Background: The water borne pathogenic fungi have recently become a big threat and lead
cause of many hazardous infectious diseases in immuno challenged people.
Objective: A universal standardized method has to be developed for instant, specific and easier
detection and diagnosis of water borne pathogenic fungi.
Method: None of the methods so far known for the detection of pathogenic microorganisms is as handy,
economic, specific and sensitive as molecular beacons. Computational approach has been employed in
the present work to detect the conserved and oft repeat sequence pattern in the r-RNA sequences of
twenty three water borne pathogenic fungal species. These species were classified in three groups and
models of probes containing secondary stem loop structures were designed for each group. Finally a
common model capable of specifically detecting all species in one hit has been designed. Molecular
beacons have been proposed by attaching donor and acceptor dyes to the designed probes
Results and Conclusion: In the present work a molecular beacon based probe has been modelled which
is capable of detecting 23 pathogenic and water borne fungal strains. This approach of designing
molecular beacons with specific sequences of rRNA can prove to be a sensitive diagnostic technique for
detecting water borne pathogenic, fungal strains in miniscule amounts.