New publucation! #2

Recently, I published a new paper on water-soluble hemi-indigo photoswitches. Basically, it describes the work that I did to design a structure of the photoswitch that binds to RNA. The paper is open-access here.

New publication!

Well, actually, I've recently published the first paper in frame of this project! Here it comes: the first application of the hemi-indigo photoswitch in the field of nucleic acids and the first example of the interaction of a photoswitchable ligand with human immunodeficiency virus (HIV) RNA. You can read the paper here (open access). 

Lighting up RNA

Since RNA has no own colour or fluorescence, it is difficult to follow the processes it participates in. To solve this problem and make RNA visible, scientists use fluorescent stains and markers - compounds that start shining in the presence of RNA. I recorded a video demonstrating the light-up effect of the molecule I recently designed upon addition of RNA.

 

Have fun by drawing RNA!

Today I want to present several options for drawing RNA and DNA. Even if you are not a chemist or biologist, it makes so much fun to play around with visualization of nucleic acid structures!

1. 2D RNA cartoons
Forna is a nice and convenient tool of RNA secondary structure visualization. You can use it directly in the browser without installing any software. Ready structures can be downloaded in png format and used further.

2. 3D RNA structures
There are a lot of specialized bioimaging programs for visualization of the 3D structures of nucleic acids, proteins etc. They are feature rich, but often very expensive. If you have no access to such items, I recommend to use Avogadro program. Avogadro is a free, open source molecular editor and visualization tool. In general, it is applicable to a wide range of molecules in computational chemistry, molecular modeling etc. A "builder for nucleic acid" tool is a pleasant option of Avogadro. However, it has some limitations in terms of sequences because it "knows" only single- and double-stranded helixes. Other forms or elements of DNA (triplex, quadruplex...) and RNA (bulges, internal loops...) are not available. But the structures look really nice!

 

3. If you don't want to draw...

... you can find a huge library of ready images of nucleic acids, proteins, viruses and other biostructures here. Here is one example:

I hope that this material will be helpful for you. Enjoy!

What is a photoswitch?

Every day from morning till evening (or even late night) we use different switches. Mainly electrical ones. In the simplest case, these useful devices allow us to switch something between two different states, for example, light on - light off. More complicated switches provide wider range of available modes. But what does the word "switch" mean in relation to a molecule? Basically, the meaning is the same: a molecule-"switch" can reversibly change its structure between two or more different forms. Like in case of "normal" switches, the molecular switch needs some external energy to perform the switching. In daily life, we use our finger as a source of energy when pressing a button. In the case of molecules, different external stimuli such as heating, light irradiation, changes of acidity, electrical current etc. can be used as an energy source for switching. If our molecule nicely and reversibly changes its structure upon irradiation with light, it is called "photoswitch". The following video shows how the compound I am working with can be switched from "orange" to "red" state by irradiation with blue LED. 

DNA vs RNA

As I have already mentioned in the previous post, everybody has at least heared the abbreviation "DNA". Many people knows how the DNA is built up and why we need it in our body. However, when I mention that I'm working with RNA, I'm often asked the following questions:"RNA? What is this? Is this like DNA? Why do we need it?" Therefore, I decided to provide an explanation and comparison of DNA and RNA. But before I started writing something on this topic I run against a wonderful publication and understood that I can hardly write something better. For this reason, I bring it to your attention: DNA vs. RNA – 5 Key Differences and Comparison
Enjoy!

Figure taken from https://www.technologynetworks.com

Have you ever seen the DNA?

In our daily life we can hear the word "DNA" very often. Sometimes we can also hear the word "RNA". At the same time, how many of you know what do the nucleic acids look like? Let's have a look!