Fiber Optic Particle Plasmon Resonance Biosensor for Label-Free Detection of Nucleic Acids and Its Application to HLA-B27 mRNA Detection in Patients with Ankylosing Spondylitis

Abstract

We developed a label-free, real-time, and highly sensitive nucleic acid biosensor based on fiber optic particle plasmon resonance (FOPPR). The biosensor employs a single-strand deoxyoligonucleotides (ssDNA) probe, conjugated to immobilized gold nanoparticles on the core surface of an optical fiber. We explore the steric effects on hybridization affinity and limit of detection (LOD), by using different ssDNA probe designs and surface chemistries, including diluent molecules of different lengths in mixed self-assembled monolayers, ssDNA probes of different oligonucleotide lengths, ssDNA probes in different orientations to accommodate target oligonucleotides with a hybridization region located unevenly in the strand. Based on the optimized ssDNA probe design and surface chemistry, we achieved LOD at sub-nM level, which makes detection of target oligonucleotides as low as 1 fmol possible in the 10-μL sensor chip. Additionally, the FOPPR biosensor shows a good correlation in determining HLA-B27 mRNA, in extracted blood samples from patients with ankylosing spondylitis (AS), with the clinically accepted real-time reverse transcription-polymerase chain reaction (RT-PCR) method. The results from this fundamental study should guide the design of ssDNA probe for anti-sense sensing. Further results through application to HLA-B27 mRNA detection illustrate the feasibility in detecting various nucleic acids of chemical and biological relevance.

Integrated Graphene Oxide with Noble Metal Nanoparticles to Develop High-Sensitivity Fiber Optic Particle Plasmon Resonance (FOPPR) Biosensor for Biomolecules Determination

“…Prior studies have indicated that the FOPPR sensor can be successfully used in various applications of chemical and biochemical domains and that it is characterized by real-time detection, high specificity and high speed. It has been experimentally proven that the sensitivity of this technology can reach the nanomolar (nM) level in bioassays [ 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. The method has many advantages; however, in order to face the detection standard for precision medicine in clinical detection, how to enhance the sensitivity and reproducibility are current topics.…”

Integration of Power-Free and Self-Contained Microfluidic Chip with Fiber Optic Particle Plasmon Resonance Aptasensor for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein

“…From the calibration curve, the limit of detection (LOD, with signal-to-noise ratio = 3:1) for the N-protein was calculated to be 2.8 nM (1.3 × 10 −7 g/mL). Based on a method correlation study from the literature [ 16 ], it was shown that the Ct value of 39.7 (≈95 copies/mL) by qRT-PCR is equivalent to the N-protein concentration of 0.71 ng/mL. By this conversion factor, our LOD is equivalent to about 1.5 × 10 4 copies/mL, which meets the acceptable LOD of 10 6 copies/mL set by the WHO target product profile [ 55 ].…”

“…Therefore, after multiple TIRs, the light transmitted through the fiber is attenuated by interaction with the AuNPs. The FOPPR biosensor has been applied to quantitative analysis of numerous different species in many different fields such as environmental analysis (e.g., heavy metal ions [ 7 , 10 , 11 ]), medical diagnostics (e.g., antinuclear antibodies [ 12 ], cytokines [ 13 , 14 ], sepsis biomarkers [ 15 ], mRNA [ 16 ], single nucleotide polymorphism [ 17 ]), food safety analysis (e.g., staphylococcus enterotoxin B [ 8 ], organophosphorous pesticides [ 18 ], antibiotics [ 19 ]), forensic science (e.g., illicit drug [ 20 ]), and agricultural analysis (e.g., orchid viruses [ 21 ]). These experimental demonstrations indicate that the FOPPR biosensor has the benefits of wide linear dynamic range, good reproducibility, and low detection limit in the analysis of real samples.…”

Trace Determination of Grouper Nervous Necrosis Virus in Contaminated Larvae and Pond Water Samples Using Label-Free Fiber Optic Nanoplasmonic Biosensor

“…Applications of the label-free FOPPR biosensor to real samples have been demonstrated. These applications include detection of antinuclear antibodies in sera [ 14 ], tumor necrosis factor-α and matrix metalloproteinases-3 in synovial fluids [ 15 ], orchid viruses in plants [ 16 ], HLA-B27 messenger RNA in blood [ 17 ], methamphetamine in urine [ 18 ], and single nucleotide polymorphismin of DNA in blood [ 19 ].…”