Tell-all DNA!

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A researcher uses a pipette to remove DNA from a micro test tube. Maggie Bartlett/NHGRI

Your spit contains a lot of information. It’s okay if you don’t believe me. Read this entire post and you will!!!

Recently, I shadowed a physician, who was collaborating with a researcher on a clinical trial. I cannot tell you about the study that they were recruiting patients for because of “confidentiality and whatnot,” but I can tell you that the study was designed to see if genetics played a role in a medical condition common in adults and kids. Every patient who agreed to participate in the study was asked to spit in a cup.

What was surprising is that more than 90 percent of the patients knew about genetic testing but were amazed by the fact that just spitting in a cup could tell them if they are predisposed to a disease or if the disease is just a random occurrence! Almost everyone today knows about the amazing DNA tests that can tell you about your heritage or (in sci-fi movies) point you to your killer. But how exactly does this work

Human DNA is made of a sequence of A, G, T and C bases. Every single human cell in the body contains 3 billion bases. Between two humans there is a 99.9 percent similarity in this sequence. The 0.1 percent difference in the bases is what makes each of us unique, except for twins (All the 3 billion bases are identical in twins).

Hair, spit, cheek cells – all of these contain DNA. Identifying if your DNA matches with someone is called DNA fingerprinting.  Let’s start by understanding how DNA is used to establish paternity or in those countless TV shows used to identify criminals.

Step 1: DNA sample is taken from two people/ DNA is found on the crime scene.

Step 2: DNA is so small in quantity that it cannot provide a proper identification.

Step 3: Science comes to the rescue.

The first step is to isolate DNA from that tiny sample using a mix of enzymes that can break down the cells and release the DNA. But because the DNA isolated is so small in quantity, the next step is to increase the quantity of DNA.

This is done using Polymerase Chain Reaction – PCR for short.  PCR’s job is like that of a Xerox machine: to make multiple copies of DNA. And, the machine in which the PCR reaction takes place is just an ultra-fancy heating block that changes the temperature rapidly enough for the PCR reaction to happen. The amazing thing is that the amount of DNA required for this reaction to happen is around 1-2μl (microliters) – an unbelievably small amount!

But like I said, PCR makes multiple copies of DNA. Imagine making millions of copies of 3 billion base pairs in one single reaction.  Thinking about it makes my head spin!

To avoid unnecessary duplication we add something called a “primer” to the PCR reaction along with DNA. Primer is an 18-22 bp sequence that decides what part of DNA is copied. Think of a primer as a roadblock, DNA polymerase enzyme (enzyme that makes multiple copies of the desired segment of DNA) cannot amplify DNA beyond the roadblock, only in between the roadblocks. Different primers can amplify different parts of DNA.

From the PCR we will have millions of copies of the desired DNA fragments. These DNA fragments can be separated based on their size using gel electrophoresis.

Gel electrophoresis involves passage of different sized DNA fragments through agarose gel (it’s pretty similar to Jell-O). DNA is negatively charged, so if you create a positively charged field at the other end, DNA will migrate from one spot to another. DNA fragments migrate in the gel based on their sizes. The smaller DNA fragment quickly moves through the matrix while the larger DNA fragments get tangled up and move slower. While running a gel, you also add something called a DNA ladder. DNA ladder is a pre-mix of different sized DNA fragments that is used as a standard ruler.  When this gel is visualized under UV light, you can see something like this:

dna sequence

To understand how this image is interpreted in cases of paternity testing, let’s assume sample A is from a kid and samples B and C are from his/her parents. In that case, what this image tells us is that sample A (kid) has a 1000bp (base pair) segment and a 500bp segment, but sample B (dad) only has a 500bp segment and sample C (mom) only has a 1000bp segment.  So, sample A (kid) could have gotten the 500bp segment from dad and 1000bp segment from mom. (Every kid gets 3 billion base pairs from mom and 3 billion base pairs from dad). But, if we randomly chose two people, there is a chance that we would get similar results, since we are 99.9 percent similar. 

Statisticians have solved this conundrum and concluded that if approximately 20 different sites on the DNA are a match, then that is enough proof to say with confidence that two people are your parents. In case of identifying genetic mutations, the bands that you see in the image are sequenced, which tells us the A-G-T-C sequence in that particular sample band, which tells us if a gene responsible for a particular disease is present in a person or not. Amazing, right?!

If after reading this post, you think you want to learn more about your ancestry check out 23andMe. Or, if you want to see what your DNA picture would look like, check out the amazing DNA portraits by DNA11. Or, if you want to try doing this really simple process at home, take a look at the PCR machine by OpenPCR.

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