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Optofluidic detection of Zika nucleic acid and protein biomarkers using multimode interference multiplexing

Alexandra Stambaugh, Joshua W. Parks, Matthew A. Stott, Gopikrishnan G. Meena, Aaron R. Hawkins, and Holger Schmidt

Open Access Open Access

Abstract

The recent massive Zika virus (ZIKV) outbreak illustrates the need for rapid and specific diagnostic techniques. Detecting ZIKV in biological samples poses unique problems: antibody detection of ZIKV is insufficient due to cross-reactivity of Zika antibodies with other flaviviruses, and nucleic acid and protein biomarkers for ZIKV are detectable at different stages of infection. Here, we describe a new optofluidic approach for the parallel detection of different molecular biomarkers using multimode interference (MMI) waveguides. We report differentiated, multiplex detection of both ZIKV biomarker types using multi-spot excitation at two visible wavelengths with over 98% fidelity by combining several analysis techniques.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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Figures (3)
Fig. 1
Fig. 1 a) Scanning electron microscope image of fabricated ARROW optofluidic device, with top down multi-mode spot quantum dot images for λ = 556 nm and λ = 633 nm shown on the right, with their respective colors (insert: photo of complete 1cm2 ARROW optofluidic chip), b) Product from the nucleic acid and protein solid-phase extraction assays used for target isolation with high specificity, c) Particle fluorescence traces detected on ARROW optofluidic chip for the protein detection complex (top: negative control (no NS1 protein); bottom: positive control (with NS1 protein)).

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Fig. 2
Fig. 2 a) Particle fluorescence trace of both nucleic acid and protein complexes detected in an MMI ARROW chip and excited first with only λ1 = 633 nm, then with only λ2 = 566 nm, and finally with λ1 and λ2, b) Fluorescence signal from a single nucleic acid complex showing 7 peaks with the signal time (Ttot) and characteristic delta t, δtR = 0.55ms, annotated on the fluorescence signal, c) Fluorescence signal from a single protein complex showing 8 peaks with the signal time (Ttot) and characteristic delta t, δtG = 0.34ms, annotated on the fluorescence signal.

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Fig. 3
Fig. 3 a) Corresponding single-particle autocorrelation signals for both a red nucleic acid signal and a green protein signal. Multiple peaks are observed at multiples of δtG, = 0.34 ms and δtR = 0.55 ms, b) Corresponding enhanced signal using shift-multiply versus δt of the signal shown in (a), signals show an increased SNR when shifted by the correct δt c) Segment of the particle fluorescence trace that was excited with both colors. Events were identified using single particle autocorrelations, shift-multiply algorithms, and total peak duration analysis. Over 98% of signals were identified. Of 215 total signals, 134 were identified as Nucleic Acid complexes, annotated by red squares and 77 were identified as Protein complexes, annotated by green circles.

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Equations (3)

Equations on this page are rendered with MathJax. Learn more.

N=  n c w 2 Lλ
S( t, δt )= ∏ m=1 N−1 F(t−m⋅δt)
N i =  T Tot,i δt i
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