Label-free detection of DNA hybridization using gold-coated tapered fiber optic biosensors (TFOBS) in a flow cell at 1310 nm and 1550 nm

https://doi.org/10.1016/j.snb.2007.12.058Get rights and content

Abstract

We had previously reported the detection of a model protein bovine serum albumin (BSA) using antibody-immobilized tapered fiber optic biosensors (TFOBS) at 1310 nm and 1550 nm under stagnant and flow conditions. Because of recent interest in pathogen detection based on DNA, in this work we explore the application of these sensors for the detection of single stranded DNA (ssDNA). We show that it is feasible to directly detect the hybridization of a 10-mer ssDNA to its complementary strand immobilized on the sensor surface. Detection was performed under flow conditions because flow reduces non-specific binding to sensor surface, eliminates optical transmission changes due to mechanical movements, and allows for instantaneous switching of samples when needed.

TFOBS were fabricated with waist diameters of 5–10 μm and total lengths of 1000–1200 μm. The taper regions were coated with 50 nm of gold and housed in a specially constructed holder which served as a flow cell. The TFOBS was immobilized with 15-mer ssDNA with a C6 extension and a thiol group, which attaches to Au〈1 1 1〉 sites. Then, the complementary 10-mer ssDNA samples were allowed to flow in from low to high concentration (750 fM to 7.5 nM) and the resulting transmission changes were recorded. It is shown that 750 fM of complementary DNA can be detected. This sensor was able to distinguish between complementary DNA from DNA with a single nucleotide mismatch in the middle position.

Introduction

Detection of DNA interactions at femtomolar concentrations has many applications, such as biotechnology [1], genetics [2], medical diagnostics [3], [4], pathogen detection [5], [6], and drug screening [7]. To date the most popular methods of detection use ssDNA probes as recognition molecules [2], [4], [5], [8], [9]. Most of these methods depend on a fluorescent-labeled probe to provide and amplify sensing signal [2], [5], [10], [11]. Although the use of fluorescent labels improves sensitivity and selectivity, such a step requires laborious and time-consuming sample preparation steps. Furthermore, nucleic acids are often present in such small amounts that they need to be amplified using polymerase chain reactions (PCR) such that enough DNA exists to cause a change in sensor signal. Thus, it is highly desirable to reduce or eliminate the need for labeling and amplification, in order to develop a rapid, reliable, and user-friendly sensor.

For the past few years, tapered fiber optic biosensors (TFOBS) have been investigated in our laboratory as an alternative detection device for biomolecules. TFOBS have been widely investigated for the monitoring of physical properties [12], [13], [14], [15], [16], chemicals [17], [18], [19], [20], [21], [22], and biological molecules [23], [24], [25], [26], [27], [28]. TFOBS has several applications in environmental monitoring, drug screening, clinical diagnostics, and national security. From a detection standpoint, some advantages of TFOBS include the exposure of evanescent field beyond the surface of the sensing region, fast and real-time response, and the ability to respond without labels. Based on the femtogram to pictogram per mL sensitivity we obtained for protein bovine serum albumin (BSA) at near-IR wavelengths and flow conditions [29], we postulate that DNA can be detected using modification to our current system, resulting in label-free and continuous detection in the flow setting, at near-IR wavelengths.

In this study, TFOBS are coated with gold and housed in a flow cell. Thiolated 15-mer single stranded (ssDNA) probes were immobilized on the TFOBS gold surface. Complementary 10-mer ssDNA target strands were then detected while they hybridized with the immobilized probes at concentrations as low as 750 fM. The sensor also showed selectivity against a single nucleotide mismatch.

Section snippets

Physics of sensing

Optical fibers are light transmission waveguides made out of silica. They consist of a cylindrical core surrounded by a cladding. The core is doped with Ge such that its refractive index (RI) becomes slightly higher than that of the cladding. Since the core has a higher RI than the cladding, light is reflected along the fiber axis when it reaches the core-cladding interface, and therefore propagates through the optical fiber by total internal reflection (TIR). Aside from the large portion of

Flow cell apparatus

The flow cell assembly was described in our previous work [29] and is shown in Fig. 1. The chamber consists of a cylindrical well 4 mm in diameter and 3 mm in depth, and is centered on a 6 mm thick Plexiglas (∼3 cm × 5 cm). The approximate volume of the sample chamber is 40 μL. A sample inlet and outlet were drilled from the side edges of the Plexiglas to the sample chamber wall, to allow fluid flow through the sample chamber. The tapered region was positioned within the sample chamber. To complete the

