How to explain the principles of nucleic acid testing to children?

Hello, my dear children and classmates! I am Li Yongle, the off-campus counselor of the Beijing Young Pioneers, from the Affiliated Middle School of Renmin University of China.

Recently, many children have done many nucleic acid tests. We all know that the purpose of nucleic acid testing is to screen for people infected with the new coronavirus. But do you know why a small cotton swab can screen out people carrying the virus from tens of millions of people? Today I will tell you what the principle of nucleic acid testing is.

1. What is nucleic acid?

In order to tell you the principles of nucleic acid testing, we first need to know what nucleic acid is.

As we all know, the human body is made up of many cells. Cells have cell membranes, which protect them. They have many organelles that can perform various functions, and a cell nucleus, which contains a substance called chromosomes. The chromosomes are wrapped with a double helix structure called deoxyribonucleic acid, or DNA for short. Do you know what DNA does?

From cells to DNA

If we magnify DNA a little more, you will find that it is made up of nucleotides one by one, just like a castle is made up of bricks one by one. There are four types of nucleotides, called A, T, C, and G. And they have a rule: A must be opposite to T, and C must be opposite to G. This is called the complementary pairing principle. Everyone must remember this principle, because nucleic acid testing uses this principle.

Deoxyribonucleotide sequence on DNA

Although there are many different kinds of organisms, their genetic information is recorded by these four nucleotides. For example, 7 musical notes can form countless beautiful melodies, and 26 English letters can also form Shakespeare's masterpieces. Using different arrangements and combinations of the four nucleotides A, T, C, and G, we can represent different genetic information of organisms. People have also given this arrangement and combination a name - gene. Each organism has its own special gene. By observing the gene, we can know which organism's DNA it is.

In addition to deoxyribonucleic acid DNA, organisms also have another type of nucleic acid called ribonucleic acid, or RNA for short. What does it do?

Since DNA is on chromosomes, which are very large and cannot get out of the cell nucleus, how can its genetic information be expressed? In the cell nucleus, cells use DNA as a template to produce single-stranded RNA, which is also composed of four nucleotides. It can also carry genetic information by pairing with DNA.

Then, the tiny RNA will come out of the nuclear pore of the cell nucleus and find a cell organelle called ribosome. RNA will tell the ribosome to produce various proteins according to the instructions of genetic information. Protein is an important part of our life, and many functions in my body are completed by protein.

From the synthesis of DNA, messenger RNA and proteins

From DNA, RNA is produced, and RNA then guides ribosomes to make proteins. The whole process is called the central dogma, which is the core function of cells. Let's make an analogy: if a cell is a factory, then DNA is the factory director, who is responsible for making production plans. However, the factory director is in the office and rarely comes out. He will not come directly to the workshop to tell the workers what to produce, but will convey it through the workshop director, who is RNA. He first listens to the instructions of the leader in the office, and then comes to the production workshop. This workshop is the ribosome. Under the guidance of the workshop director, the workers in the workshop produce proteins. The efficiency of cell production is very high. The efficiency of any enterprise in the world is far behind that of a cell.

Cell Factory

Do you understand what I have said? There are two types of nucleic acids: DNA and RNA, both of which can carry genetic information. We humans use DNA as the main genetic material, and RNA is the messenger of DNA. But there are also some viruses that do not have DNA, but directly use RNA for inheritance. The new coronavirus is such a virus. If we want to determine whether a person has the new coronavirus, we have to see whether there is an RNA sequence corresponding to the new coronavirus in the person's cells.

2. How nucleic acids replicate

However, when the white blood cell probe is poked into our throat or nose, it can only pick up very few cells, and if there is virus, the content is very low. Moreover, with tens of thousands of people undergoing nucleic acid testing every day, it is too difficult to find one or two infected people. What should we do?

Everyone thinks: It is very difficult to find a needle in a haystack, but if the needles in the haystack can reproduce, 1 becomes 2, 2 becomes 4, 4 becomes 8... I let it reproduce 40 times, then one needle will become 1 trillion needles. Wouldn't it be much easier to find them then?

So, if we want to conduct nucleic acid testing, we must first allow the virus's nucleic acid to replicate. Do you know what the nucleic acid replication process is like in nature?

Our cells divide every day, and when cells divide, DNA is replicated. We can imagine that if a factory opens a branch, it must train a new factory manager. In this process, many biological catalysts, enzymes, play an important role. They can use the nucleotides in the cell to replicate new DNA. You can think of enzymes as tools, such as screws and bottle openers. With these tools, nucleotides can form DNA. Without these tools, DNA cannot be replicated at all, just like if you don’t have a bottle opener, you can’t open a bottle of beverage.

The specific process of DNA replication is as follows:

First, under the action of helicase, the double helix structure of DNA will open and form two single strands.

Helicase unwinds the DNA double strands

Subsequently, under the action of primer enzymes, the nucleotides in the cell will form a short primer on the original DNA chain according to the principle of complementary pairing. The role of primers is very important. It can lay the foundation for the subsequent DNA replication, a bit like the classmate who starts the chorus or the tour guide in a tour group. Without primers, DNA cannot be replicated.

Primer formation

Then, the third enzyme, DNA polymerase, appeared. Under its catalytic action, the nucleotides in the cell will be connected to the primer one by one according to the principle of base complementary pairing to form two new DNA chains. It is just like children, using their dexterous hands to build blocks one by one according to the blueprint.

DNA replication

Finally, there's something called DNA ligase, which repairs the gaps in the new strand, like a final check on the building blocks.

In this way, a new double-stranded DNA is formed. You see, now one pair of DNA strands becomes two pairs, achieving DNA replication.

However, the speed of DNA replication in the biological world is not fast. Take the fastest dividing bacteria as an example. Under suitable environmental conditions, they divide once every 30 minutes. If they replicate at this speed, it will take about 20 hours to reproduce 40 times. Can we use artificial methods to speed up this process?

Bacterial division

3. Polymerase chain reaction

40 years ago, there was an American scientist named Mullis who invented a method to replicate nucleic acids outside cells at a very fast speed. People call this method polymerase chain reaction, or PCR for short. This is a very important biological method. If you want to laugh at a biology student who is not good at learning, you can say: he can't even do PCR. The current nucleic acid test uses the PCR method.

Mullis

The specific steps of PCR are:

First, heat the nucleic acid sample to 94-98 degrees Celsius for 20 to 30 seconds. At high temperatures, the DNA will denature, unwind the double helix, and become two single strands. You see, this step is the same as the function of the helicase in biological cells.

Then, the sample temperature is lowered to 50-65 degrees Celsius for 20 to 40 seconds, and specific primers are added. Do you remember the role of primers? Primers are a short sequence of nucleotides that adhere to a specific segment of the original DNA according to the principle of complementary pairing, giving a start to the subsequent DNA replication.

The third step is to raise the sample temperature to 75 to 80 degrees Celsius and add enough nucleotides and DNA polymerase. These nucleotides are like building blocks. According to the principle of base complementary pairing, they adhere to the back of the primer on the original DNA to form a new DNA chain.

Finally, repeat these three steps.

Simply put, the PCR method is to use temperature control to artificially replicate nucleic acids. Because one cycle is very short, the replication speed is very fast. For example: Normally, a chicken lays one egg a day. We want to increase the egg-laying speed. What should we do? We can adjust the lighting, so that the chicken shed has lights for 6 hours and no lights for 6 hours. The chicken will think that 1 day is 12 hours, and it will lay an egg every 12 hours.

Similarly, after one cycle, we can replicate DNA once, which only takes about 4 minutes. If we repeat this cycle over and over again, DNA can be replicated again and again. Replicating 40 times only takes more than 2 hours, but DNA can be replicated 1 trillion times.

During the process of inventing PCR, there was a problem. That is, the polymerase in the third step must be resistant to high temperatures. However, most enzymes in the biological world cannot withstand such high temperatures. What should be done? Fortunately, there is a female scientist from Taiwan, China, Qian Jiayun. She found that there are many hot springs in Yellowstone Park in the United States. There are some thermophilic bacteria in these hot springs that can live in high temperatures. Through her research on these bacteria, she discovered a DNA polymerase that can withstand high temperatures, solving the biggest problem of PCR.

Qian Jiayun

IV. Steps of nucleic acid testing

After understanding what nucleic acids are, DNA replication in organisms, and the artificial PCR method, we can explain the principles of nucleic acid testing for the new coronavirus.

The coronavirus has a protein shell covered with spikes - the key for the virus to invade our human cells. Inside the shell, the virus's genetic material is ribonucleic acid, also known as RNA. We want to check whether there is RNA sequence of the new coronavirus in the sample.

COVID-19 Model

After the sample is sent to the laboratory, the staff will first use some chemicals to dissolve the protein shell of the virus to release the RNA inside. This process is called lysis. After that, chemicals are added for washing, and the sample is placed in a centrifuge to separate the nucleic acid from other impurities. After several steps, we can obtain relatively pure RNA.

Lysis, washing and centrifugation

However, RNA is unstable and easily broken, so it cannot be directly amplified by PCR. Therefore, we must first use the RNA template to copy the DNA corresponding to the viral RNA. This process is called reverse transcription, and then perform PCR amplification on this DNA representing the virus.

