(618c) 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)).