Effect of gold thickness

Prior to performing DNA experiments, the ideal gold thickness was obtained by determining its effect on the TFOBS response due to Protein G (PG) immobilization. PG was chosen as the test analyte because its mechanism of attachment is similar to that of ssDNA, but can be used at higher concentrations and is of lower cost. Since the Denton Desk II System was capable of sputtering 100–1000 nm of gold, the experimental thicknesses were set within that range. In order to limit the number of

Conclusions

Through the use of a model system, we have shown that DNA hybridization can be detected using the TFOBS. The notable aspects of our detection system are intensity-based sensing, the use of near-IR wavelengths, and the ability to detect label-free DNA. The detection limit is comparable to many detection systems, and there should be some effort dedicated to lowering the limit. After the optimization of detection limit, the next step would be the detection of DNA from live cells.

Angela Leung received her BASc in biomedical engineering from University of Toronto in 2003. She is currently a final year doctoral student in Drexel University, where she is anticipating a PhD in chemical and biological engineering in June 2007. Her research area is in biosensors, particularly low concentration protein and DNA detection and design and fabrication of tapered fiber optic sensors and devices. Her interest also includes development of validation methods for bioprocesses and

References (34)

Cited by (56)

  • Carbon quantum dots functionalized tapered optical fiber for highly sensitive and specific detection of Leptospira DNA

    2023, Optics and Laser Technology
    Citation Excerpt :

    The LOD of 1.0 fM is in fact the highest LOD achieved among other reported DNA biosensors that use nanomaterial coating such as electrical based sensor by Kurkina et. al, (2 fM) [31] and S. Guo et al. (3 nM) [32], as well as in optical biosensor by Y. Huang et al. (1 pM) [33] and L. Angela et al. (7.5 pM) [34]. Ultimately, CQDs has successfully enhanced the DNA detection with the attainment of higher sensitivity, higher affinity and low LOD.

  • A biosensor based on a modified S-taper fiber for target protein detection

    2020, Nanotechnology and Precision Engineering
    Citation Excerpt :

    The protein biosensor plays an important role in the discrimination field because of its biocompatibility and adaptability to a wide variety of assay conditions, such as variable blood3 and different clotting factors.4 A variety of biosensors have been proposed for the detection of protein interactions, including two kinds of optical fiber grating binding structures for thrombin detection,3,5,6 MZ interferometer based photonic crystal fiber immune sensors for interactions between an antigen and antibody,7 a unique pattern microfiber biosensor for DNA hybridization,8–12 fiber optic SPR biosensing DNA-protein interactions,2,13 and nonadiabatic tapered optical fiber sensor for bovine serum albumin detection on an antibody-immobilized surface.14 Specific protein detection is an important part of protein biosensing as the investigation of protein interactions is essential for revealing roles in cellular function and is helpful for understanding life activities and pharmaceutical design.15

  • Fabrication of ultra-long tapered optical fibers

    2020, Microelectronic Engineering
View all citing articles on Scopus

Angela Leung received her BASc in biomedical engineering from University of Toronto in 2003. She is currently a final year doctoral student in Drexel University, where she is anticipating a PhD in chemical and biological engineering in June 2007. Her research area is in biosensors, particularly low concentration protein and DNA detection and design and fabrication of tapered fiber optic sensors and devices. Her interest also includes development of validation methods for bioprocesses and biomedical devices.

P.M. Shankar received his MSc (1972) in physics from Kerala University, India, MTech (1975) in applied optics and PhD in electrical engineering (1980) from Indian Institute of Technology, Delhi, India. He was a visiting scholar at the School of Electrical Engineering, University of Sydney, Australia, from 1981 to 1982. He joined Drexel University in 1982 and is currently the Allen Rothwarf Professor and interim department head of Electrical and Computer Engineering. He is the author of the textbook ‘Introduction to Wireless Systems’, published by John Wiley & Sons, 2002. His research interests are in wireless communications, fiber sensors, biosensors, and statistical signal processing for medical applications.

Raj Mutharasan received his BS degree (1969) in chemical engineering from IIT Madras (India) and a PhD (1973)in chemical engineering from Drexel University. He joined the faculty ranks at Drexel University in 1974 after a post doctoral year at University of Toronto, Canada. He was appointed to the position of Frank A. Fletcher Professor of Chemical and Biological Engineering in 1995. His research interests are in biophysics, biophotonics and cantilever for sensor development, and process biotechnology. He has published extensively and is the author of several patents. He is a Fellow of American Institute of Chemical Engineers and American Institute for Medical and Biological Engineering.

View full text