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Ellipsometric-based novel DNA biosensor for label-free, real-time detection of Bordetella parapertussis

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Abstract

Pertussis (or whooping cough) is a contagious disease mainly affecting infants and children and predominantly caused by Bordetella pertussis followed by Bordetella parapertussis. B. parapertussis causes a milder cough but usually symptomatically appears like B. pertussis infection. Thus the epidemiology of illness caused by B. parapertussis is not well understood. In this study, a sensitive and specific method for the rapid diagnosis of B. parapertussis is presented. The covalent immobilization of thiol-terminated DNA oligonucleotides (ss DNA SAM) on a silicon surface by disulfide bond formation is investigated with atomic force microscopy (AFM) and ellipsometry. The measurements indicated an average layer thickness of 5 ± 0.84 nm for 2 μg/μl concentration and 24 h incubation time. This thickness changed to 8.4 ± 0.92 nm for the same concentration (2 μg/μl) by altering the incubation time to 48 h. Ellipsometric data recorded before and after hybridization of B. parapertussis revealed an increase in mean grain area from 91 nm2 to 227 nm2 and a change in the refractive index from 1.489 to 1.648 for 2 μg/μl B. parapertussis, respectively. This change in the refractive index was used to evaluate the amount of adsorbed molecules and their density. The results showed that the density of adsorbed molecules increased from 0.2 to 0.97 g/cm3 after B. parapertussis attachment, respectively. To confirm the hybridization of B. parapertussis to ss DNA SAM, the ds DNA SAM was denatured and the ss DNA SAM surface was reproduced with an average height variation of 6.42 ± 0.75 nm. This showed the stability of the DNA film that can be tuned by varying the concentration and incubation time, thus providing a robust method for the label-free detection of B. parapertussis other than routinely used PCR detection.

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Acknowledgements

This work was supported by the Higher Education Commission, Pakistan (HEC) development grant for ‘Designing and Fabrication of Micro and Nano Devices’ and the department of physics, COMSATS institute of Information Technology, Islamabad, Pakistan.

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Authors and Affiliations

  1. Department of Physics, Air University, PAF Complex, E-9, Islamabad, 44000, Pakistan

    S. Rafique

  2. Department of Microbiology, COMSATS Institute of Information Technology, Islamabad, 44000, Pakistan

    M. Idrees & H. Bokhari

  3. Centre for Micro & Nano Devices, Department of Physics, Faculty of Science, COMSATS Institute of Information Technology, Park Road Campus, Islamabad, 44000, Pakistan

    A. S. Bhatti

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Rafique, S., Idrees, M., Bokhari, H. et al. Ellipsometric-based novel DNA biosensor for label-free, real-time detection of Bordetella parapertussis. J Biol Phys 45, 275–291 (2019). https://doi.org/10.1007/s10867-019-09528-2

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