Making complementary DNA from RNA

Researchers already know the RNA sequence of the virus, so they can make primers for viral nucleic acid. Do you remember primers? They can attach to DNA and start DNA replication. Because this primer is targeted at viral nucleic acid, its sequence can only be complementary to viral nucleic acid, so it can only attach to viral nucleic acid and ignore other DNA. During amplification, only the nucleic acid of this virus will be replicated.

In fact, my country has also made contributions to the world in this regard. In January 2020, when the novel coronavirus had just begun to spread, the Chinese Center for Disease Control and Prevention (CDC) released the RNA sequencing results of the novel coronavirus and recommended sequences for making primers, which were announced to the world.

Then, it is the PCR amplification process. Today's PCR machines are fully automatic. Just put the sample, primers, polymerase, and nucleotides in, press the button, and the machine will automatically heat up and cool down. Moreover, one machine can test 96 tubes of samples at the same time. If the nucleic acid of 10 people is mixed in one tube of sample, 960 people can be tested at one time. If the test takes 4 hours at a time, one machine can test 5760 people a day. Now you know why the nucleic acid test of tens of millions of people a day is done, right?

PCR Machine

Think about it: if there is no viral nucleic acid in the sample, no matter how many times it is replicated, it will not have any effect; but if there is viral nucleic acid in the sample, after several replications, the viral nucleic acid will increase. Moreover, this difference can be observed in real time, because we also added a fluorescent probe to the sample - a short nucleotide sequence connecting two groups.

Fluorescent probes cannot emit light

This fluorescent probe can attach to viral nucleic acid, and its two ends are connected to a fluorescent group and a quenching group. Normally, when the probe is irradiated with ultraviolet light, the fluorescent group of the probe cannot emit light, because the quenching group will deprive the fluorescent group of its energy. However, if the probe is disassembled, the fluorescent group and the quenching group are separated, and the fluorescent group can emit light under ultraviolet light. It's like when you put money under the ultraviolet light of a banknote detector, you will find that the anti-counterfeiting mark on the money will glow.

The quencher and fluorescent groups are separated, and the fluorescent group emits light under ultraviolet light

During the PCR amplification process, the fluorescent probe first attaches to the viral nucleic acid. When the viral nucleic acid replicates, it finds that the probe is blocking the way and will remove it without hesitation. At this time, the fluorescent group and the quenching group are separated, and we can detect fluorescence.

Probe luminescence principle

During the PCR process, we continuously irradiate the sample with ultraviolet light. If we gradually see fluorescence emitted by the sample, it means that the viral nucleic acid is increasing. This is called real-time quantitative fluorescence PCR.

Real-time quantitative fluorescence PCR

People set 10 times the fluorescence value emitted by the initial sample as the threshold. When the fluorescence intensity exceeds the threshold, the number of PCR cycles is called the Ct value. Obviously, the smaller the Ct value, the higher the virus concentration in the initial sample, and the person is infected with the virus; if the Ct value is large, it means that there is no virus in the sample, or the virus content in the sample is very low. In my country, a Ct value below 37 is defined as positive, a Ct value greater than 40 is defined as negative, and a value between 37 and 40 is defined as suspected.

Classmates, this lesson is over. What have we learned? Let's make a summary!

First, we learned what nucleic acid is: Nucleic acid is biological genetic material, which is divided into two types: DNA and RNA. We humans rely on DNA for inheritance, and the genetic material of the new coronavirus is RNA. Nucleic acid testing is to detect whether there is viral RNA in the sample.

Then, we learned about the DNA replication process. The DNA double helix structure opens and forms a new DNA chain according to the principle of complementary base pairing, and one pair of DNA becomes two pairs.

Then, we learned to replicate DNA artificially, which is the PCR method. It is very efficient and can replicate once every few minutes. We also know that the high-temperature resistant enzyme in PCR was discovered by scientists in Taiwan, China.

Finally, we learned the entire nucleic acid testing process. First, the nucleic acid must be purified, then the RNA nucleic acid must be converted into DNA nucleic acid, then the DNA nucleic acid must be amplified, and finally, it must be irradiated with ultraviolet light and fluorescence must be observed to determine the virus content.

Children, now you know the principle of nucleic acid testing! In fact, this method can not only be used to detect the new coronavirus, but it is also of great significance to the entire biotechnology and medical fields. For example, we often see in movies and TV shows that the police can lock the murderer by extracting a little DNA from the murderer at the crime scene, which is the use of this technology.

In addition, in the past, patients were dying of infection with a virus or bacteria, but because they did not know what bacteria or virus it was, they delayed treatment. Now with this detection method, we can take samples from patients and test the nucleic acid sequence of each suspected bacteria or virus. The successful test indicates which microorganism is infected. This method is saving more and more lives.

How is it? Isn't biology interesting? Today's Young Pioneers class ends here! Children and classmates, get out of class is over!

END