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Engineered electromagnetic fields in plasmonic nanopores enable enhanced optical detection and their use in single molecule sequencing. Here, a plasmonic nanopore prepared in a thick nanoporous film is used to investigate the interaction between the metal and a long-chain double strand DNA molecule. We discuss how the matrix of nanoporous metal can interact with the molecule thanks to: i) transient aspecific interactions between the porous surface and DNA and ii) optical forces exerted by the localized field in a metallic nanostructure. A duration of interaction up to tens of milliseconds enables to collect high signal-to-noise Raman vibrations allowing an easy label-free reading of information from the DNA molecule. Moreover, in order to further increase the event of detection rate, we tested a polymeric porous hydrogel placed beneath the solid-state membrane. This approach enables a slowdown of the molecule diffusion, thus increasing the number of detected interactions by a factor of about 20.
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The programmable assembly of DNA strands is a promising tool for building tailored bottom-up nanostructures. Here, we present a plasmonic nanosystem obtained by the base-pairing mediated aggregation of gold nanoparticles (NPs) which are separately functionalized with two different single-stranded DNA chains. Their controlled assembly is mediated by a complementary DNA bridge sequence. We monitor the formation of DNA assembled NP aggregates in solution, and we study their Surface Enhanced Raman Scattering (SERS) response by comparison with the single NP constituents. We interpret the revealed SERS signatures in terms of the molecular and NP organization at the nanoscale, demonstrating that the action of the DNA bridge molecule yields regular NP aggregates with controlled interparticle distance and reproducible SERS response. This demonstrates the potential of the present system as a stable, biocompatible, and recyclable SERS sensor.
Surface enhanced Raman scattering (SERS) process results in a tremendous increase of Raman scattering cross section of molecules adsorbed to plasmonic metals and influenced by numerous physico-chemical factors such as geometry and optical properties of the metal surface, orientation of chemisorbed molecules and chemical environment. While SERS holds promise for single molecule sensitivity and optical sensing of DNA sequences, more detailed understanding of the rich physico-chemical interplay between various factors is needed to enhance predictive power of existing and future SERS-based DNA sensing platforms. In this work we report on experimental results indicating that SERS spectra of adsorbed single-stranded DNA (ssDNA) isomers depend on the order on which individual bases appear in the 3-base long ssDNA due to intra-molecular interaction between DNA bases. Furthermore, we experimentally demonstrate that the effect holds under more general conditions when the molecules dont experience chemical enhancement due to resonant charge transfer effect and also under standard Raman scattering without electromagnetic or chemical enhancements. Our numerical simulations qualitatively support the experimental findings and indicate that base permutation results in modification of both Raman and chemically enhanced Raman spectra.
Recently, studies have been carried out on attempts to combine surface-enhanced Surface-enhanced Raman spectroscopy (SERS) substrates that can be based on either localized surface plasmon (LSP) or surface plasmon polaritons (SPP) structures. By combining these two systems, the drawbacks of each other can be solved. However, the manufacturing methods involved so far are sophisticated, labor-intensive, expensive, and also technically demanding. We propose a facile method for the fabrication of a flexible plasmonic nanoslit SERS sensor. We utilized the pattern on periodic optical disks (DVD-R) as a cheap substitute for printing the periodic pattern on PDMS with soft imprint lithography. Ag nanoslit (AgNS) was fabricated by serial bideposition using a dynamic oblique angle deposition (DOD) technique. The nanoslit structures were physically and optically characterized, and the experimental results were compared to the numerical simulation studies; Monte Carlo and the finite-difference time-domain (FDTD) simulation. The Ag nanoslit structure showed an excellent SERS enhancement, and its biosensing capability was demonstrated by the sensing of bilirubin.
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {em block length} $2n$ as well as on the {em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-stranded DNA translocations through conical quartz nanopores with mean opening diameter 15 nm. We observe an entropic barrier limited, length dependent translocation frequency at 4M LiCl salt concentration and a drift-dominated, length independent translocation frequency at 1M KCl salt concentration. These observations are described by a unifying convection-diffusion equation which includes the contribution of an entropic barrier for polymer entry.
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