Label-Free MicroRNA Optical Biosensors

Abstract

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection of miRNA. The optical approach for a label-free miRNA sensor is very promising and many assays have demonstrated ultra-sensitivity (aM) with a fast response time. Here, we review the most relevant label-free microRNA optical biosensors and the nanomaterials used to enhance the performance of the optical biosensors.

Keywords: label-free; microRNA; nanomaterials; optical sensor.

Figure 1

Principle of surface plasmon resonance (SPR) sensor: (a) prior to binding and (b) analyte binding where the number of analytes captured results in a change in the index of refraction (RI) near the surface of the metal layer.

Figure 2

(a) Surface plasmon resonance biosensor based on the attenuated total reflection (ATR) method and (b) spectrum shifts observed before and after change in the refractive index as the result of a biorecognition event.

Figure 3

(a) Schematic representation of the antibody-based assay for detection of miRNA-122. (b) Sensor response to the miRNA and antibody. Reproduced with permission from [71]. Copyright American Chemical Society, 2010.

Figure 4

(a) Fraunhofer compact SPR biosensor (left) with chips and flow cells (right) and (b) schematic representation of the arrangement of the three 1D spot arrays (channel 1, channel 2 and channel 3) on the gold surface illuminated by three side-by side distinct stripes lights (1, 2 and 3). Reproduced with permission from [25,72]. Copyright John Wiley and Sons, 2011 and Walter De Gruyter GmbH, 2016.

Figure 5

(a) Preparation of two-dimensional antimonene nanosheets. (b) Faraday–Tyndall effect used to verify the existence of antimonene nanosheets in the solution. Reproduced with permission from [44]. Copyright Springer Nature, 2019.

Figure 6

Fabrication of the microRNA sensor integrated with antimonene nanomaterials. (I) The antimonene nanosheets casted on Au substrate. (II) AuNR-ssDNAs adsorption. (III) miRNA binds to complementary AuNR-ssDNA to form a double-strand with complementary AuNR-ssDNA. (IV) AuNR-ssDNA released from the antimonene nanosheets. Reproduced with permission from [44]. Copyright Springer Nature, 2019.

Figure 7

Illustration of the reflected light from the biorecognition event on the array being detected via a CCD camera for each array spot as the change of intensity of the reflected light.

Figure 8

miRNAs detection mechanism using a combination of surface polyadenylation chemistry and nanoparticle amplified SPRi detection.

Figure 9

(A) Fabrication procedure for fabricating gold-islanded biochip with hydrophilic/hydrophobic spacer: ① gilding, ② photoresist spin-coating, ③ patterned exposure and developing, ④ gold etching, ⑤ CYTOP spin-coating and baking, ⑥ stripping excessive CYTOP and photoresist; (B) Image of the chip wetted by water; (C) Image of the chip dropped with hydrophilic samples. Reproduced with permission from [75]. Copyright American Chemical Society, 2017.

Figure 10

Schematic diagram for a localized surface plasmon excited in a small metallic particle.

Figure 11

LSPR-based sensor using transmission attenuation configuration. Reproduced with permission from [94]. Copyright MDPI, 2018.

Figure 12

Plasmonic biosensors based on nanoprisms: (a) Chemically synthesized gold nanoprisms covalently attached onto glass coverslip via 3-mercaptopropyltriethoxysilane-functionalized. (b) Surface modification of gold nanoprisms equimolar mixture of SH-C6-ssDNA-X and PEG6-SH in PBS buffer (pH 7.4). (c) Incubation of sensor in miR-X solution and formation of DNA duplex. (d) Extinction spectrum of the surface modification with SH-C6-ssDNA-X and PEG6-SH (blue curve) and after incubation with miR-X (red curve). (e) Plot of Δλ_LSPR versus log of miR-X concentrations. Reproduced with permission from [62]. Copyright American Chemical Society, 2014.

Figure 13

Surface modification of LSPR sensor. (a) AFM micrographs after functionalization with 1:1 ratio of HS-C6-ssDNA-21/PEG6-SH (b) and after hybridization with 100 nM miR-21 in 40% human plasma. (c) bare gold nanoprisms. (d) plot of the change in surface area of the gold nanoprisms after each surface modification. Reproduced with permission from [62]. Copyright American Chemical Society, 2014.

Figure 14

(a) Mach–Zehnder interferometer and (b) Young interferometer biosensor configurations. Reproduced with permission from [96]. Copyright Elsevier, 2014.

Figure 15

Schematic diagram of the MZI biosensor platform (a) TEM image of the cross section of the waveguide. (b) SEM images of mode converter, and (c) a silicon nitride grating coupler. (d) Photograph image of MZI biosensor. (e) Output intensity displaying a 4πphase shift after the target miRNA recognition. Reproduced with permission from [31]. Copyright Elsevier, 2015.

Figure 16

Microfiber-capillary optofluidic sensor fabricated by Liang et. al (a) Schematic diagram of the fabrication process of the sensor. (b) Image of the sensor platform. (c) SEM image of the cross-section and side view of the sensor. Reproduced with permission from [79]. Copyright Elsevier, 2017.

Figure 17

WGMs supported upon total internal reflection can be understood by either geometrical optics (left) or wave optics (right).

Figure 18

Schematic diagram of the microring biosensor system for miRNA detection. (a) The microring is functionalized with a capture DNA sequence (green curve). The capture of the target miRNA (purple curve) causes a shift in the wavelength required to achieve optical resonance. (b) SEM image showing six microrings on a sensor array chip. (c) The wavelength shift after miRNA recognition of the selected miRNAs. Reproduced with permission from [73]. Copyright John Wiley and Son, 2010.

Figure 19

Schematic diagram of the Anti-DNA-RNA amplification experiment. A complementary DNA modified microring is exposed to target miRNA followed by the anti-DNA-RNA antibody for signal amplification.