Washington: As we have learned from the COVID-19 pandemic, disease-causing microorganisms can quickly switch to versions that evade detection and treatment. However, researchers presenting in ACS Infectious Diseases have discovered a process that could help detect these elusive infections. His “AutoPLP“focus creates nucleic acid probes that are fast, accurate and easy to detect novel variants.
Pathogens are detected by evaluating genetic material in various diagnoses, such as those based on Polymerase chain reaction (PCR). Rolling Circle Magnification (RCA) works in a similar way to PCR, but does not require the complex temperature cycling that PCR requires.
Both techniques require nucleic acid probes with sequences that match those of the target pathogen at specific locations, but RCA uses “highly specific”padlock probes(PLP). As a pathogen mutates, its genetic sequence also changes, and researchers have to keep redesigning their probes. So Sowmya Krishnan, Ruben Soares, M. Michael Gromiha, and Narayanan Madaboosi wanted to create a tool that could not only design these PLPs automatically but also, for the first time, systematically consider all the technical parameters needed at once to make the entire process be easier and more robust.
His tool, a computer program called “AutoPLP”, was named after the PLPs he designs. The program can take the genome sequences of similar pathogens as input and run a series of analyzes and database searches, generating a set of custom PLP sequences.
The team used the program to design probes against the rabies virus, a virus that is transmitted between animals and people, and Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, and compared them with previously reported ones. For rabies virus, AutoPLP targeted three genes, producing probes with a higher and narrower range of melting temperatures than those in the literature. For M. tuberculosis, they designed a total of 13 probes specifically targeting two genes responsible for drug-resistant strains with the program. The researchers say this tool could help speed up the discovery of new pathogen variants, helping to combat them quickly and effectively through precise molecular diagnostics.
