Detection of tomato leaf curl New Delhi virus DNA using U-bent optical fiber-based LSPR probes

• The ssDNA of Tomato leaf curl virus was successfully detected using a plasmonic U-bent fiber-optic probe. • The primer cDNA interaction on the gold nanoparticles immobilized fiber surface was monitored and receptor probes were developed for the detection of begomovirus DNAs. • The detection limit of viral ssDNA using both forward as well as reverse primers were found 50 ± 10 ng/μL and the selection of receptor probe types were determined from the conjugation efficiency. • The response time of these surface plasmon-mediated complementary oligonucleotide probes was found 10 min. • The positive detection of viral ssDNA was confirmed compared to non-infected ssDNA from similar genera of begomovirus of two different genetic strains and thus, the selectivity of the sensor was established. The detection of Tomato leaf curl New Delhi virus (ToLCNDV) DNA has been presented using U-bent fiber optic sensor (FOS) by an evanescent wave absorption method in the visible region. The localized surface plasmon resonance (LSPR) based FOS was developed by immobilizing gold nanoparticles on the amine-functionalized surface and the receptor probe was prepared by attaching a short segment of the complementary DNA (cDNA) on this surface. Further, the cDNA attachment was confirmed by monitoring the real-time change in LSPR absorption spectra. The conjugation protocol of single-strand DNA (ssDNA) from the viral genome of ToLCNDV was established like antibody-antigen-based assays by observing the real-time change in absorption kinetics. Consequently, a linear correlation between ssDNA concentration and the conjugation-dependent change in refractive index (RI) has been observed. The limit of detection (LOD) using two different cDNA immobilized FOS probes was determined to be 50±10 ng/μL and the change in RI was found 12.5±1.3×10 −4 RIU/Abs. From this systematic binding study, a straightforward target-specific sensor has been constructed using a digital electronic logic gate analogy. This device has significant commercial potential for the development of a portable LSPR sensor for real-time detection of plant pathogens in addition to the possibility of multi-target environments.