Nucleic acid functionalized fiber optic probes for sensing in evanescent wave: optimization and application

Abstract

Nucleic acid functionalized evanescent wave fiber optic (EWFO) biosensors have attracted much attention due to their remarkable advantages in both device configuration and sensing performance. One critical technique in EWFO biosensor fabrication is its surface modification, which requires (1) minimal nonspecific adsorption and (2) high-quality DNA immobilization to guarantee satisfactory sensing performances. Focusing on these two requirements, a series of optimizations have been conducted in this work to develop reliable DNA-functionalized EWFO probes. Firstly, the surface planeness of EWFO probes were found to be greatly improved by a novel HF/HNO₃ mixture etching solution. Both atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) were conducted to investigate the morphological structures and surface chemical compositions. Besides, EWFO sensing performances adopting moderate immobilization of irrelevant DNA were investigated for optimization purposes. Furthermore, a split aptamer based sandwich-type EWFO sensor was developed using adenosine (Ade) as the model target (LOD = 25 μM). To the best of our knowledge, this study is the first case to focus on the optimization of etching solution compositions in the fabrication of combination tapered fibers, which provides experimental basis for the understanding of the silica-etching mechanism using HF/HNO₃ mixture solution and may further inspire related researches.

Fig. 1. SEM images of combination tapered fiber surfaces obtained using etching solutions (a)–(e).

Fig. 2. AFM images of different SiO₂ chip surfaces before etching (a) and after etching by HF (b) and HF/HNO₃ (10 : 3) mixture solutions (c). Scan rate: 1 Hz. The obtained AFM data were analyzed using NanoScope Analysis 1.8, and the calculated profile roughness parameters, roughness average (R_a) and RMS roughness (R_q), were labeled in the bottom of this figure. Height ranges (δh) of each areas were calculated based on the differences from obtained height bars.

Fig. 3. XPS spectra of SiO₂ etched by HF pure solution and HF/HNO₃ (10 : 3) mixture solution: (a and b) survey; (c) Si 2p; (d) F 1s; (e) O 1s; (f) N 1s.

Fig. 4. Comparison of fibers etched merely by HF and by HF/HNO₃ mixture solution (c). (a) Schematic illustration (left) and the sensing performances (SNRs, right) of the two wet-process strategies. The capture DNA and C6-linker are depicted as blue strands, and black polygonal line, respectively. The SEM images of fiber surface are included. (b) EWFO signal traces of the experimental groups (exp., CT-Cy5.5) and control groups (ctr., A20-Cy5.5).

Fig. 5. Effect of irrelevant ssDNA mixed immobilization on EWFO hybridization signals. (a) Schematic illustration (left) and the sensing performances (SNRs, right) of fibers fabricated with/without mixers. The capture DNA (C6-DNA) and mixed DNA (A10) are depicted as blue and red strands, respectively. (b) EWFO signal traces of the experimental groups (exp., CT-Cy5.5) and control groups (ctr., A20-Cy5.5) based on fibers fabricated with/without mixers.

Fig. 6. Detection of Ade using the optimized EWFO sensing platform. (a) Schematic illustration of the sandwich-type assembly based Ade detection strategy using Ade split aptamer (ASA1 and ASA2). (b) Calibration curve of Ade.