This article was written in collaboration with Nanome contributor Robert Ramji.

A New Frontier of Cell Exploration

We’re drawing on the awesome Molecule of the Month series from RCSB’s education portal PDB-101, which has been running since January of 2000! Our goal here is to expand on their articles by taking you on a guided tour of these molecules in VR, hopefully making some of the more abstract details about what makes these molecules so interesting easier to understand. Be sure to check out their website and articles at pdb101.rcsb.org!

The discovery of Green Fluorescent Protein (GFP) changed science forever. GFP’s fluorescent properties cause it to glow when exposed to light. This fluorescent glow enables scientists to track this protein (and anything it is bound to), providing a window into many otherwise unobservable processes, including some of the inner workings of cells.

This month, our spotlight is on Fluorescent RNA Aptamers, which can be thought of as the RNA version of GFP. The discovery of these new molecules enables us to add fluorescent tags to RNA much in the way that GFP lets us tag proteins and many other things. One of the molecules in this family is named “Spinach”, and has already been used to image RNA within live cells. This should open up new insights into the RNA-related mechanisms of cells in the future.

Green Fluorescent Protein (GFP)

These aptamers are short chains of RNA with the special property of binding to certain fluorophores, which are small fluorescent molecules. These fluorophore-binding aptamers can be engineered into natural RNAs, so that when we add those fluorophores into the cell, the aptamers now built into the RNA will bind them and allow the motion of the RNA to be tracked within the cell via fluorescence, mimicking the way GFP enables us to track proteins.

One of the coolest parts of Spinach is the way it enhances the brightness of the fluorophore it binds to. Fluorescence is the process of absorbing photons (light) and then re-emitting that energy as another photon.

Under normal circumstances, these fluorophores release the energy absorbed from these photons through motion.

The structure of the aptamer, however, confines the fluorophore. The confined fluorophore is forced to release the absorbed energy as light. As a result, the fluorophores confined within the RNA aptamers are hundreds to thousands of times brighter than the unbound fluorophores. This creates contrast within the cell during imaging, enabling scientists to see where the RNA is within the cell!

Here at Nanome, we’re hopeful that this technology will enable scientists to gain a deeper understanding of RNA’s roles within the cell. If you’re interested in learning more, check out the links below, and take a look at these molecules yourself in Nanome! (You can download it for free at nanome.ai. ) Stay tuned for our next Molecule of the Month!

References:

http://science.sciencemag.org/content/333/6042/642

https://www.sciencedirect.com/science/article/pii/S0165614717301281

https://pdb101.rcsb.org/motm/229

https://pdb101.rcsb.org/motm/42

Steve McCloskey

Steve is an Alumni from the first class of Nanoengineering at the University of California, San Diego. Steve’s work is focused on emerging technologies applied to Science, Technology, Engineering, and Mathematics (STEM).

During his time at UC San Diego Steve worked directly with the founding Chair of the Nanoengineering Department, Ken Vecchio helping set the foundation for the Nanoengineering Materials Research Center and developing thermodynamic processing methods for Iron-based Superelastic alloys.

After graduating from UCSD he founded Nanome Inc to build Virtual Reality solutions for Scientists and Engineers working at the nanoscale, specifically protein engineering and small molecule drug development. Steve is also a founder of the Matryx blockchain platform which provides a secure framework for collaborative design and development for STEM.

Robert Ramji

Rob is a senior at UCSD double majoring in NanoEngineering and Chinese Studies. When he’s not working on Molecule of the Month, he can usually be found working on Molecular Dynamics simulations codes in lab, discussing the finer points of Chinese slang with his friends, or out enjoying the San Diego weather. He can be reached via email at rob@nanome.ai