The Ultimate Guide To DNA

DNA molecules can be found within a cell, meaning that they cannot be viewed with the naked eye. This means that in order to view DNA molecules, you will have to use a microscope.

The Ultimate Guide To DNA

Light microscopes allow us to view the nucleus of a cell that contains DNA, but in order to see the DNA molecule itself, you need to use an electron microscope.

Electron microscopes allow us to view the molecules in detail, providing us with plenty of research such as the length and width of the DNA.

This is useful for all kinds of research, especially when it comes to researching diseases in the bid to find a cure for all kinds of illnesses.

In this guide, we’ll be taking you through everything you need to know about DNA and the various microscopy methods that you can use to view DNA molecules, depending on what kind of research or experiment you want to conduct.

This allows you to properly research DNA in the way that will help your thesis. 

What Is DNA?

Before we delve into the various microscopy techniques, it’s essential to understand what DNA actually is.

The full name of DNA is Deoxyribonucleic acid which is a polymer that consists of two polynucleotide chains that coil around one another to create a double helix that carries specific genetic instructions that determine the development, function, growth, and reproduction of all organisms and various viruses. 

When discussing DNA, we often think of ourselves as we are formed of DNA. But what is DNA used for?

As mentioned before, scientists can study DNA to research all kinds of diseases to find a cure as well as use DNA to discover new species, organisms, and viruses. 

What Is The Structure Of DNA?

DNA carries all sorts of crucial information including the genetic and hereditary material of the organism. It is found in the nucleus of every cell and is made from repeated patterns that consist of six molecules.

Regardless of whether you are looking into the DNA structure of a virus or a human, you will find that the DNA’s pattern consists of these six molecules as it requires all six to thrive.

In order to research DNA properly, it’s important to learn and understand what each molecule is and why it is there. 

These six molecules are: 

Deoxyribose

This is a phosphate group that is known as a five-carbon sugar.

Adenine

Adenine is commonly referred to as A in the repeated pattern and is a nitrogenous base. 

Cytosine

Cytosine is commonly referred to as C in the repeated pattern and is a nitrogenous base. 

Guanine

Guanine is commonly referred to as G in the repeated pattern and is a nitrogenous base. 

Thymine

Thymine is commonly referred to as T in the repeated pattern and is a nitrogenous base. 

The actual structure of DNA is a double helix that allows for the development of the organism and is used to protect the base atoms.

The basic units of DNA are known as Nucleotides which consist of a single phosphate molecule with one nitrogenous base and a single molecule of sugar. 

Microscopy

The best way to view DNA is through a process called Microscopy. There are various methods of microscopy that you can use to view the DNA molecules with differing results and detail for each. 

Light microscopes have limited resources, meaning that you may only have approximately 0.25um resolution, while an electron microscope can achieve 0.2 nanometers in resolution, meaning that you are able to view the DNA molecules in detail.

This is because electron microscopes utilize electron beams compared to the visible light that is utilized by light microscopes. 

In this section, we’ll be delving into the various microscopy methods you can use. 

Atomic Force Microscopy

Atomic Force Microscopy is commonly known as AFM and is an electron microscope technique that is used to study DNA.

Specifically, researchers commonly use AFM in order to look into the length of the DNA strands. In this section, we’ll be delving into how Atomic Force Microscopy is conducted.

Here is everything you need to know about Atomic Force Microscopy:

What Is Needed For AFM

Before you begin, you need to make sure that you have gathered the right equipment and materials. Here is a basic list of what you will need:

  • AC glow-discharge
  • AFM microscope
  • DNA samples (such as X174 virion DNA)
  • Formaldehyde
  • Freshly-cleaved ruby mica circle
  • Magnesium acetate
  • Water

How To Observe DNA Using Atomic Force Microscopy

If you are dealing with single-stranded DNA, make sure you follow these instructions:

  1. Prepping the materials: The first thing you need to do is prep the materials by soaking the ruby mica circles in 33 mM of magnesium acetate. Make sure that the ruby mica circles have been freshly cleaved and are soaked between 4 and 24 hours. 
  2. Removing the magnesium acetate: Now the excess magnesium acetate needs to be removed by sonicating the ruby mica circles in millipore water for approximately five minutes.
  3. Dry using compressed air: Once you are confident that all magnesium acetate has been removed, you need to ensure that the ruby mica circle is dried using compressed air.
  4. Exposing the ruby mica circles: You now need to expose the ruby mica circles to AC glow-discharge for approximately 20 seconds in 100 millitor air.
  5. Inverting the circles: Right after you have exposed the ruby mica circles, invert the circles via 7 microliter drops of single-stranded DNA strands within 0.5% of formaldehyde and approximately 15 mm ammonium acetate. This will help to deposit the parafilm.
  6. Let the materials stand before rinsing: Leave the materials to stand for approximately four minutes before rinsing the circles with around three drops of water.
  7. Dry using compressed air: Once again, make sure you are drying the materials using compressed air.
  8. Storing the materials: Lastly, store the materials within a desiccator that is on drierite if you are not using the materials immediately. If you are using double-stranded DNA, then you need to follow the same procedure as above but make sure that you are not using the ammonium acetate or formaldehyde.  

AFM Imaging

AFM imaging can be carried out using III AFM or Nanoscope II under 100% propanol. Here, we will be delving into how an O-ring can be used to apply propanol when the sample is placed on the device. 

