For decades, nearly every DNA sequencing technology shared one fundamental idea.
If you wanted to determine the sequence of DNA, you first had to copy it.
Frederick Sanger's chain-termination method relied on DNA polymerase synthesising a complementary DNA strand. Modern next-generation sequencing (NGS) platforms such as Illumina also depend on DNA synthesis. Although the technologies differ considerably, they share the same underlying philosophy: observe DNA while it is being copied.
Oxford Nanopore Technologies asked a completely different question.
What if we did not copy the DNA at all?
What if we measured the molecule itself?
Rather than observing DNA synthesis, Oxford Nanopore measures the physical properties of individual DNA or RNA molecules as they pass through an extremely small biological nanopore.
Measuring DNA Instead of Copying It
To appreciate why Oxford Nanopore sequencing is different, it is useful to consider what previous sequencing technologies actually measure.
Sanger sequencing measures fluorescence emitted by chain-terminating DNA fragments.
Illumina sequencing measures fluorescence generated during DNA synthesis.
Neither technology observes the original DNA molecule directly.
In Oxford Nanopore sequencing, instead of copying DNA, a single DNA molecule is guided through a microscopic protein pore embedded within a synthetic membrane.
An electrical voltage is applied across the membrane.
Because DNA carries a negative charge, it is drawn through the nanopore by the electrical field.
As the DNA passes through the pore, it partially blocks the flow of ions moving through the nanopore.
This causes tiny changes in the electrical current.
These electrical current changes are the data produced by the instrument.
This is perhaps the most important concept to understand.
Oxford Nanopore sequencers do not directly observe the letters A, T, G, or C.
They observe electrical current.
What Does the Instrument Actually Measure?
Imagine looking at the output from an Oxford Nanopore sequencer.
Instead of seeing DNA bases, you might see a stream of electrical current measurements such as:
83.4 pA
82.7 pA
80.9 pA
84.1 pA
81.6 pA
To a human observer these numbers appear meaningless.
However, sophisticated neural network algorithms have been trained using millions of sequencing examples.
These algorithms learn the relationship between electrical current patterns and the DNA sequences that produce them.
The process of converting electrical signals into DNA sequence is known as basecalling.
Unlike earlier sequencing technologies, the instrument never directly identifies DNA bases.
Instead, it measures physics, while software reconstructs biology.
Why Doesn't the Nanopore Read One Base at a Time?
An obvious question arises.
If DNA consists of individual nucleotides, why doesn't the nanopore simply identify each base separately?
The answer lies in the size of the nanopore.
The sensing region of the pore is physically larger than a single nucleotide.
At any given moment, several neighbouring nucleotides occupy the narrowest region of the pore simultaneously.
Consequently, the electrical current reflects the combined influence of multiple adjacent bases rather than one nucleotide alone.
Rather than recognising individual bases directly, the basecalling software learns to interpret these complex electrical signatures into DNA sequence.
The Importance of the Motor Protein
DNA would naturally pass through the nanopore far too quickly to measure accurately.
Without regulation, millions of nucleotides could pass through the pore every second.
To solve this problem, Oxford Nanopore attaches a specialised motor protein to each DNA molecule.
The motor protein controls the movement of DNA through the nanopore one small step at a time.
You can think of the motor protein as the gearbox of the sequencing system.
Instead of allowing DNA to rush through uncontrollably, it feeds the molecule through the nanopore at a carefully regulated speed, giving the electronics sufficient time to record precise electrical measurements.
Without the motor protein, nanopore sequencing would not be possible.
Why Can Oxford Nanopore Produce Such Long Reads?
Traditional sequencing technologies are ultimately limited by the chemistry required to repeatedly copy DNA.
Oxford Nanopore does not repeatedly synthesise DNA.
It simply continues measuring until the DNA molecule reaches its end.
Consequently, read length is determined primarily by the size and quality of the DNA molecules extracted from the sample.
