In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocation velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here we present a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane, for synchronized optical and electronic detection of biomolecules. Proof of principle experiments are conducted showing that the Pyrex substrates have substantially lowers ionic current noise arising from both laser illumination and platform capacitance. Furthermore, using confocal microscopy and a partially metallic pore we demonstrate high signal-to-noise synchronized optical and electronic detection of dsDNA.

Nanopores are valuable tools for single-molecule sensing and biomolecular analysis. This can not only be seen from their prevalence in academic and industrial research, but in the growing capabilities at the cutting edge of the field. Recently the demand for improved structural resolution and accelerated analytical throughput has led to the incorporation of additional detection methods, such as fluorescence spectroscopy. The most frequently used solid-state nanopore platforms consist of a bulk silicon substrate and silicon nitride membrane. Although these platforms have many potential uses, they exhibit high photo-induced ionic current noise when probed with light. Due to the high translocation velocity of molecules, high bandwidth electrical measurements are essential for structural information to be investigated via resistive pulse sensing. Consequently, the applicability of Si substrate based nanopore sensors to synchronized optical and electrical measurements is limited at high-bandwidth and high-laser-power. This chapter describes the development and application of a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane. Proof-of-principle experiments are presented that show a Pyrex substrate greatly reduces ionic current noise arising from both platform capacitance and laser illumination. Furthermore, using confocal microscopy and a partially metallic nanopore as a zero mode waveguide, high signal-to-noise synchronized optical and electrical detection of dsDNA is demonstrated.

No abstract

In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocate on velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here, we investigate the influence of light illumination in the solid-state nanopore device fabricated either on Si substrate and quartz substrate. As has been well known, the noise signal in the solid state nanopore structure has been one of the major concerns. And the strong increase of ionic noise upon laser light illumination has been investigated before. Without light illumination, the noise signal which is characterized either by RMS value or more importantly by the power spectrum (pA2/Hz versus frequency Hz) typically shows about 40 pA in a Si substrate and 5.3 pA in a quartz substrate in RMS values and shows much improved noise characteristics on quartz substrate both in low frequency and high frequency. In general, it has been known that there are four different types of noise sources of ionic current obtained from the patch clamp system which shows different frequency dependency; 1. Voltage noise including RC noise showing f2 relationship, 2. dielectric noise which is proportional to f, 3. Johnson noise (thermal noise or Nyquist noise) and shot noise which are independent to f, and 4. Flicker noise related to a combination of noise showing 1/fa characteristics. However, upon irradiation with laser light in Si device, a completely different PSD was observed. PSD has the corner frequency, which is located at few hundreds Hz. This frequency dependence of this noise source is inconsistent with that of surface charge protonation noise or temperature-dependent thermal and dielectric noise. And, this peaks absence within the quartz-SiNx platforms power spectrum suggests the source of noise is related to the Si substrate. The optical transparency of the SiNx membrane and photon energy (2.54 eV) is sufficient for electron-hole pair generation in the Si substrate (band gap ∼1.1 eV), reported to promote photoreduction of H+ at p-type Si interfaces. Therefore, the increase in noise is via electrochemical reaction at the silicon/electrolyte surface by the excitation electron-hole pairs. In this sense, quartz device has only insignificant increase with laser illumination. Increase in thermal and dielectric noise term by localized heating can explain the small noise increase. This observation may also be quite important since there are many researchers who would like to utilize spectroscopic way of sequencing the DNA in a nanopore system.