Solid-State Nanopore Tutorial

This solid-state nanopore tutorial is intended primarily as a tool by which to quickly get researchers new to the field up to speed on the essentials of nanopore research, but even expert users may find useful information ways to refine your workflows and get the most out of your valuable time. This course is a living document, that is regularly updated with new information and optimization as NNi's suite of nanopore tools grows.

This course is divided into several major sections. We discuss how to make a pore, including best practices and how to optimize your protocols to maximize success for any desired pore size. We cover detecting molecules with a nanopore, including DNA, proteins, and general tips for optimizing conditions for these and other more exotic polymers. We get into the weeds of signal transduction and dissect the signal that we read from our amplifiers, understanding not only what the signal means about the molecule but also how our hardware distorts the signal read and how to avoid mistaking hardware artefacts for physical effects. Finally, we present an overview of nanopore signal processing and analysis using our upcoming suite of software tools.

The Table of Contents below will help you navigate the course material. For new researchers starting training we strongly recommend reading through the course in the order presented prior to delving into the references. Note that the references herein are not intended to be a comprehensive overview of the field, but rather are a gateway and guide to provide new users with a foundation on which to begin building an understanding the current state of nanopore research, with a focus on the modern methods of nanopore fabrication that NNi is working to facilitate.

NNi is here to help. Should you have any questions relating either to the course specifically or nanopores in general, we would love to hear from you how we can be of assistance.

Table of Contents

1. Nanopore basics

2. How to make a solid-state nanopore

   1. Piranha cleaning tutorial

   2. NNi Nanopore Fabrication Software Tutorial

3. Characterizing a nanopore electrically

   1. How to measure the size of your pore electrically

   2. Nanopore noise measurement tutorial

4. How to detect molecules with a solid-state nanopore

5. Understanding your amplifier

6. Analyzing your data

   1. Visualizing your data

   2. Fitting events

   3. Visualizing event metadata

   4. Clustering and substructure labeling

   5. Event database filtering

   6. Capture rate analysis

   7. Analysis example: double-stranded DNA

   8. Coming soon

Last Updated: 2021-09-24