Molecule of the Month: DNA-Sequencing Nanopores

DNA sequencing has revolutionized the study of biology, revealing the information that encodes the processes of life. The Human Genome Project took a total of 13 years and cost almost 3 billion dollars using the conventional Sanger chain-termination method. As the enthusiasm for genomics continues to grow, the need for faster, better and more cost-effective sequencing techniques is increasingly clear. Nanopore sequencing is a rapidly developing tool to meet these demands, with devices often costing less than $1000. Today, this technology is used everywhere - from Antarctica to the International Space Station!

Nanopore sequencing decodes a DNA strand as it is drawn through a tiny pore embedded in a membrane. Compared to conventional DNA sequencing approaches, nanopore sequencing directly detects nucleotides without relying on DNA synthesis/amplification. This technique also enables sequencing of long fragments of DNA, which can be used to piece together entire genomes of organisms quickly and reliably. A single device houses thousands of individual nanopores and yet is simple, inexpensive and can even fit in your pocket. Scientists are currently minimizing challenges such as reducing error rates and increasing yields per run.

Nanopore sequencers are composed of nanopores embedded in a membrane that splits a salt solution into two chambers. A voltage is applied across the membrane, which causes ionic flow that can be measured. When a DNA strand is pulled through the pore, the ion flow is partially blocked, leading to a reduction in the observed current. The four types of nucleic acid bases are each associated with a different level of ion current change, which enables their identification. Commercially-available sequencers currently use derivatives of the bacterial protein CsgG as the go-to nanopore. CsgG, shown here from PDB ID 4uv3, is an ungated, non-selective outer membrane protein with a pore diameter of about 1 nanometer, which allows the easy passage of single-stranded DNA. To improve its DNA-reading ability, CsgG has been engineered to reshape the nanopore, as described below, resulting in greater yields and more accurate sequencing reads.

Precise control of the DNA strand is required to maintain efficient sequencing rates as it passes through the nanopore. Free DNA strands pass through pores too fast to get a clear read of each base. Scientists have found that they can regulate the speed by adding DNA-binding enzymes such as polymerases or helicases to the nanopore machinery. Bacteriophage phi29 DNA polymerase is shown here (PDB ID 1xhz). It acts as a stepper motor to slow down the DNA. In association with phi29 DNA polymerase, DNA ratchets through the CsgG pore at single nucleotide resolution.

Other pore-forming membrane proteins are abundant in nature. α-hemolysin (PDB ID 7ahl), a bacterial toxin, was the first biological nanopore used for sequencing. It features a long channel with a range of pore diameters (1.5-2.5 nanometers), making it suboptimal for discerning individual nucleic acid bases. The mycobacterial protein, MspA (PDB ID 1uun), is a naturally occurring nanopore with a shorter sensing region. This is an advantage, because in pores with shorter sensing regions, fewer nucleotides influence the characteristics of the recorded current, resulting in more accurate sequence reading. Since MspA exhibits a channel diameter of about 1.2 nanometers and a shorter sensing region, it is a better sequencer compared to α-hemolysin.