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DNA Profiling

What do you think of when you hear the three letters DNA? Do you think of genetics, labs, or perhaps something else? Well, you probably think of something at least remotely scientific because you have probably previously learned that DNA carries the genetic information of living beings. DNA is the basis of how our genes are transferred from generation to generation. Since DNA makes up almost all living organisms, we can use DNA to create genetically modified organisms, study diseases, profile humans, and even figure out lineages. Keep reading to get more clues about how researchers and forensic scientists use DNA profiling to make the world better! 

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DNA Profiling

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What do you think of when you hear the three letters DNA? Do you think of genetics, labs, or perhaps something else? Well, you probably think of something at least remotely scientific because you have probably previously learned that DNA carries the genetic information of living beings. DNA is the basis of how our genes are transferred from generation to generation. Since DNA makes up almost all living organisms, we can use DNA to create genetically modified organisms, study diseases, profile humans, and even figure out lineages. Keep reading to get more clues about how researchers and forensic scientists use DNA profiling to make the world better!

DNA profiling definition

DNA profiling involves identifying individuals or samples through DNA.

DNA profiling can also be referred to as DNA fingerprinting, and Alec Jeffries, a geneticist at the University of Leicester in 1984, first invented it.

We can identify individuals or samples using DNA because even though most of the genome is identical in different humans (~99.9%), there are some key differences.

A genome is all the genetic information in an organism.

The human genome includes the coding regions and non-coding regions of DNA.

The parts of DNA that vary in humans are called genetic markers; since their locations are known, we can use them to identify individuals. The different types of genetic markers in humans are:

  • Short tandem repeats (STRs)

  • Single Nucleotide Polymorphisms (SNPs)

  • Restriction fragment length polymorphisms (RFLPs)

Short tandem repeats (STRs): A short sequence of repeating nucleotide units. It is usually 2 to 6 base pairs long and is the most common DNA profiling method.

There are a bunch of different STRs throughout the genome. Different STRs have different repeating units in different locations shown below:

DNA Profiling Types of STRS Study SmarterFigure 1: Two Different STRs are shown. Daniela Lin, Study Smarter Originals.

In Figure 1, examples of two different STRs are shown. The first one, STR-1, is made up of GAC and has two repeats. The second one, STR-2, has two repeats but is made up of CAG.

To understand DNA profiling, let’s focus on just one STR illustrated in Figure 3. Humans all have short tandem repeats; it's the length or the number of nucleotides that varies between all of us.

Nucleotides are the building blocks of DNA.

DNA stands for deoxyribonucleic acid, and it stores the genetic information of living organisms. DNA is shown in figure 2 in blue.

STRs are non-coding DNA or DNA not involved in protein synthesis, meaning there’s no impact on our health to have different numbers.

DNA Profiling STRs comparison between Humans Study Smarter Figure 2: Humans with varied STRs shown. Daniela Lin, Study Smarter Originals.

Figure 2 shows that the number of repeats between the same STRs (STR-1 GAC) differs from person to person. Person 1 has six base pairs or two repeats, person 2 has three repeats or nine base pairs, and finally, person 3 has four repeats or twelve base pairs in the same place in the genome.

STRs still take a long time to map, but you only have to map at specific genome points. It’s good for DNA profiling, as explained above.

Now that we’ve gone over the basics of STRs let’s move on to learning about the other two genetic markers. Then we’ll reevaluate these genetic markers to make DNA profiles in the next section.

Single nucleotide polymorphisms (SNPs) are areas where there’s a single nucleotide change in the genome between different humans.

In this example, four different humans’ nucleotide sequence at one point in their genome is shown below:

  1. GACGACCTA

  2. GACGACCAA

  3. GACGACCGA

  4. GACGACCCA

In the example shown above, the letters highlighted in red are SNPs because each human has a different nucleotide at that spot.

SNPs are more common than STRs because the probability of finding one different nucleotide at different points is higher than finding different numbers of repeats. As a result, SNPs also allow us to get a more complete genetic view.

The bad thing about SNPs is that you need to map the entire genome, making it take longer than STRs. Next-generation sequencing, a type of efficient sequencing technology, has made it more accessible.

SNPs are better than STRs at comparing genes between populations and making family trees.

The last part of this section explains what restriction fragment length polymorphisms (RFLPs) are.

