Research 101: DNA
Talking about DNAโฆseems like such a simple topic, right? Well, using DNA in a lab is not as straightforward as it may seem. A lot of information that is published relies on DNA in different contexts. I thought it would therefore be a good addition to my Research 101 series and highlight how researchers use DNA in their studies.
If youโre interested, you can also find my other Research 101 articles using this link!
What is DNA?
Iโm sure anyone who has had any amount of education knows that DNA is essentially the building block of life; it is the blueprint of our cells. It contains all genetic information passed from parent to child and basically controls what you are (maybe not personality/behaviorallyโฆalthough there are some interesting ideas that DNA might contribute to behavior in major ways, such as addiction).
If you want a piece of trivia knowledge, DNA stands for deoxyribonucleic acid. But people only say the full word when they want to sound extra smart (maybe just my opinion). Structurally, itโs comprised of two strands that wrap around each other in a double helix. The exact structure of this can vary, but the most well-known DNA is a right-handed helix. (Imagine going up a spiral staircase with your right hand on the railing โ thatโs a right-handed helix).
The strands themselves are made up of a sugar molecule called deoxyribose (which is a 5-carbon ring, if you want more trivia), connected by phosphate groups. The strands are then linked together by a variety of โbasesโ (so-named because they are basic, nitrogenous molecules) called nucleotides. Yet another bit of trivia knowledge, these bases are adenine (A), thymine (T), guanine (G), and cytosine (C). These four letters are it โ the source of all your genetic information is comprised of a mess of Aโs, Tโs, Gโs, and Cโs. Life is so simple…right?
One last bit of trivia for you, DNA is negatively charged, due to those phosphate groups on the backbone.
Anyway, we have a lot of DNA. If we took the DNA from one of our cells and stretched it out, it would be about 2 meters long. If we took all the DNA from all our cells, it would work out to about twice the diameter of the solar system. Almost too much to comprehend. All this information is highly condensed into chromosomes in our cellsโ nucleus. When a particular piece of information is needed (say to transcribe a gene) or a cell needs to replicate its DNA to divide, these ultra-condensed chromosomes are unpacked and then repacked later. Itโs truly a remarkable process.
Where do we get the DNA?
Itโs surprisingly easy to get DNA. The barebones method is gathering some cells, breaking them open (called lysing), and separating the DNA from the rest of the cellular components to get pure DNA. The cells can be obtained from tissue samples (from model organisms or humans) or cell culture.
There are ways to purify DNA from โscratchโ so to speak, but most people I know use commercial kits. Most of the time, these kits use a column-based purification system. Essentially, there is a column that contains a kind of cotton-y (itโs not actually cotton, but itโs a good descriptor) filter layer that binds DNA, and the other cellular components are washed through. At the end, the DNA can be eluted all alone by unbinding it from the filter, and voilร ! Fresh, pure DNA.
What can the DNA tell us?
The main piece of information DNA can tell us is the โstateโ of our genes. This can be identifying mutations, determining if certain genes are present or not, and identifying specific proteins that interact with DNA. Iโm likely missing some applications, but essentially analyzing DNA can inform us of the genetic โstateโ of the sample and how this effects phenotypes (like disease states, physical appearances, etc.). This is important, by informing how certain mutations or loss of certain genes can affect how cells act.
For example, DNA extracted from patient tumors are sequenced to identify what mutations are present. The presence of different mutations can inform what chemotherapies are administered, because some mutations render certain treatments useless, but other mutations respond well to the same medication. This can happen in breast cancer, where patients can become resistant to hormonal-based treatments due to the cancer cells generating additional mutations. Therefore, it’s important that patient tumors are sequenced throughout treatments, to ensure the best possible outcomes.
Side note: if you want more information on cancer and mutations, I wrote a post about it a while back!
How do we analyze DNA?
DNA is most frequently analyzed through polymerase chain reaction (PCR) and sequencing. PCR is used to amplify specific sections of DNA, while sequencing is more unbiased and identifies the actual sequences of the nucleotide bases (those A/T/G/Cโs we talked about earlier), and doesn’t have to be contained through one specific section of DNA.
PCR is mostly used when the sequence is known. It’s important to note that the output from PCR doesn’t provide the specific sequence information, like sequencing can. Instead, PCR products are most often run on gels to see if the target gene is present. Often (as I do almost daily), the PCR products are then sent for sequencing to confirm the A/T/G/C sequence. I wonโt go into more specifics of when we use each method (or how we do them), but they can each be used to identify the information I described above โ mutations, presence of genes, etc. Determining which specific method is used is a balance of time, resources, and the downstream applications we want to use the information for.
Conclusion
Hopefully this was at least semi-interesting! Iโm writing these articles to be more informative, because I feel like the โvoidโ between scientists and non-scientists is partially due to the fact non-researchers donโt really know what us research scientists do in lab every day. Maybe this can help generate a better understanding of how mundane โ I meanโฆexciting โ the every day lab work is, and how big discoveries are made.
I want to include one sort of disclaimer here โ there are a lot of commercial DNA testing kits out there now. Thereโs Ancestry DNA, 23andMe, Helixโฆmy Google search has shown even National Geographic has a DNA testing kit. The issue with a lot of these kits is once you send your sample (usually in the form of saliva), your genetic data is โownedโ by the company. This means they can sell your information to whatever third parties might pay them for it, without your consent. This is partially good, because it can provide researchers and research organizations with a lot of genetic information that they donโt have to go out and solicit – saving time and resources. Plus, your personal identifiers are removed, so itโs not like anyone can find you.
However, your genetic information is valuable data. You’re paying these companies to get your DNA sequenced, but theyโre making even more money on top of that. Outside of getting your results, where is the benefit to you? It does seem a bit unfair that you donโt get any monetary benefit from using these kits. I imagine that the ownership and sharing of genetic information like this will become more regulated in the next few years. Iโm not telling you not to use these kits. They are pretty cool and itโs fun to see what your DNA can tell you, but you should also be aware that your genetic data is valuable, and you should benefit from that the same way these companies are.
Further reading:
