Would you define "marker" a little better. I'm a little confused about it's meaning.

It's a standardized test solution of specific marked DNA which allows scientists to have a comparison to the sample DNA placed in the wells.

Taq polymerase is acquired from bacteria ,it is DNA pol III (responsible for elongation in prokaryotes) of a prokaryote. So, how can it elongate a eukaryotic DNA in PCR when it is meant to elongate a prokaryotic DNA?

While there can be differences in the DNA from different species, those differences generally do not affect the ability to be copied by different DNA polymerases. It is perhaps surprising, but we frequently take DNA from one organism and put it into another and have it replicated and even transcribed and translated! (To do this we put the DNA into something called a vector, which provides the right signals to the host cell so that these processes can happen.)

During the annealing process, isn't there a possibility of the DNA templates joining back to each other instead of the primer or what measures are taken to ensure that doesn't happen. Also, when does the polymerization of a cycle stops

Yes, the binding of primers to each other is possible. These are often called "primer dimers."

if we don't know the exact sequence of the gene, what ways can we can still use PCR to amplify that gene?

PCR is usually used for amplification of known genes. Why? Because you need to have primers. how are you going to design or to use pre-existing primers if you do not know what sequence to they are aligned to? So to start the PCR, one has to design degenerate primers. First, to obtain reference sequence, use Bioinformatic software and databases NCBI, and Ensembl for finding _most similar gene sequences_ from closely related species. Once one finds it, use Ensembl to recreate exon sequences and therefore primers. https://www.researchgate.net/post/How_can_I_design_primer_for_unknown_DNA_sequence_of_different_species https://bitesizebio.com/18992/a-primer-for-designing-degenerate-primers/

In PCR, why is the reaction cooled when the primers have to be attached?

The heat denatures the DNA, meaning it keeps the single strands of DNA from forming secondary structures and annealing to other DNA. Since primers are short pieces of DNA, they will also be denatured and unable to anneal in the high heat. The heat separates double stranded DNA into single strands to allow the opportunity for primers to anneal to the single stranded DNA when the reaction cools. Primers are most often used in extreme excess which increases the probability of annealing. It's not 100% efficient because of course the DNA can always bind with its complimentary strand again, but it doesn't have to be because of the exponential amplification.

What is a genetic marker?

*Genetic marker* is known gene or DNA sequence (with a known location on the chromosome) used to identify individual or species.

Are restriction enzymes used during PCR or are they the same as the primers?

Hello dixit.anusha02, At first - restriction enzymes are enzymes, i.e. biological macromolecules. Some of them occur naturally in cells to destroy damaged DNA. Primers on the contrary are short artificial pieces of single-strand DNA, where the amplification starts. As you see, restriction enzymes and primers have quite little in common. In the PCR you need the DNA sample, nucleotides, buffer solution and primers. The PCR is used to produce many identical DNA samples. The restriction enzymes are used for a restriction digest, where the DNA is cut into pieces. This is useful for an analysis of the DNA (I can't explain it in a sentence). You often have to make a PCR before a restriction digest in order to have enough DNA for it, but as you see these are two different things. I hope this helps!

Main content

Polymerase chain reaction (PCR)

Google Classroom

A technique used to amplify, or make many copies of, a specific target region of DNA.

Key points:

Polymerase chain reaction, or PCR, is a technique to make many copies of a specific DNA region in vitro (in a test tube rather than an organism).
PCR relies on a thermostable DNA polymerase, Taq polymerase, and requires DNA primers designed specifically for the DNA region of interest.
In PCR, the reaction is repeatedly cycled through a series of temperature changes, which allow many copies of the target region to be produced.
PCR has many research and practical applications. It is routinely used in DNA cloning, medical diagnostics, and forensic analysis of DNA.

What is PCR?

Polymerase chain reaction (PCR) is a common laboratory technique used to make many copies (millions or billions!) of a particular region of DNA. This DNA region can be anything the experimenter is interested in. For example, it might be a gene whose function a researcher wants to understand, or a genetic marker used by forensic scientists to match crime scene DNA with suspects.

Typically, the goal of PCR is to make enough of the target DNA region that it can be analyzed or used in some other way. For instance, DNA amplified by PCR may be sent for sequencing, visualized by gel electrophoresis, or cloned into a plasmid for further experiments.

PCR is used in many areas of biology and medicine, including molecular biology research, medical diagnostics, and even some branches of ecology.

Taq polymerase

Like DNA replication in an organism, PCR requires a DNA polymerase enzyme that makes new strands of DNA, using existing strands as templates. The DNA polymerase typically used in PCR is called Taq polymerase, after the heat-tolerant bacterium from which it was isolated (Thermus aquaticus).

T. aquaticus lives in hot springs and hydrothermal vents. Its DNA polymerase is very heat-stable and is most active around

70 ° C

(a temperature at which a human or E. coli DNA polymerase would be nonfunctional). This heat-stability makes Taq polymerase ideal for PCR. As we'll see, high temperature is used repeatedly in PCR to denature the template DNA, or separate its strands.

PCR primers

Like other DNA polymerases, Taq polymerase can only make DNA if it's given a primer, a short sequence of nucleotides that provides a starting point for DNA synthesis. In a PCR reaction, the experimenter determines the region of DNA that will be copied, or amplified, by the primers she or he chooses.

PCR primers are short pieces of single-stranded DNA, usually around

20

nucleotides in length. Two primers are used in each PCR reaction, and they are designed so that they flank the target region (region that should be copied). That is, they are given sequences that will make them bind to opposite strands of the template DNA, just at the edges of the region to be copied. The primers bind to the template by complementary base pairing.

When the primers are bound to the template, they can be extended by the polymerase, and the region that lies between them will get copied.

Both primers, when bound, point “inward” – that is, in the 5’ to 3’ direction towards the region to be copied. Like other DNA polymerases, Taq polymerase can only synthesize DNA in the 5’ to 3’ direction. When the primers are extended, the region that lies between them will thus be copied.

The steps of PCR

The key ingredients of a PCR reaction are Taq polymerase, primers, template DNA, and nucleotides (DNA building blocks). The ingredients are assembled in a tube, along with cofactors needed by the enzyme, and are put through repeated cycles of heating and cooling that allow DNA to be synthesized.

The basic steps are:

Denaturation ( $96 ° C$ ‍): Heat the reaction strongly to separate, or denature, the DNA strands. This provides single-stranded template for the next step.
Annealing ( $55$ ‍ $-$ ‍ $65$ ‍ $° C$ ‍): Cool the reaction so the primers can bind to their complementary sequences on the single-stranded template DNA.
Extension ( $72 ° C$ ‍): Raise the reaction temperatures so Taq polymerase extends the primers, synthesizing new strands of DNA.

This cycle repeats

25

-

35

times in a typical PCR reaction, which generally takes

2

-

4

hours, depending on the length of the DNA region being copied. If the reaction is efficient (works well), the target region can go from just one or a few copies to billions.

That’s because it’s not just the original DNA that’s used as a template each time. Instead, the new DNA that’s made in one round can serve as a template in the next round of DNA synthesis. There are many copies of the primers and many molecules of Taq polymerase floating around in the reaction, so the number of DNA molecules can roughly double in each round of cycling. This pattern of exponential growth is shown in the image below.

Using gel electrophoresis to visualize the results of PCR

The results of a PCR reaction are usually visualized (made visible) using gel electrophoresis. Gel electrophoresis is a technique in which fragments of DNA are pulled through a gel matrix by an electric current, and it separates DNA fragments according to size. A standard, or DNA ladder, is typically included so that the size of the fragments in the PCR sample can be determined.

DNA fragments of the same length form a "band" on the gel, which can be seen by eye if the gel is stained with a DNA-binding dye. For example, a PCR reaction producing a

400

base pair (bp) fragment would look like this on a gel:

A DNA band contains many, many copies of the target DNA region, not just one or a few copies. Because DNA is microscopic, lots of copies of it must be present before we can see it by eye. This is a big part of why PCR is an important tool: it produces enough copies of a DNA sequence that we can see or manipulate that region of DNA.

Applications of PCR

Using PCR, a DNA sequence can be amplified millions or billions of times, producing enough DNA copies to be analyzed using other techniques. For instance, the DNA may be visualized by gel electrophoresis, sent for sequencing, or digested with restriction enzymes and cloned into a plasmid.

PCR is used in many research labs, and it also has practical applications in forensics, genetic testing, and diagnostics. For instance, PCR is used to amplify genes associated with genetic disorders from the DNA of patients (or from fetal DNA, in the case of prenatal testing). PCR can also be used to test for a bacterium or DNA virus in a patient's body: if the pathogen is present, it may be possible to amplify regions of its DNA from a blood or tissue sample.

Sample problem: PCR in forensics

Suppose that you are working in a forensics lab. You have just received a DNA sample from a hair left at a crime scene, along with DNA samples from three possible suspects. Your job is to examine a particular genetic marker and see whether any of the three suspects matches the hair DNA for this marker.

The marker comes in two alleles, or versions. One contains a single repeat (brown region below), while the other contains two copies of the repeat. In a PCR reaction with primers that flank the repeat region, the first allele produces a

200

bp

DNA fragment, while the second produces a

300

bp

DNA fragment:

You perform PCR on the four DNA samples and visualize the results by gel electrophoresis, as shown below:

Which suspect's DNA matches the DNA from the crime scene at this marker?

Humans are diploid, meaning that they have two copies of most of their DNA. Thus, there will be two copies of the marker we are examining in each of the DNA samples.

If a person has two different alleles of the marker (is heterozygous), two different-sized bands (

200

bp and

300

bp) will be amplified during PCR. These will appear as bands of DNA in the gel at the

200

bp and

300

bp locations.

If a person has two copies of the same allele (is homozygous), only one band will be amplified during PCR. If the person is homozygous for the

200

bp allele, only a

200

bp band will be visible on the gel. Similarly, if the person is homozygous for the

300

bp allele, only a

300

bp band will be visible on the gel.

The marker genotypes of the DNA samples are:

Crime scene DNA: homozygous $200$ ‍ bp allele
Suspect $1$ ‍: homozygous $300$ ‍ bp allele
Suspect $2$ ‍: heterozygous
Suspect $3$ ‍ homozygous $200$ ‍ bp allele

Both the DNA sample from the crime scene and the DNA sample from suspect

3

are homozygous for the

200

bp version of the marker. That is, the two samples match for this marker.

More about PCR and forensics

In real forensic tests of DNA from a crime scene, technicians would do an analysis conceptually similar to the one in the example above. However, a number of different markers (not just the single marker in the example) would be compared between the crime scene DNA and the suspects' DNA.

Also, the markers used in a typical forensic analysis don't come in just two different forms. Instead, they're highly polymorphic (poly = many, morph = form). That is, they come in many alleles that vary in tiny increments of length.

The most commonly used type of markers in forensics, called short tandem repeats (STRs), consist of many repeating copies of the same short nucleotide sequence (typically,

2

5

nucleotides long). One allele of an STR might have

20

repeats, while another might have

18

, and another just

10

^{1}

By examining multiple markers, each of which comes in many allele forms, forensic scientists can build a unique genetic "fingerprint" from a DNA sample. In a typical STR analysis using

13

markers, the odds of a false positive (two people having the same DNA "fingerprint") are less than

1

10

billion

^{1}

Although we may think of DNA evidence being used to convict criminals, it has played a crucial role in exonerating falsely accused people (including some who had been jailed for many years). Forensic analysis is also used to establish paternity and to identify human remains from disaster scenes.

Attribution:

This article is a modified derivative of "The polymerase chain reaction," by CK-12 Foundation (CC BY-NC 3.0).

The modified article is licensed under a CC BY-NC-SA 4.0 license.

Works cited:

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Forensic evidence and genetic profiles. (10th ed., pp. 430-431). San Francisco, CA: Pearson.

References:

Kimball, J. W. (2014, May 3). PCR. In Kimball's biology pages. Retrieved from http://www.biology-pages.info/P/PCR.html.

OpenStax College, Biology. (2016, March 23). Biotechnology. In OpenStax CNX. Retrieved from http://cnx.org/contents/GFy_h8cu@10.8:exg4e4AU@7/Biotechnology.

Reece, J. B., Taylor, M. R., Simon, E. J., and Dickey, J. L. (2012). DNA profiling. In Campbell biology: Concepts & connections (7th ed., pp 242-246).

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Amplifying DNA: The polymerase chain reaction (PCR) and its use in DNA cloning. (10th ed., pp. 414-416). San Francisco, CA: Pearson.

Wilkin, D. (2016, March 23). Biotechnology and forensic science - advanced. In CK-12. Retrieved from http://www.ck12.org/biology/Biotechnology-and-Forensic-Science/lesson/Biotechnology-and-Forensic-Science-Advanced-BIO-ADV/.

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Forrest T
Posted 7 years ago. Direct link to Forrest T's post “Would you define "marker"...”
Would you define "marker" a little better. I'm a little confused about it's meaning.
Button navigates to signup pageComment on Forrest T's post “Would you define "marker"...”
(31 votes)
Answer
- Parth Malaviya
  Posted 7 years ago. Direct link to Parth Malaviya's post “It's a standardized test ...”
  It's a standardized test solution of specific marked DNA which allows scientists to have a comparison to the sample DNA placed in the wells.
  Comment on Parth Malaviya's post “It's a standardized test ...”
  (24 votes)
Ayomide Ayodeji
Posted 7 years ago. Direct link to Ayomide Ayodeji's post “During the annealing proc...”
During the annealing process, isn't there a possibility of the DNA templates joining back to each other instead of the primer or what measures are taken to ensure that doesn't happen. Also, when does the polymerization of a cycle stops
Button navigates to signup pageComment on Ayomide Ayodeji's post “During the annealing proc...”
(6 votes)
Answer
- Miriam
  Posted 7 years ago. Direct link to Miriam's post “Yes, the binding of prime...”
  Yes, the binding of primers to each other is possible. These are often called "primer dimers."
  Button navigates to signup page
  (6 votes)
ayezaali176
Posted 6 years ago. Direct link to ayezaali176's post “Taq polymerase is acquire...”
Taq polymerase is acquired from bacteria ,it is DNA pol III (responsible for elongation in prokaryotes) of a prokaryote. So, how can it elongate a eukaryotic DNA in PCR when it is meant to elongate a prokaryotic DNA?
Button navigates to signup pageButton navigates to signup page
(8 votes)
Answer
- tyersome
  Posted 6 years ago. Direct link to tyersome's post “While there can be differ...”
  While there can be differences in the DNA from different species, those differences generally do not affect the ability to be copied by different DNA polymerases.
  
  It is perhaps surprising, but we frequently take DNA from one organism and put it into another and have it replicated and even transcribed and translated!
  (To do this we put the DNA into something called a vector, which provides the right signals to the host cell so that these processes can happen.)
  Button navigates to signup page
  (3 votes)
KEVIN
Posted 9 months ago. Direct link to KEVIN's post “How do they manufacture a...”
How do they manufacture all the primers for PCR with them being so small and needing to have an exact nucleotide sequence? Same with all the specific enzymes.
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(6 votes)
Answer
SULAGNA NANDI
Posted a year ago. Direct link to SULAGNA NANDI's post “"The most commonly used t...”
"The most commonly used type of markers in forensics, called short tandem repeats (STRs), consist of many repeating copies of the same short nucleotide sequence (typically, 22 to 55 nucleotides long). One allele of an STR might have 20 repeats, while another might have
18, and another just 10."

Is the human genome known to contain a lot of different short tandem repeats? And a lot of variation in the number of repeats for each STR?
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(5 votes)
Answer
- Aradhya
  Posted 5 months ago. Direct link to Aradhya's post “Yes ,Short tandem repeats...”
  Yes ,Short tandem repeats account for approximately 3% of the human genome and the number of repeats in STR markers can be highly variable among individuals.
  Button navigates to signup page
  (1 vote)
Ebonie Lopez
Posted 4 years ago. Direct link to Ebonie Lopez's post “if we don't know the exac...”
if we don't know the exact sequence of the gene, what ways can we can still use PCR to amplify that gene?
Button navigates to signup pageButton navigates to signup page
(4 votes)
Answer
- Ivana - Science trainee
  Posted 4 years ago. Direct link to Ivana - Science trainee's post “PCR is usually used for a...”
  PCR is usually used for amplification of known genes. Why? Because you need to have primers. how are you going to design or to use pre-existing primers if you do not know what sequence to they are aligned to?
  
