Modelling the Next Generation Treatment for Cancer and Tuberculosis

I, as well as other experts in the field of nanotechnology often exclaim that it is so revolutionary and that it can solve this problem and that problem, that it can make existing inventions obsolete, and so on. A lot of you probably think this is just ALL BARK, NO BITE.

Well today, I am here to back up MY BARK, WITH SOME BITE.

In order to gain some experience and learn more in nanotechnology, I decided to model and simulate a DNA origami nanostructure, which can be used to develop much less harmful and more efficient treatments for various types of cancer and lung disease Tuberculosis (TB).

This article is going to be the first out of two pieces of content related to this project, here I will go into depth about how the science behind it works and how I modelled it, while the YouTube video will be to display the final product and simulate the self-assembly (video is linked at the bottom).

Background

DNA, the more common term for Deoxyribonucleic acid, is essentially the recipe book for our entire body. It is a molecule that stores the genetic instructions for the four main aspects of living things: development, function, growth and reproduction.

DNA in our bodies is stored in its famous double helix structure, which is two strands, coiled around each other. The best comparison is to a severely twisted ladder. The reason for this structure has to do with its length and the bonds between the nucleotides, but we’ll get into that a little later. Each strand contains four DNA bases that run the length of the strand. Each base is made up of one deoxyribose molecule (carbon-based sugar), one phosphate group and one of four nucleotides:

  • Adenine — the DNA base is labelled ‘A’ and often colour-coded green
  • Thymine — the base is ‘T’ and colour-coded red
  • Guanine — the base is labelled ‘G’ and colour-coded blue
  • Cytosine — the base is labelled ‘C’ and colour-coded yellow

A single nucleotide change in your DNA can change something like your ability to smell something, whether you have freckles or not, and even cure diseases like Sickle Cell Anemia.

Returning to the structure of the DNA, the strands are held together by the bonds between the bases. Adenine, or A, exclusively bonds with Thymine or T, while Guanine exclusively bonds with Cytosine.

A single nucleotide change in your DNA can change something like your ability to smell something, whether you have freckles or not, and even cure diseases like Sickle Cell Anemia.

The pattern of the bases seems very basic, but in detail, is unimaginable complex because it provides the instructions for the creation of proteins and RNA molecules. Proteins and RNA molecules are the two main ‘builders’ and ‘transporters’ of everything in our bodies. I want to keep this part nice and short, so I won’t go into too much detail about those since it is not relevant, but for those of you interested, here’s a great video to watch if you want to learn more.

As you can imagine, our entire DNA is very long, containing over 3 billion base pairs of DNA at the Nanoscale. What’s even crazier is that the entire human genome (all the DNA in the human body) is stored at the centre of every single cell.

If you think about it logically, it makes sense for that to be where it lies. Continuing with my previous analogy of the recipe book, where is the recipe book found? In the heart of the kitchen, with everything else going on around it. Similarly, the genome is stored in the centre, the nucleus, of the smallest unit of life, the cell.

Have you ever tried to fit a long cable into a small package? Except it isn’t a small package, it’s so incredibly small, only a couple of micrometres in size. That’s sort of what is happening with the genome, but instead of pushing hard and randomly stuffing, it is organized in a very simple structure.

First, the DNA strands are coiled into the double helix. Next, the double helix is tightly wrapped around histone proteins, called a nucleosome. Lastly, all the nucleosomes are tightly wound and coiled together into structures called chromosomes, in which we have a total of 46 in the entire genome. 23 are from your mother, 23 from your father. All the chromosomes then fit into the nucleus of the cell.

DNA Strands ➡ Double Helix ➡ Nucleosome ➡ Chromosomes ➡ Genome

DNA ≠ Nanotechnology. Unless…

For everyone who watched my video or understands the basics of nanotechnology, you know that the entire field of nanotechnology is based on the control and manipulation of matter at the nanoscale. For those of you who haven’t watched it, here you go).

As I was thinking about what project to build in nanotech, I was also learning about gene editing, which are methods to edit specific DNA bases, when it hit me. DNA has massive applications and is at the nanoscale. It seemed perfect. Apparently, I wasn’t the only one who thought this was a super cool field.

I jumped on my computer and searched this up, I was shocked to discover the massive field of…

DNA Nanotechnology

DNA nanotechnology is a pretty big sub-field of nanotechnology, with its whole purpose being to use DNA as engineering materials to design and manufacture nanostructures for specific uses.

The great thing about using DNA as building blocks is that it solves the biggest challenge in nanomedicine, hands-down. I am not saying that we can suddenly use DNA nanotech for everything because it certainly has its limitations, but the discovery and implementation of using DNA eradicated the challenge of biocompatibility. Exactly what it sounds like, biocompatibility is the ability of a material to be compatible (-compatibility) with a living organism (bio-). The DNA is naturally not only found in the human genome but also arguably the most important part of our entire body. Therefore, the body is not alarmed and/or doesn’t trigger an immune or Reticuloendothelial system response.

All of the applications of DNA-engineered nanostructures fall under one of these two categories:

  1. Using it as an arrangement tool for other molecules — applications in biology, chemistry, enzymes, protein folding and nanoelectronics and more
  2. Performing in action in the body using the nanostructure, taking advantage of its superior biocompatibility — applications in targeted drug delivery, disease diagnostics, countless disease treatments, mimicking membrane proteins and more

For my project, I chose to focus on the second point because it was more applicable in the real-world through nanomedicine, as well as it was easier to develop concrete results and solutions.

Now I am going to walk you through how I was able to build, from scratch, a hollow 3D DNA Origami Nanostructure to cure Cancer. The actual visualization and simulation will be displayed in my YouTube video, linked above.

So, what does it solve?

An important thing to keep in mind is that DNA nanotechnology is just a biocompatible version of normal nanofabrication. It goes without saying that almost all of its applications lie in nanomedicine, where the DNA aspect makes the most difference. That said, while these nanostructures can technically be used for all the applications in the human body, they have their limitations and they excel in a few key fields.

The most obvious one is targeted drug delivery, which is the field of technologies that deliver and control the release of drugs to very specific parts of the body. Usually, the drugs are infused with nanoparticles or other carriers of a similar nature, but with DNA nanotechnology we can simply design and assemble the perfect structure we need to deliver the drugs, fully customized to the experiment.

In our DNA nanostructure, instead of incorporating targeting ligands, peptides, or antibodies, we can use a very simple and ingenious tool that several Danish scientists developed. Essentially, an extra two short strands of DNA are attached from the top face to the desired side face, holding it closed. However, whenever the structure comes into proximity of certain molecules referred to as the DNA ‘keys’ the strands bind to that instead, swinging the lid opening and releasing the contents inside.

The next set of applications is in the field of observation and studying of the actions of molecules, or the interactions between molecules. The DNA nanostructure can be used to conduct a 3D structural analysis of macromolecules, to conduct electricity across lipid membranes, to control the release of fluorophores (a fluorescent compound that can emit light) for easier observation, and more. DNA nanotubes have been used to study molecular motors, which get their name by being molecules that transport cargo along protein microtubules.

DNA nanotechnology doesn't have to be, and in fact, rarely are passive nanostructures (once again, if you don’t know what that is, watch my video above), they actually perform functions at the nanoscale in the human body. In this study, scientists created a nanostructure with a swinging arm that could transfer substrates between enzymes (Substrate: A molecule acted upon by an enzyme. Enzyme: A protein that carries out a specific chemical reaction).

You knew this was coming as soon as you saw the previous application: Nanobots! Nanobots are exactly what they sound like, robots at the nanoscale. This is one of the largest applications of DNA nanotechnology and scientists have already created complicated nanobots comprised of DNA plus other nanomaterials that can move, “walk” around, carry and deliver items and more. This is only the very, very, very, beginning of expanding field of DNA nanobots.

What I Did — Step 1: Design

The first step to actually building a DNA origami nanostructure is deciding exactly which 2D or 3D shape you want to build. This can depend on a number of factors, the most prominent one being what is the desired impact of this experiment? If applicable, which diseases can it help cure?

For this project, I decided to use DNA nanotechnology for targeted drug delivery. Going a little more detailed, I wanted my simulated nanostructure to be able to cure a real-world disease.

After doing lots of research, and asking myself all the questions and more, I discovered that I could tackle two problems at once, by modelling a DNA Origami Cube or Box, with the application of developing much more efficient and less harmful treatments for various types of Cancer and Tuberculosis.

I want to keep this article short and sweet, so I won’t go into all the details of how it can develop much better treatments, but if you are curious here is a paper that explains it for Tuberculosis and here is a great paper that explains DNA origami applications for Cancer therapy

What I did — Step 2: Modelling

Now comes the most defining stage in this entire process, modelling the 3D shape in a program called caDNAno. There are a lot of parts in this stage and it is very complex, so I am going to explain what each part does and how it works.

Before we DNA origami works by using one very long strand of DNA (7000+ bases) called the scaffold strand, which is highlighted in blue. This strand is typically from an M13 Bacteriophage, which is exactly what caDNAno uses.

Attached to the original scaffold strands are short strands of DNA, between 20–40 bases usually, called staple strands which create the complex folds and attachments between parts of the nanostructure.

First, we begin with the desired DNA scaffold, which is stretched out over multiple different strands, as you can see on the left. Each circle in the square lattice represents a single double helix strand of DNA.

Now because we are modelling an open DNA origami cube, the simplest way to do so is to build the four side faces, attach them to each other, then add the bottom and connect that to all four faces, then add the top and only attach it to one face (to give the open effect).

This is the model of a single, flat 3D face. The blue scaffold strand starts anywhere and continues throughout every double helix strand, and it has to continue throughout every part of the 3D nanostructure, for it to form.

A single cube face

The crossovers you see between the different strands are to make sure they are attached nice and tight, to resemble the face of a cube. Whereas, the small multi-coloured strands are the DNA staples.

Now, we repeat.

After that, all the other faces are done similarly, and we must connect them to one another. If you visually the net of a square being put together, each square edge is connected to two other squares, with the ones on the end having to loop around. So, next, I did that by connecting the staple strands from one face directly to the staple strands in the other desired faces.

All four side faces

The time for creating the top and bottom faces has arrived. For the bottom face, we must create it and then connect each side to the base of one of the side faces, once again by connecting the colourful staple strands from each face

All four side faces plus the bottom face

For the top face, we must create it and then only connect one edge to the top edge of any side face. Once we do that, we have our final model (the top face is in the bottom right).

All six cube faces, all interconnected and ready for self-assembly

Now our DNA nanostructure is ready for self-assembly and visualization. If you want to check that out, watch my video below!

Conclusion

I learned so much from this project and I had lots of fun at the same time. If you want to see the final product and watch its self-assembly, make sure to click the video below.

The fact that I modelled and simulated the next generation of treatments by designing a DNA nanostructure is undeniable proof that nanotechnology can not only change the world, but that anyone can do it.

Feel free to connect with me on LinkedIn if you enjoyed this article, or email me at aahaanmaini@gmail.com if you have any questions/want to discuss more! If you want to stay up to date on all of the cool things I am doing with Nanotechnology, subscribe to my monthly newsletter!

--

--

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store
Aahaan Maini

Aahaan Maini

16-year-old ML dev currently building Circulate to tackle the blood shortage in India