Colton McOmber Nanotech 4/18/2020

On the topic of D.N.A. Nanoengineering

What is D.N.A. Nanoengineering?

To describe what DNA Nanoengineering is you would have to know what DNA is, what

its components are, what Nanoengineering is, and how it works. In this paper I would like to start

by explaining DNA.

DNA stands for Deoxyribonucleic Acid and is the blueprint/building block of all life.

Everything that is considered living and even some that are in between living and non-living, like

viruses, use DNA to replicate. DNA is small and follows a set of rules due to the nature of its

components that makes it consistent to work with and observe. Nanoengineering is exactly what

it sounds like it is, engineering on the nano scale. It is building things or making things

approximately about the size of atoms. There is some form of nanoengineering in every aspect of

society today and even some traces of it over a thousand years ago.

When combined all together DNA nanoengineering is a bottom-up building process

where one uses DNA as a way of manipulating other things or to shape DNA on a nanoscale.

DNA is easy to harvest and easy to manipulate. It sounds perfect right? Well there are some pros

and cons to using DNA that we will go over in this paper.

History of DNA Nanoengineering

The idea of using DNA as a construction material was an idea thought up by Nadrian

Seeman, which was later augmented by Paul Rothemund into what is commonly referred to (and

affectionately) as DNA origami, DNA Lego, and other such names. Paul Rothemund believes

that all life is formed with an organic computer that follows an organic computer code, DNA, so

why not use that code the same way you could use normal computer codes? Mr. Rothemund
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came up with the idea of using single strand DNA that was found in a viral organism referred to

as M13 bacteriophage as a base building block for DNA origami. This would be his “code”.

The Science involved in DNA Nanoengineering or DNA Origami

 Atomic Structure of DNA

No matter where in the world you look you will find DNA, and all DNA found in

all living organisms are composed of the same molecules. DNA is formed with chains of

molecules called nucleotides. Nucleotides are composed of a sugar molecules called

Deoxyribose, or if you are looking at RNA its Ribose, which is connected to a phosphate

group and a nitrogen-containment spot for 1 of 4 bases named Adenine, Cytosine,

Guanine, and Thymine. In RNA Uracil will replace Thymine in the nucleotide.

So, in one Nucleotide you can find 3 different molecules. The Deoxyribose sugar

molecule is Ribose with the loss of an oxygen atom, its chemical formula is C5-H10-O4.

The next molecule is called a phosphate group because it is composed of one phosphorus

atom surrounded and attached to four oxygen atoms with a chemical formula of PO43-.

The last molecule in the Nucleotide is the nitrogen-containment spot for the bases

which is composed of nitrogen and houses one of the following: 1) Adenine, containing

Carbon, Nitrogen, and Hydrogen atoms with a chemical formula of C5-H5-N5; 2)

Cytosine, containing Carbon, Hydrogen, and Nitrogen atoms with a chemical formula of

C4-H5-N30; 3) Guanine, containing Carbon, Hydrogen, and Nitrogen atoms with a

chemical formula of C5-H5-N50; and 4) Thymine, containing Nitrogen, Hydrogen,

Oxygen, and Carbon with a chemical formula of C5-H6-N2-O2.

 How does It Bond

Colton McOmber Nanotech 4/18/2020

DNA bonds through two processes of bonding known as hydrogen bonding and

covalent bonding with the DNA linking up on the phosphate groups with covalent

bonding while the nitrogen-bases link up with hydrogen bonding. Covalent bonding

occurs with the sharing of electrons between two atoms and is a very stable and strong

form of bonding. Hydrogen boding is the attraction of a hydrogen atom to a nitrogen,

oxygen, or a fluorine atom.

This Hydrogen bonding involving Thymine to Adenine and Guanine to Cytosine

is the major component of DNA origami. Because Adenine and Thymine only link up

with each other and Guanine only linking up to Cytosine, it forms a consistent “computer

code” that you can work with to shape the DNA in any form. Usually when two single

strands of DNA link up, they will form a long single strand double helix with the

nitrogen-bases attaching the two separate strands together respective to what bases are

laid out in sequence through hydrogen bonding. But, as we will discuss next, it can be

changed from a double helix into whatever shape is needed.

Benefits to Humanity

As stated above the shaping of DNA is a core part of DNA origami. A single strand of

DNA could look like this (ACGGAGTTGAAACGTAGT), with each letter representing one of

the four bases discussed above in a Nucleotide. When another strand that is designed to link up

with the first strand of DNA is introduced it will look like this: 1st

strand (ACGGAGTTGAAACGTAGT) and

2nd strand (TGCCTCAACTTTGCATCA).

In DNA origami you take single strands of DNA and introduce “staples” to them that will

help mold their shape. Staples are short DNA strands that connect to the long single strands of
Colton McOmber Nanotech 4/18/2020

DNA and bend them by attaching to one end of the strand and then only attaching again further

down on the long single strand of DNA. This idea of using staples to form patterns is a major

factor in DNA origami and was developed by Mr. Rothemund.

 Bottom up Nanofabrication

Because of the how simple and programmable DNA is, it is a great method of

bottom up Nanofabrication. Bottom up Nanofabrication is when you build

Nanostructures from bases atoms and molecules. With DNA you can shape it into

whatever form you can think of which makes it ideal for moving and attaching other

objects at the Nanoscale.

 Movement of medicine

One such way of moving and attaching objects at the nanoscale is making a DNA

box on the nanoscale and putting a poison or medicine inside that can kill or heal

something. Then you attach a latch that opens the box when it receives a “key”. This

“key” being the destination and or cell/virus you want to die or heal. When the “key” is

found and the box is opened it releases its contents onto the designated target, in this case

the “key” and then the only cell/virus that is affected by the poison or medicine is the

designated target.

This is extremely helpful in the case of cancer which spreads throughout the body

and is hard to find when it reaches a certain stage and it is no longer contained in a

certain area. Modern day solutions to cancer include a type of treatment called

chemotherapy which releases a large amount of chemicals into the body which are

designed to kill the cancer cells. The only problem is that it kills more than just the cancer

cells, it also kills many of the weaker cells in your body. So, people on chemotherapy
Colton McOmber Nanotech 4/18/2020

lose their hair and become visibly weaker when they take this form of therapy. With

DNA nanostructures encasing this chemical and delivering it only to the cancer cells, the

people would not lose their hair and go through painful sessions of chemotherapy.

One downside to DNA nanostructures is that when they are introduced into the

body, they quickly end up inside the bladder and don’t have enough time to spread

throughout the body properly. This can be fixed by coating them with a type of oil but

then the latch on the DNA nanostructure has a hard time finding the key because it is

covered in this oil.

 Movement/Placement of Nanomaterials

Another way to use DNA Origami is by setting them up as a kind of scaffold that

hold nanomaterials in place such as Gold collides, Gold nanoparticles, Carbon nanotubes,

and Quantum dots to name a few. When the desired structure is attached to the DNA

nano scaffold it makes it easy to move and to place in designated locations due to the

DNA nanostructures being quite a bit larger than the other nanomaterials. When the DNA

nano scaffold is in place you then can dissolve the DNA structure in some form of

solution, remove the solution and have the desired nanomaterials in their designated spot.

This makes it ideal for exceedingly small, very precise instruments whether electronic or

chemical.

Movement of medicine and movement/placement of nanomaterials are only two of many ways to

use DNA Origami on the microscale.

Thank you.

Works Cited
Colton McOmber Nanotech 4/18/2020

 Precise Control of Gold Nanoparticles on DNA Origami for Logic Operation.

Authors: Chen Kuiting, Li Xiang, Yang Jing.

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sessmgr01&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d%3d#AN=139451195&db=asn

 Pharmacophore Nanoarrays on DNA Origami Substrates as a Single‐Molecule

Assay for Fragment‐Based Drug Discovery. Authors: Kielar Charlotte, Reddavide

Francesco, Tubbenhauer Stefan, Cui Meiying, Xu Xiaodan, Grudnmeier Guido,

Zhang Yixin, Keller Adrian.

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 DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels.

Authors: Kurokawa Tatsuki, Kiyonaka Shigeki, Nakata Eiji, Endo Masayuki, koyama

Shohei, Mori Emiko, Tran Nam Ha, Dinh Huyen, Suzuki Yuki, Hidaka Kumi, Kawata

Masaaki, Sato Chikara, Sugiyama Hiroshi, Morii Takashi, Mori Yasuo.

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%40sessionmgr103&bdata=JnNpdGU9ZWhvc3QtbGl2ZQ%3d

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 Basic principles of Nanotechnology.

Authors: Wesley C. Sanders

Colton McOmber Nanotech 4/18/2020

 Paul Rothemund: The astonishing promise of DNA folding.

https://www.youtube.com/watch?v=WhGG__boRxU&t=586s

 DNA Origami: Folded DNA as a Building Material for Molecular Devices - P.

Rothemund - 5/25/16.

https://www.youtube.com/watch?v=yPkQsrQwpj8