Microgap Structured Optical Sensor for Fast Label-Free DNA Detection

Abstract

DNA detection technology has developed rapidly due to its extensive application in clinical diagnostics, bioengineering, environmental monitoring, and food science areas.Currently developed methods such as surface Plasmon resonance (SPR) methods, fluorescent dye labeled methods and electrochemical methods, usually have the problems of bulky size, high equipment cost and time-consuming algorithms, so limiting their application for in vivo detection. In this work, an intrinsic Fabry-Perot interferometric (IFPI) based DNA sensor is presented with the intrinsic advantages of small size, low cost and corrosion-tolerance. This sensor has experimentally demonstrated its high sensitivity and selectivity.In theory, DNA detection is realized by interrogating the sensor's optical cavity length variation resulting from hybridization event. First, a microgap structure based IFPI sensor is fabricated with simple etching and splicing technology. Subsequently, considering the sugar phosphate backbone of DNA, layer-by-layer electrostatic self-assembly technique is adopted to attach the single strand capture DNA to the sensor endface. When the target DNA strand binds to the single-stranded DNA successfully, the optical cavity length of sensor will be increased. Finally, by demodulating the sensor spectrum, DNA hybridization event can be judged qualitatively.This sensor can realize DNA detection without attached label, which save the experiment expense and time. Also the hybridization detection is finished within a few minutes.This quick response feature makes it more attractive in diagnose application. Since the iii sensitivity and specificity are the most widely used statistics to describe a diagnostic test, so these characteristics are used to evaluate this biosensor. Experimental results demonstrate that this sensor has a sensitivity of 6nmol/ml and can identify a 2 bp mismatch. Since this sensor is optical fiber based, it has robust structure and small size ( 125μm ). If extra etching process is applied to the sensor, the size can be further reduced. This promises the sensor potential application of in-cell detection. Further investigation can be focused on the nanofabrication of this DNA sensor, and this is very meaningful topic not only for diagnostic test but also in many other applications such as food industry, environment monitoring.iv Acknowledgement

Photonic Biosensor Assays to Detect and Distinguish Subspecies of Francisella tularensis

“…Because of its sugar phosphate backbone, DNA is considered an anionic polyelectrolyte that can be immobilized onto the surface of the 125-μm diameter fiber tip by LbL/ESA. The 26-base ssDNA-A oligonucleotide probe to F. tularensis ( Table 1 ) was immobilized on the fiber tip by electrostatic self-assembly [ 24 , 29 , 37 ]. Representative cavity thickness changes resulting from immobilization of the ssDNA-A probe are shown in Figure 5 .…”

“…A conventional FFPI consists of an input fiber, an air cavity subject to perturbation by the substance of interest, and a second reflecting surface, which may be either a second fiber or a diaphragm [ 15 – 17 , 19 , 22 ], forming a two-beam interferometer. A single cavity FFPI may also be formed by generating an air-filled microgap between two spliced optical fibers [ 37 ]. Such sensors are intended to observe the perturbation of only a single cavity.…”

Molecular beacons immobilized within suspended core optical fiber for specific DNA detection

“…Among biosensors, DNA sensors are an important subclass as DNA detection and/or profiling is a fundamental step in numerous applications in Medical, Pharmacy, Forensics, and Archaeology. Attempts to use optical fibers, including microstructured optical fibers (MOFs) for DNA detection have been reported [2][3][4][5][6][7]. The intrinsic optical fiber based DNA sensors developed to date, in which the fiber itself serves as a sensing element, have largely been based on the use of label-free sensing principles [2][3][4][5][6][7].…”

“…The intrinsic optical fiber based DNA sensors developed to date, in which the fiber itself serves as a sensing element, have largely been based on the use of label-free sensing principles [2][3][4][5][6][7]. In this case, localized variations in the refractive index of a DNA sensitive layer (the probe), immobilized on the surface [2][3][4] or at the end [5] of an optical fiber upon hybridization with its cDNA sequence (the target), induce a wavelength shift [2][3][4] or optical path length change [5]. Consequently the presence of the target sequence binding with the immobilized probe can be inferred.…”

“…Consequently the presence of the target sequence binding with the immobilized probe can be inferred. The optical transduction mechanism used for label-free detection is typically a fiber grating [2][3][4], a Fabry-Perot interferometer [5], or surface plasmon resonance [6]. For DNA sensing label-free approaches have the drawback that they do not generally work at room temperature.…”