Polarization-Multiplexed Bloch Surface Wave Sensing of Single-Strand DNA Growth

TL;DR

The paper tackles real-time, label-free refractometric sensing of birefringent interfacial dynamics during biomolecular growth. It introduces polarization-multiplexed Bloch Surface Wave sensing on a tailored 1D photonic crystal to simultaneously monitor TE and TM modes, enabling direct access to time-resolved birefringence. A two-stage Transfer Matrix Method model is developed: a surface-sensitivity stage confines changes to a thin layer ($t_{SL}\approx 10$ nm) to separate isotropic from birefringent signals, followed by a birefringent slab model for vertical DNA growth, with nonlinear least-squares fitting to recover $n_{ ext{DNA,TE}}$, $n_{ ext{DNA,TM}}$, and $t_{ ext{DNA}}(t)$ from $\\lambda_{ ext{res}}^{TE}(t)$ and $\\lambda_{ ext{res}}^{TM}(t)$. The study reports a final ssDNA thickness of about $620\ ext{nm}$ and a birefringence of $\\Delta n \\approx 0.006$, demonstrating the method's ability to resolve dynamic anisotropic interfacial processes and providing a framework for time-resolved, label-free analysis of biomolecular interfaces.

Abstract

Refractometric biosensing is a vital label-free tool for the real time detection and interaction analysis of biological and chemical substances. Nanophotonic platforms like Surface Plasmon Resonance (SPR) have played a critical role in providing refractometric sensing capabilities for clinical diagnostics and environmental monitoring. However, traditional systems operating in a single-polarization state cannot fully characterize complex optical properties such as birefringence, which is crucial to resolve many complex biological interactions. Although Bloch Surface Wave (BSW) sensors can support both TE and TM modes, a key capability SPR lacks, they have historically been implemented in single-mode configurations. In this paper, we present a polarization multiplexed BSW refractometric sensing system, simultaneously tracking the resonant wavelength shifts of both TE and TM BSW modes through time. Our technique was applied to investigate single-strand DNA growth during rolling circle amplification (RCA). To accurately recover the time-dependent birefringence, capturing dynamics of the DNA growth and orientation of its chains, we implemented a two-stage modeling approach based on the TMM. First, we utilized a wavelength-dependent surface sensitivity model, confining refractive index changes to the immediate layer above the crystal, to distinguish isotropic background dynamics from birefringent signals. Following the onset of RCA, we transitioned to a model that accounted for the vertical growth of the DNA layers in time. By fitting this model to the TE and TM resonant shifts, we monitor the growth rate of the single-strand DNA layer as well as the refractive index along the two polarization components. Our findings demonstrate the platform's ability to resolve the structural evolution of complex bimolecular interactions associated with conformational changes.

Figures (10)

• Figure 1: a) Diagram of the Rolling Circle Amplification (RCA) process, showing how the padlock probe (PLP) is used to grow the single-strand DNA (ss-DNA). b) Experimental data of the shift in resonant wavelength for TE and TM BSW modes as a function of time from the growth of the ssDNA via RCA.
• Figure 2: Optical schematic of the multiplexed BSW sensing system.
• Figure 3: a) Example reflectivity spectra, $R(\lambda)$, for a BSW with and without a perturbation applied to the bulk refractive index of the superstrate. The spectra were calculated using TMM and the wavelength at which these spectra are at a minimum represent the resonant wavelength. In this example, $\Delta n = 20$ mRIU with an associated $\Delta \lambda_{\mathrm{res}} = 3.2$ nm giving a $S_{\mathrm{bulk}} = 324$$\mathrm{nm}/\mathrm{RIU}$. b) Example field enhancement distribution of our 1DPC without any perturbations applied to our superstrate comprised of an aqueous solution.
• Figure 4: a) Diagram of the 1DPC sensor in the Kretschmann configuration with a 10 nm PLL layer above the 1DPC and a thin Surface Layer, SL, above the PLL layer prior to the aqueous bulk superstrate. b) Refractometric surface layer sensitivity as a function of the thickness of the surface layer. c) Modeled surface sensitivity as a function of the index change applied to the surface layer. d) Modeled bulk sensitivity as a function of the index change applied to the bulk superstrate. e) Exponential decay coefficient, $\alpha$, fitted to the simulated electric field distribution of the exponentially decaying field inside the superstrate as a function of refractive index applied to the bulk and surface layers.
• Figure 5: a) Refractometric surface sensitivity as a function of resonant wavelength. b) Experimentally measured resonant wavelength shifts converted to refractive index modifications as a function of time within the surface layer. c) Time dependent birefringence of the surface layer with and without removing the linear phase from the TE data.