Lights, Fluorescence, Action: Live Imaging And Detection Of Genetic Sequences Using Molecular Probes

By: Mili Chizhik  |  August 31, 2020

By Mili Chizhik, News Editor

Amidst the COVID-19 pandemic, one can understand the importance of biological research and how it can impact each individual’s life. 

After my original summer plans fell through, I applied to a virtual summer internship at YU that allowed students to help research various subjects with the YU faculty. One lab that participated in this program was Dr. Irina Catrina’s research lab, where the researchers are trying to find ways to image genetic sequences by using molecular probes or beacons. In simpler terms, if one wants to find a certain gene that encodes for a certain protein, or if one wants to locate a specific genetic sequence within an area of an organism, a probe can be used to determine whether it is present. A molecular beacon or probe is an oligonucleotide ‒‒ a short DNA or RNA molecule ‒‒ that is complementary, or attracted, to the genetic sequence that one wants to image and locate. To create a probe that will find the proper target, one has to identify the specific gene they want and find the probe that will provide the most stable and spontaneous results. 

For example, picture magnets ‒‒ they are attracted to each other and will move towards each other unless something obstructs their ways. Just like the two magnets want to come close to each other, the probe’s two ends will fold over and bond to each other, forming a hairpin-like shape. At the bottoms of the ends is a quencher dye and a fluorophore (something that releases a fluorescent light), and when they are together, no light is released (i.e. the light is quenched when together, otherwise a light/fluorescence is released and not quenched). When the probe is in the presence of the target sequence and it is more thermodynamically stable to bind to the target sequence than the original conformation (hairpin loop), light/fluorescence will be released because the quencher dye and fluorophore are not together (the fluorophore is not quenched by the quencher due). With this fluorescence/light, one can identify whether the target sequence is present.

By using various programs written in Python, one can input a file of the target genetic sequence and the program will provide a list of many potential probes that can be used to image the genetic material. 

Using these techniques, researchers can learn more about genetic sequences in countless organisms. They can also help detect pathogens like the COVID-19 pathogen. When the nasal cavity is swabbed during the COVID-19 test, the contents are put in a solution and are broken down into smaller genetic components that can be detected by these probes and through fluorescence. Thus, it is very important and relevant for each individual to understand what impact the research has on the world and try to help further the advancements and breakthroughs of science.