Follow these steps for AFM imaging: 

  1. Placing the alcohol on the cantileve: Firstly, place a drop or two of alcohol on the cantilever which is located inside the fluid cell.
  2. Position the cantilever: Make sure that you position the cantilever on top of the O-ring and ensure that it is clamped securely in place.
  3. Ensure that the fluid amount is sufficient: Double-check that the amount of fluid that you have used is sufficient. You can be sure of this by looking at the light path. If there are no bubbles on the light path, this means that you have used an appropriate amount of fluid.
  4. Handling the cantilever: When you are handling the cantilever, make sure that you are using as little force as possible in order to prevent lifting the sample.
  5. Measuring the DNA: Now, you can measure the DNA strands as the images will be enlarged and there should be a fine chain that is evident across the DNA contours.
  6. The drawback of this method is that you are only provided with a top view of the DNA strand, meaning that the images and detail that you can see are limited. 

DNA Electron Microscopy

DNA Electron Microscopy

One method that is most commonly used is DNA Electron Microscopy. Before you begin the procedure, you need to make sure that you have gathered the appropriate equipment and materials in advance.

What Is Needed For DNA Electron Microscopy?

Here are the materials and equipment that you will need for the process:

  • DNA samples such as nucleic acids
  • Electron microscope
  • Formaldehyde
  • Heavy metal salts such as lanthanum nitrate, lead perchlorate, or uranyl acetate

How To Observe The DNA Using DNA Electron Microscopy

Here is how you can observe DNA using DNA Electron Microscopy:

  1. Use a glass nebulizer to spray the DNA: Firstly, you will need to use a glass nebulizer to spray the DNA on a grid using a freshly cleaved mica when possible.
  2. Adding the latex spheres: Now, you need to add the latex spheres which are used as reference particles during the process.
  3. Spreading the DNA solution: Spread protein and the DNA solution onto a water surface using a Langmuir trough. This helps to spread the nucleic acid to ensure that the DNA is retained on the surface.
  4. Staining the solution: The preparation stage is now complete, and the DNA solution is ready for staining.
  5. Apply the nucleic acid to the staining solution: To stain the DNA solution, you need to apply the nucleic acid to the grids that are then immersed within the staining solution. Make sure that the nucleic acid is applied between 10 minutes and four hours to ensure that the staining is thorough.
  6. Rinsing the grids: Once you are confident that the nucleic acid has been thoroughly immersed in the staining solution, make sure you use redistilled water to rinse the grids. You should rinse the grids three times and make sure the water is at a pH of 6.0 before viewing it under the microscope.
  7. Observe the DNA molecules: Lastly, you’ll be able to observe the DNA molecules when you use the heavy salts that provide a high level of contrast. 

Scanning Tunneling Microscopy 

Scanning Tunneling Microscopy is known as STM and is a method that can be used for viewing DNA molecules. What makes STM such a great option is that you are able to view the DNA in great detail as you will be able to view the objects at their atomic level.

In this section, we’ll be taking you through how you can use STM for imaging through numerous methods:

Method 1

  1. Placing the DNA solution: Firstly, place a drop of DNA solution onto the substrate.
  2. Drying the solution: Once you have placed the DNA solution on the substrate, let the solution air dry for some time.
  3. Stabilizing the DNA solution: Now, you need to stabilize the solution by containing it within 10mM of potassium chloride.
  4. Sonicating the solution: Use a Biosonik IV probe sonicator on the solution for approximately 30 minutes at 160 W.
  5. Imaging the solution: Now you will be able to image the solution as the STM can be carried out.

Method 2 

The second method is the same as the first, but there are some differences that can change the imaging results. 

Firstly, the solution needs to be vacuumed dried, and contained within 10mM ammonium acetate. The sonication stage should also be skipped. 

Method 3

  1. Placing the water on parafilm: Firstly, place approximately 10 microliters of distilled water onto a parafilm piece, causing the phage to burst, which in turn will release the DNA.
  2. Adding the DNA droplets: Now, you will need to add droplets of lysed DNA particles with approximately 10 microliters of the solution.
  3. Placing the substrate: Placing a substrate onto the droplet briefly will help to pick up the particles that are lysed.
  4. Identifying the DNA via imaging: Now you can view the DNA strands via imaging. What is great about STM is that you are able to see the width and height of the DNA as well as clearly viewing their parallel arrangements. 

Frequently Asked Questions

Can DNA Be Seen Under A Microscope?

DNA molecules can be seen under a microscope. Bear in mind that basic microscopes won’t show much detail in the molecules.

However, if you have an advanced microscope, you’ll be able to see the DNA molecules in a lot of detail, which is essential for all kinds of research. 

When Can We See The DNA When Looking At A Cell Under A Microscope?

When observing DNA molecules under a microscope, you will be able to see the cell divide into two separate cells during the cytokinesis process.

You may also be able to see the telophase process meaning that the DNA molecules will be present at either pole. 

Can We Photograph DNA?

Thanks to advanced technology, it is possible to photograph DNA. This is thanks to the various techniques that can pull strands of DNA between two silicone pillars and then use an electron microscope to photograph them.

This was developed by a researcher located at the University of Genoa in Italy. 

Why Is DNA White And Stringy?

DNA tends to be white and stringy when there is lots of it. This is evident when using alcohol in your testing as alcohol has a lower density than water meaning that it will float on top.

This is because the DNA will precipitate and not dissolve, causing the DNA to clump together. 

Conclusion

In conclusion, DNA cannot be seen with the naked eye because the DNA molecules are located within the cells. In order to view DNA molecules, you have to use a microscope.

The more advanced your microscope is, the more detailed the DNA molecules will appear. 

By understanding how DNA molecules work and how you can view them, you’ll be able to conduct all kinds of experiments and research, no matter what field you are working in. 

Jennifer Dawkins

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