Restriction fragment length polymorphisms (RFLPs) are DNA fragments that differ between people as a result of them being snipped by enzymes.

Enzymes are proteins that help speed up reactions. Restriction enzymes are a type of enzyme usually made by bacteria that can cut DNA at specific sites.

Homologous DNA sequences are genes inherited from common ancestors and have known variability.

Don’t worry about knowing what gel electrophoresis is or exactly how RFLP works; we will compare it to the method used to profile DNA today in the next section.

This method is no longer used for DNA profiling because other techniques we will discuss next are faster and cheaper. This is because RFLPs involves all the steps described above and need to build a probe or a single-stranded sequence of DNA or RNA used to search for complementary sequences.

We need to use probes for RFLPs because many indiscernible fragments can be made when restriction enzymes snip genomes.

DNA profiling steps

Now that we understand what DNA profiling is and why it works. We can now learn how we create them.

  1. We need to collect a DNA sample:

  • We can obtain this from any substance with cells (e.g., blood, saliva, hair, fingernails, etc.)

  1. We need to extract the DNA from the sample collected:

  • First, we must break open the cells by adding chemicals like alcohol or detergents.

  • Next, we must separate DNA from other cell components like lipids or proteins.

  1. We need to amplify the STR fragments:

PCR of polymerase chain reaction is a method used to make millions or billions of copies of a pre-selected region of DNA. In DNA profiling, researchers want to amplify genetic markers to compare to DNA collected from potential suspects.

We amplify STRs by using DNA primers that only bind to the DNA on each region of the STR, as shown in Figure 3. The primers allow DNA polymerase to bind and make copies. After a while, we end up with a ton of copies!

DNA Profiling PCR Primers Study Smarter Figure 3: DNA polymerase and primers enable PCR to work. Daniela Lin, Study Smarter Originals.

  1. We use gel electrophoresis to determine the length of STRs:

  • STR fragments can be separated by gel electrophoresis because smaller fragments move through the gel faster than larger ones.

  • The number of bands and where they are in the gel electrophoresis make our DNA profile.

  • We need to compare our results to a DNA ladder or a mix of DNA fragments whose size we know, as shown in Figure 4.

DNA Profiling Gel Electrophoresis Study Smarter

Figure 4: Gel electrophoresis illustrated. Daniela Lin, Study Smarter Originals.

The longer STR fragments stay nearer to the negative part than shorter STR fragments because the longer DNA fragments have to push through the agarose gel more. The DNA moves from the negative to the positive end because it's negatively charged due to the presence of phosphate groups.

Another type of electrophoresis we use in DNA profiling is called capillary electrophoresis. Like gel electrophoresis, capillary electrophoresis features the same first three steps.

  1. Collect DNA sample(s).

  2. Extract DNA sample(s).

  3. Amplify STR fragments.

When we amplify primers, we do the exact procedure explained above with gel electrophoresis, except our primers are fluorescent.

  1. This step is different as we determine the length of STRs using capillary electrophoresis:

  • We use a laser and detector to make an electropherogram or a plot of our DNA profile.

  • The number of peaks and where they are located on the graph create our DNA profile. Like gel electrophoresis, we also use a DNA ladder to determine the size and length of an STR, as illustrated in Figure 5.

DNA Profiling Capillary Electrophoresis Study SmarterFigure 5: Capillary electrophoresis shown. Daniela Lin, Study Smarter Originals.

Similarly to gel electrophoresis, the longer STR fragments stay nearer to the negative part (anode) than shorter STR fragments because the longer DNA fragments have to push through the capillary tube more. The DNA moves from the negative to the positive (cathode) end because it is negatively charged due to the presence of phosphate groups.

DNA profiling examples

Determine the parentage of the child shown below. Assume all DNA profiling procedures were followed correctly.

DNA Profiling Parentage Example 1 Study SmarterFigure 6: The parentage problem is shown. Daniela Lin, Study Smarter Originals.

To determine the child's father, we need to look at the DNA bands in Figure 6. For the mom, three bands match the child’s; this means three other bands must come from the father.

Humans have 23 pairs of homologous chromosomes, or 23 x 2= 46. Of the 46, 23 come from dad, and 23 come from mom. Each pair of homologous chromosomes have the same genes, but variations might result in potentially different alleles. What this means for us is that every human has two copies of every STR in their genome.

