Nanopore Zero-Mode Waveguides for DNA Sequencing and Beyond

Abstract

Single-molecule techniques are becoming more practical and useful in academic research and commercial healthcare devices. A prime example of this is single-molecule DNA sequencing, which is now achievable using either nanopores or single-molecule real time (SMRT) methods. In these platforms, read lengths exceed those of bulk sequencing methods by orders of magnitude, and sensitivity to epigenetic modifications is allowed in cases where DNA amplification is not necessary. However, since sequencing and epigenetic analysis require native DNA fragments, a critical part of accessing this information is loading of the DNA into a readout device with high sensitivity. While typical DNA library input requirements are in the 100's of ng, ideally one would want to probe single cell amounts, or pg-level DNA. In this work, we have utilized micro and nano fabrication to construct zero-mode waveguides that contain nanopores in their base, and show that these devices can be used for extremely sensitive DNA capture and sequencing. The device, a nanopore-zero-mode waveguide (NZMW), allows sub nanogram levels of DNA to be efficiently drawn for analysis in seconds, and does not exhibit a bias towards low-molecular weight DNA as in diffusion-based methods. We will discuss the implications of such a device on DNA sequencing, RNA sequencing, as well as other single-molecule biophysical studies where only precious samples are available.