Detection of unamplified genomic DNA by a PNA-based microstructured optical fiber (MOF) Bragg-grating optofluidic system

• Published in: Biosensors & bioelectronics Vol. 63; pp. 248 - 254
• Main Authors: Bertucci, Alessandro, Manicardi, Alex, Candiani, Alessandro, Giannetti, Sara, Cucinotta, Annamaria, Spoto, Giuseppe, Konstantaki, Maria, Pissadakis, Stavros, Selleri, Stefano, Corradini, Roberto
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 15.01.2015; Elsevier
• Subjects: Biological and medical sciences; Biophotonics; Biosensing Techniques - instrumentation; Biotechnology; Chromosome Mapping - instrumentation; Computer simulation; Deoxyribonucleic acid; Devices; DNA - analysis; DNA - chemistry; DNA - genetics; DNA detection; Equipment Design; Equipment Failure Analysis; Fiber Optic Technology - instrumentation; Fiber optics; Finite element method; Fundamental and applied biological sciences. Psychology; Microfluidic Analytical Techniques - instrumentation; Miniaturization; Nucleic Acid Amplification Techniques; Optical Devices; Optical fibers; Optofluidics; Peptide nucleic acids; Peptide Nucleic Acids - chemistry; Peptide Nucleic Acids - genetics; Photonic crystal fibers; Refractometry - instrumentation; Samples; Statistical methods; Optofluidics; DNA detection; Peptide nucleic acids; Photonic crystal fibers; Biophotonics; DNA; Genomics; Crystals; Peptide nucleic acid; Detection; Optical fiber
• ISSN: 0956-5663; 1873-4235
• DOI: 10.1016/j.bios.2014.07.047

Microstructured optical fibers containing microchannels and Bragg grating inscribed were internally functionalized with a peptide nucleic acid (PNA) probe specific for a gene tract of the genetically modified Roundup Ready soy. These fibers were used as an optofluidic device for the detection of DNA by measuring the shift in the wavelength of the reflected IR light. Enhancement of optical read-out was obtained using streptavidin coated gold-nanoparticles interacting with the genomic DNA captured in the fiber channels (0%, 0.1%, 1% and 10% RR-Soy), enabling to achieve statistically significant, label-free, and amplification-free detection of target DNA in low concentrations, low percentages, and very low sample volumes. Computer simulations of the fiber optics based on the finite element method (FEM) were consistent with the formation of a layer of organic material with an average thickness of 39nm for the highest percentage (10% RR soy) analysed. •We produced LMA-10 microstructured optical fibers (MOFs) with Bragg grating.•Microchannels of the MOF were modified with a PNA probe on the inner surface.•Detection of unamplified DNA was obtained using the modified MOFs and AuNPs.•The Bragg-grating reflection band shifts observed were dependent on % of target DNA.•Finite element method calculation were used for modelling the sensing process.