3D ‘printouts’ at the nanoscale using self-assembling DNA

structures&

Expanding the DNA alphabet: 'Extra' DNA base found to be

stable in mammals

Ana Mercedes Vanegas Torres3rd SemesterUPB Teacher: Lina M. Martínez

INTRODUCTION

What is the essential molecule for life? The answer is really easy, DNA! It is the responsible for the growth and maintenance of life, because it holds the instructions for an organism's development and reproduction

DNA is a long polymer of simple units called nucleotides, which are held together by a backbone made of sugars and phosphate groups.This backbone carries four types of molecules called bases and it is the sequence of these four bases that encodes information. The main role of DNA in the cell is the long-term storage of information.

If this molecule has any change, our cells starts working incorrectly triggering a disease.

3D ‘printouts’ at the nanoscale using self-assembling DNA structures(July

23,2015)

There is a new technique that makes possible to synthesize 3D DNA origami structures that are also able to tolerate the low salt concentrations inside the body

This opens the way for completely new biological applications of DNA nanotechnology

“We can now make structures that were impossible to design previously and we can do it in the same way as one might draw a 3D structure for printing out in macroscopic scale, but instead of making it out of plastic, we print it in DNA at the nanoscale.”

How is this new technique developed?

The user draws the desired structure, in the form of a polygon object, in 3D software

They calculate the DNA sequences needed to produce the structure using graph-theoretic algorithms and optimization techniques

The synthesized DNA sequences are combined in a salt solution They assemble themselves into

the correct structure.

Using this technique, the team has built a ball, spiral, rod and bottle-shaped structure, and a DNA printout of the so-called Stanford Bunny, which is a common test model for 3D modelling.

“An advantage of the automated design process is that one can now deal systematically with even quite complex structures. Advanced computing methods are likely to be a key enabler in the scaling of DNA nanotechnology from fundamental studies towards groundbreaking applications,” says Professor Pekka Orponen, who directed the team at the Aalto University Computer Science Department.

What are the possible applications ?

The team at Karolinska Institutet has previously made a DNA nano-caliper used for studying cell signalling.

The new technique makes it possible to conduct similar biological experiments in a way that resembles conditions within cells even more closely.

I have something

to say

In my opinion this discovery is a great contribution to modern medicine, because doctors and scientists hope to use our genetic information to diagnose, treat, prevent and cure many illnesses. That’s why, I think that we should investigate more about DNA structure, because if we learn more about life at the level of atoms and molecules we could identify specific explanation of many diseases and treat the real cause.

Expanding the DNA alphabet: 'Extra' DNA base found to be stable in mammals(June 22, 2015)

Researchers from the University of Cambridge and the Babraham Institute have found that a naturally occurring modified DNA base appears to be stably incorporated in the DNA of many mammalian tissues, possibly representing an expansion of the functional DNA alphabet.

'This modification to DNA is found in very specific positions in the genome -- the places which regulate genes,' said the paper's lead author Dr. Martin Bachman

They have found a rare 'extra' base, known as 5-formylcytosine (5fC)

In addition to the DNA bases G, C, A and T, there are also small chemical modifications, or epigenetic marks, which affect how the DNA sequence is interpreted and control how certain genes are switched on or off.

It had been thought that 5fC was a 'transitional' state of the cytosine base which was then being removed from DNA by dedicated repair enzymes.

5fC

Epigenetic mark

When TET enzymes add oxygen to methylated DNA

* It is a DNA molecule with smaller molecules of methyl attached to the cytosine base

However, this new research has found that 5fC can actually be stable in living tissue, making it likely that it plays a key role in the genome.

They feed some cells and living mice with an amino acid called L-methionine, enriched for naturally occurring stable isotopes of carbon and hydrogen.

Method applied by the researchers

Then they measure the uptake of these isotopes to 5fC in DNA.

The lack of uptake in the non-dividing adult brain tissue pointed to the fact that 5fC can be a stable modification: if it was a transient molecule, this uptake of isotopes would be high.

The researchers believe that 5fC might alter the way DNA is recognised by proteins. 'Unmodified DNA interacts with a specific set of proteins, and the presence of 5fC could change these interactions either directly or indirectly by changing the shape of the DNA duplex,' said Bachman.

'A different shape means that a DNA molecule could then attract different proteins and transcription factors, which could in turn change the way that genes are expressed.'

I think that this discovery is really useful because scientists can look forward for the real function of this extra base and what effects causes in our body, telling us if they are good or bad, keeping in mind that this 'extra' base has a key role in the regulation of gene expression.

Medical UtilityOne of the most important applications of DNA nanostructures is that they have also been used to make targeted capsules able to deliver cancer drugs direct to tumour cells, which can reduce the amount of drugs needed.

'5fC will alter the thinking of people in the study of development and the role that these modifications may play in the development of certain diseases,'

Thanks to molecular biology, scientists have observed each one of the components of the DNA molecule, so for them it is easy to identify if there is something wrong, for example if a part of the molecule is missing and it causes a specific disease, so they could treat it and in some cases cure it.

If we know and understand the essential role of DNA in our organism, we could search for different mechanisms to find the answer to so many diseases that today apparently doesn’t have any treatment or cure, and in this way contributing to medical advances.

Bibliography

3D ‘printouts’ at the nanoscale using self-assembling DNA structures, Karolinska Institutet, 2015. (internet) 2015 Julio (Fecha de acceso Julio 30 de 2015) Disponible en: http://ki.se/en/news/3d-printouts-at-the-nanoscale-using-self-assembling-dna-structures

Expanding the DNA alphabet: 'Extra' DNA base found to be stable in mammals, of Cambridge and the Babraham Institute, 2015. (internet) 2015 Julio (Fecha de acceso Julio 30 de 2015) Disponible en: http://www.sciencedaily.com/releases/2015/06/150622122726.htm