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

TL;DR

This paper introduces a polarization multiplexed Bloch Surface Wave sensing system capable of real-time, label-free detection of single-strand DNA growth, revealing detailed birefringence and structural dynamics during biological interactions.

Contribution

The work presents the first implementation of a dual-polarization BSW sensor for real-time DNA growth analysis, enabling simultaneous tracking of TE and TM modes to resolve birefringence.

Findings

Successfully monitored DNA layer growth rate over time.

Differentiated isotropic and birefringent signals during DNA amplification.

Demonstrated structural evolution analysis of complex biomolecular interactions.

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.