If the extracted DNA is 20 kilobases long, the instrument can potentially sequence 20 kilobases continuously.
If the DNA is several hundred kilobases long, equally long reads are possible.
Under carefully optimised laboratory conditions, reads exceeding one million bases have been demonstrated.
This ability to generate ultra-long reads has transformed applications such as genome assembly, structural variant detection, repetitive sequence analysis, and complete bacterial genome sequencing.
Sequencing in Real Time
Another unique feature of Oxford Nanopore sequencing is that sequencing begins producing useful information immediately.
As soon as DNA molecules begin passing through nanopores, electrical signals are generated.
These signals can be basecalled while sequencing is still in progress.
Alignment, taxonomic classification, and genome assembly can begin long before the sequencing run has finished.
This real-time capability has proven particularly valuable during infectious disease outbreaks, environmental sequencing, and situations requiring rapid identification of pathogens.
Native DNA and Epigenetics
Because Oxford Nanopore measures native DNA molecules directly, it can often detect more than the DNA sequence alone.
Chemical modifications such as DNA methylation subtly alter the way DNA interacts with the nanopore.
These changes produce characteristic alterations in the electrical signal.
Rather than requiring additional chemical treatments to study DNA methylation, Oxford Nanopore can frequently infer these modifications directly from the sequencing data.
Similarly, the platform is capable of sequencing native RNA molecules, allowing researchers to study RNA directly rather than sequencing DNA copies produced by reverse transcription.
Oxford Nanopore versus Sanger Sequencing
Although both technologies determine DNA sequence, they do so using fundamentally different approaches.
Sanger sequencing observes DNA synthesis.
Oxford Nanopore observes the DNA molecule itself.
Sanger sequencing measures fluorescence.
Oxford Nanopore measures electrical current.
Sanger sequencing analyses millions of copied DNA fragments.
Oxford Nanopore analyses individual DNA molecules.
Sanger sequencing typically produces highly accurate reads approaching 700–1,000 bases.
Oxford Nanopore produces much longer reads, often extending tens or hundreds of kilobases, while enabling real-time sequencing and direct detection of certain DNA modifications.
Sanger sequencing remains one of the best methods for validating small DNA regions, while Oxford Nanopore excels when long reads, structural variation, rapid sequencing, or epigenetic analysis are required.
One Technology, Multiple Instruments
Oxford Nanopore has a few instruments depending on the data output requirements.
They have a Flongle, MinION, GridION, or PromethION.
Each system uses:
biological nanopores
motor proteins
ionic current measurements
neural-network basecalling
The primary difference is simply the number of nanopores operating simultaneously.
Flongle provides a low-cost solution for small experiments.
MinION places a sequencing laboratory into a portable device that can fit into a pocket.
GridION allows multiple sequencing flow cells to operate simultaneously within a laboratory.
PromethION scales the same technology to support population-scale sequencing projects.
This is similar to increasing the number of processor cores in a computer.
A Different Way of Thinking About Sequencing
Previous sequencing technologies asked:
"How can we observe DNA while it is being copied?"
Oxford Nanopore asks:
"Can we measure the molecule directly?"
That philosophical shift has enabled ultra-long reads, real-time sequencing, direct RNA sequencing, epigenetic analysis, and portable sequencing platforms capable of operating almost anywhere in the world.
Ultimately, the Oxford Nanopore workflow can be summarised in a single diagram:
DNA molecule
↓
Motor protein
↓
Nanopore
↓
Electrical current
↓
Neural-network basecaller
↓
DNA sequence
Everything before the final step is fundamentally a physics experiment.
Everything after it is computational biology.
Related posts
What Is Next-Generation Sequencing? NGS Vs Sanger Explained
https://adwoabiotech.blogspot.com/2026/06/what-is-next-generation-sequencing-ngs.html
Sanger Sequencing Explained: How One Missing Oxygen Changed DNA Sequencing Forever
https://adwoabiotech.blogspot.com/2026/06/sanger-sequencing-explained-how-one.html
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