  So to start the PCR, one has to design degenerate primers.
  First, to obtain reference sequence, use Bioinformatic software and databases NCBI, and Ensembl for finding most similar gene sequences from closely related species.
  
  Once one finds it, use Ensembl to recreate exon sequences and therefore primers.
  
  https://www.researchgate.net/post/How_can_I_design_primer_for_unknown_DNA_sequence_of_different_species
  https://bitesizebio.com/18992/a-primer-for-designing-degenerate-primers/
  Button navigates to signup page
  (3 votes)
Mishgan Fatima
Posted 5 years ago. Direct link to Mishgan Fatima's post “What is a genetic marker?”
What is a genetic marker?
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(2 votes)
Answer
- Ivana - Science trainee
  Posted 5 years ago. Direct link to Ivana - Science trainee's post “*Genetic marker* is known...”
  Genetic marker is known gene or DNA sequence (with a known location on the chromosome) used to identify individual or species.
  Comment on Ivana - Science trainee's post “*Genetic marker* is known...”
  (6 votes)
SULAGNA NANDI
Posted a year ago. Direct link to SULAGNA NANDI's post “Is 20 nucleotides really ...”
Is 20 nucleotides really long enough for a primer? What if there's another (non-target) DNA region flanked with the sequence that matches the chosen primer on both of its sides? Or is the probability of a non-target DNA sequence having the same flank sequences as the target DNA sequence negligible?

Also, do the flank sequences have to be palindromic? Is this why the same primer sequence can be used on either side of the target DNA sequence? Or do two different primer sequences have to be used, one for each flank?
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(4 votes)
Answer
dixit.anusha02
Posted 6 years ago. Direct link to dixit.anusha02's post “Are restriction enzymes u...”
Are restriction enzymes used during PCR or are they the same as the primers?
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(2 votes)
Answer
- Okapi
  Posted 6 years ago. Direct link to Okapi's post “Hello dixit.anusha02, At...”
  Hello dixit.anusha02,
  At first - restriction enzymes are enzymes, i.e. biological macromolecules. Some of them occur naturally in cells to destroy damaged DNA.
  Primers on the contrary are short artificial pieces of single-strand DNA, where the amplification starts. As you see, restriction enzymes and primers have quite little in common.
  In the PCR you need the DNA sample, nucleotides, buffer solution and primers. The PCR is used to produce many identical DNA samples.
  The restriction enzymes are used for a restriction digest, where the DNA is cut into pieces. This is useful for an analysis of the DNA (I can't explain it in a sentence). You often have to make a PCR before a restriction digest in order to have enough DNA for it, but as you see these are two different things. I hope this helps!
  Comment on Okapi's post “Hello dixit.anusha02, At...”
  (5 votes)
autumn
Posted 4 years ago. Direct link to autumn's post “In PCR, why is the reacti...”
In PCR, why is the reaction cooled when the primers have to be attached?
Button navigates to signup pageButton navigates to signup page
(3 votes)
Answer
- zoefreeman13
  Posted 3 years ago. Direct link to zoefreeman13's post “The heat denatures the DN...”
  The heat denatures the DNA, meaning it keeps the single strands of DNA from forming secondary structures and annealing to other DNA. Since primers are short pieces of DNA, they will also be denatured and unable to anneal in the high heat. The heat separates double stranded DNA into single strands to allow the opportunity for primers to anneal to the single stranded DNA when the reaction cools. Primers are most often used in extreme excess which increases the probability of annealing. It's not 100% efficient because of course the DNA can always bind with its complimentary strand again, but it doesn't have to be because of the exponential amplification.
  Button navigates to signup page
  (3 votes)

AP®︎/College Biology

Course: AP®︎/College Biology > Unit 6