Multiplexed Nucleic Acid Sensing by Target-Induced Nanoparticle Aggregation with Optical Fiber Cone Arrays

     Environmental monitoring, food safety and disease diagnostics require a rapid and portable sensing platform capable of detecting nucleic acid signatures (DNA/RNA) of multi target pathogens for point-of-care application. Although Real-Time PCR (RT-PCR), a commercial detection kit, can analyse two or more targets in a same reaction, it is expensive, bulky and requires complex data interpretation and hence not suitable for field application.  Additionally, detection of targets using RT-PCR  requires fluorescence (FL) labeling of primer oligo sequence, which is tedious, time-consuming and limited to target numbers.

To overcome the shortcomings of existing technologies, we report a novel optical fiber sensing platform, which has the potential to detect hundreds of targets in one fiber bundle (1 mm diameter). Each fiber core (~7000 cores in one bundle) can be individually addressed for target analyte sensing using a laser. Several probes (DNA oligoprobes specific to target pathogen of interest) can be functionalized onto one fiber bundle using a photoactivation process. Instead of FL labeling, gold (Au) nanoparticles, that are chemically stable and absorb strongly at certain wavelength, will be used to indicate the presence of target DNA. Target nucleic molecules present in the sample solution act as a bridge between the gold particles functionalized with complementary target sequence and the oligoprobes on the optical fiber array by partially hybridizing with both. In one variation, each optical fiber tip is sharpened by wet etching into a conical shape with a radius curvature less than 100 nm.  The conic geometry enhance diffusion transport rate of the nanoparticles as compare to flat surface. Upon capture of gold particles by target DNA on the optical array, an increase in the absorption spectrum confirms the presence of target molecules that can be detected by a portable endoscopy microscope. Further, optical fiber bundle can be easily integrated with a microfluidic channel, where diffusion limitation and sample volume can be optimized. Ion-selective membranes are synthesized near the fiber array to allow analyte concentration by a new depletion zone microfluidic technology (Senapati et al, Topics in Current Chemistry (2011)). Another strategy to reduce the assay time and enhance the sensitivity is to coat the conic tip array with metal and photoconductive material such that plasmonics and optoelectronic dielectrophoresis can be employed to rapidly trap and concentrate the target molecules, as we have done in our earlier biosensor designs (Basuray et al, ACSNano(2009); Cheng et al, LabChip(2010)).

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