likely in Africa, where the hot humid climate is not conducive to the fossilization process. For example, there is evidence that another hominin species known as Homo erectus existed, but scientists have not yet been able to sequence DNA from the fossilized remains that were found.

In my next blog post, I will discuss how our ancestors mated with the Neanderthal and Denisovan people and the imprints that this left on our genetic signatures. Until next week, carry on with curiosity!

 

Works Cited

Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., … & Cagan, A. (2013). Great ape genetic diversity and population history. Nature, 499(7459), 471-475.

Smithsonian’s National Museum of Natural History. (n.d.). Homo neanderthalensis | The Smithsonian Institution’s Human Origins Program. Retrieved July 05, 2016, from http://humanorigins.si.edu/evidence/human-fossils/species/homo-neanderthalensis