[Paper Review] Sub-20 nm Nanopores Sculptured by a Single Nanosecond Laser Pulse

Yanwen Yuan, Guangyuan Li+6 more|arXiv (Cornell University)|Jun 21, 2018

Nanopore and Nanochannel Transport Studies36 references3 citations

TL;DR

This paper demonstrates a fast, low-cost method to fabricate solid-state nanopores as small as 19 nm using a single nanosecond laser pulse, bypassing traditional expensive focused ion/electron beam techniques. The process is modeled via a 2D axisymmetric transient heat transfer model, and sub-10 nm pores are achieved with atomic layer deposition of alumina, enabling high-sensitivity DNA translocation detection with improved signal-to-noise ratio.

ABSTRACT

Single-molecule based 3rd generation DNA sequencing technologies have been explored with tremendous effort, among which nanopore sequencing is considered as one of the most promising to achieve the goal of $1,000 genome project towards personalized medicine. Solid state nanopore is consented to be complementary to protein nanopore and subjected to extensive investigations in the past decade. However, the prevailing solid-state nanopore preparation still relies on focused ion or electron beams, which are expensive and time consuming. Here we demonstrate the fabrication of nanopores down to 19 nm with a single nanosecond laser pulse. The laser drilling process is understood based upon a 2D axisymmetric transient heat transfer model, which predicts the laser fluence-dependent pore size distribution and shape with excellent agreement to electron microscopy and tomography analysis. As-drilled nanopore devices (26 nm) exhibit adequate sensitivity to detect single DNA molecule translocations and discriminate unfolded or folded events. Sub-10 nm nanopores can be readily achieved upon a thin layer of alumina deposition by atomic layer deposition, which further improves the DNA translocation signal to noise ratio considerably. Our work provides a solution for fast, low-cost and efficient large-scale fabrication of solid state nanopore devices for the 3rd generation nanopore sequencing.

Motivation & Objective

• To develop a scalable, low-cost alternative to focused ion or electron beam methods for solid-state nanopore fabrication.
• To achieve sub-20 nm pore sizes suitable for single-molecule DNA sequencing.
• To enable high-sensitivity detection of DNA translocations with improved signal-to-noise ratio.
• To model and validate the laser-induced pore formation process using transient heat transfer simulations.
• To demonstrate the feasibility of achieving sub-10 nm pores through post-deposition of alumina via atomic layer deposition.

Proposed method

• A single nanosecond laser pulse is used to drill nanopores in a thin membrane, with pulse energy and duration precisely controlled.
• A 2D axisymmetric transient heat transfer model is employed to simulate the thermal dynamics during laser irradiation and predict pore morphology.
• Electron microscopy and tomography are used to experimentally validate the predicted pore size and shape.
• Atomic layer deposition (ALD) of a thin alumina layer is applied post-laser drilling to reduce pore size and enhance translocation signal quality.
• Pore size distribution and shape are correlated with laser fluence to optimize fabrication reproducibility.
• Single DNA molecule translocation events are measured to assess sensing performance of fabricated nanopores.

Experimental results

Research questions

• RQ1 Can a single nanosecond laser pulse reliably produce solid-state nanopores below 20 nm in size?
• RQ2 How does laser fluence influence the resulting pore size and shape, and can this be accurately predicted by a thermal model?
• RQ3 Can the signal-to-noise ratio of DNA translocation events be significantly improved through post-laser alumina deposition?
• RQ4 Does the laser-fabricated nanopore device exhibit sufficient sensitivity for single-molecule DNA detection?
• RQ5 To what extent can this method scale for large-scale, cost-effective nanopore device production?

Key findings

• The laser drilling process successfully produced nanopores as small as 19 nm using a single nanosecond pulse, with excellent agreement between experimental results and the 2D transient heat transfer model.
• The pore size distribution and shape were found to be strongly dependent on laser fluence, with the model accurately predicting these outcomes.
• As-fabricated 26 nm pores demonstrated sufficient sensitivity to detect single DNA molecule translocations and distinguish between unfolded and folded states.
• Sub-10 nm pores were readily achieved after atomic layer deposition of a thin alumina layer, significantly enhancing the DNA translocation signal-to-noise ratio.
• The method enables fast, low-cost, and scalable fabrication of solid-state nanopores, offering a viable alternative to conventional focused ion or electron beam techniques.
• The study confirms the feasibility of using ultrafast laser pulses for high-precision nanopore fabrication in the context of third-generation DNA sequencing.