For instance, if we have STR-1 GAC 2 (shown in Figure 1)

Knowing this, we can determine that dad number 2 has three bands that are the same as the child’s, making him the father.

DNA Profiling Parentage Example 1 Solution Study Smarter

Figure 7: Parentage analysis results shown. Daniela Lin, Study Smarter Originals

The child’s DNA bands come from the mother (pink) and the father (blue) shown in Figure 7. Why is this? As explained above, each copy of an STR comes from one parent.

Cons of DNA profiling

After understanding all the wonders DNA profiling can do, we should also consider some cons of DNA profiling.

  1. DNA samples are delicate and can be ruined quickl by contamination, so we can no longer test them.

  2. We need a lot of samples for the test to be accurate. For example, we need 13 STRs to test with PCR.

  3. Improper procedures and handling could lead to inaccurate results. For instance, we need to ensure that the gel, buffer, and current are all okay when we perform gel electrophoresis.

  4. User needs to interpret the results correctly for the test to be valid.

  5. DNA samples can be easily gathered, meaning we could have a lot of data that means nothing. For example, if the crime scene has copious amounts of DNA, then forensic scientists must compare every single one to rule out suspects.

Risks of DNA profiling

This section will discuss the ethical issues or risks of building DNA profiles.

  1. Privacy and data protection:

  • DNA databases and banks can be subject to hacking which can lead to new ways for scammers to commit identity theft.

  • DNA databases can be stored indefinitely and don't guarantee anonymity which could be used not only by the federal government but also by sites like 23andMe, depending on who the database belongs to.

  1. DNA evidence doesn’t always tell the correct story:

  • What we mean by this is sometimes crime scenes could be so overly contaminated that DNA will tell us that so and the so person was here, but it won’t tell you if that’s the person you’re looking for. Maybe the DNA was there at the wrong place and time.

  • There’s also human error and bias that could influence DNA evidence. For instance, researchers have shown that forensic scientists can arrive at wildly different results with the same DNA mixtures.

  • Due to the United States history and potential human error, racial bias can be a potential risk with DNA profiling.

Although there are potential cons and risks to DNA profiling, there are also a lot of positives. DNA profiling has rightfully freed many innocent people because as long as the procedures are followed, DNA is accurate. DNA profiling has also been used for adopted individuals to find their biological relatives, identify genetic diseases, etc. Overall, DNA profiling can be a great advent depending on how we as a society use it.

DNA Profiling - Key takeaways

  • DNA profiling involves identifying individuals or samples through DNA.

  • The reason we can identify individuals or samples using DNA is that even though most of the genome is identical in different humans (~99.9%), there are some key differences.

  • The parts of DNA that vary in humans are called genetic markers. Since their locations are known, we can use them to identify individuals: short tandem repeats, short nucleotide polymorphisms, and restriction fragment length polymorphisms.

  • The main techniques we use to build DNA profiles are gel and capillary electrophoresis.

  • Although DNA profiling has been a ha tool in paternity and genetic testing, it also comes with disadvantages and risks. For example, it could impact privacy and be prone to human error.


References

  1. Aziza Ahmed, Ethical Concerns of DNA Databases used for Crime Control, Harvard Law, 2019.

Frequently Asked Questions about DNA Profiling

DNA profiling involves identifying individuals or samples through DNA. 

We can get a DNA profile from urine but it’s not as good as blood. This is because there’s a low epithelial and low blood cell count which can affect the DNA in the urine. 

DNA profiling is used to solve crimes as we can use genetic markers such as short tandem repeats, amplify them with PCR and then use gel electrophoresis to separate the short tandem repeats by length. After separating them, we can compare the DNA collected from the crime scene to the suspect’s DNA. 

DNA profiling works in the following steps: 

  1. Collect the DNA sample

  2. Extract the DNA sample

  3. Amplify STR fragments 

  4. Use gel or capillary electrophoresis to determine length of STRs and compare them to known DNA mixtures. 

The purpose of DNA profiling is to mostly accurately identify the DNA found in a crime scene. Although DNA profiling can also be used to test for paternity. 

Test your knowledge with multiple choice flashcards

What is DNA profiling?

Why are genetic markers important?

What are different types of genetic markers?

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