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Sunday, July 12, 2026

DNA Nanoballs: How MGI's DNBSEQ Rewrites Sequencing

July 12, 2026 0 Comment

Picture a single strand of DNA curling up into a tight little ball, thousands of identical copies of itself packed into a space smaller than a red blood cell. Now imagine spreading billions of these balls across a chip, each one sitting in its own private parking spot, and reading every single one of them at once. That, in essence, is what MGI's DNBSEQ platform does every time it runs. No PCR thermal cycling. No bridge amplification. Just a ball of DNA and a very patient camera.

If you have been following this series, you already know the cast of characters. We started with Sanger sequencing, the original workhorse that gave us the first human genome, one careful read at a time. Then came the next-generation revolution: Illumina's bridge amplification and reversible terminator chemistry, Oxford Nanopore's electrical current reading of DNA threading through a protein pore, PacBio's real-time single-molecule imaging, and Ion Torrent's clever trick of measuring pH instead of light. Today we add a sixth platform to the lineup, one that has quietly become one of the most widely used sequencing technologies outside the United States: MGI's DNBSEQ.

Where did this technology come from?

DNBSEQ traces its roots back to Complete Genomics, a California company that published a landmark paper in Sciencein 2010 describing a method for sequencing a human genome using what they called self-assembling DNA nanoarrays (Drmanac et al., 2010). The idea was radical for its time: instead of amplifying DNA fragments with PCR, which introduces its own errors and biases, why not let the DNA circularize and replicate itself using a gentler, more faithful process? Complete Genomics was later acquired by the Chinese genomics company BGI, and its sequencing chemistry evolved into what we now call DNBSEQ, developed and commercialized by MGI Tech, BGI's technology arm.

Why does it matter that this technology skips PCR? Anyone who has tried to amplify an AT-rich genome like Plasmodium falciparum, sitting at roughly 80 percent AT content, knows the frustration of GC bias, dropout regions, and uneven coverage that standard PCR-based library prep can introduce. A method that avoids repeated PCR cycling has an obvious appeal for exactly this kind of genome.

So how does a DNA nanoball actually form?

The process starts in a familiar place. Double-stranded DNA fragments, each carrying adapter sequences at their ends, are heated until they denature into single strands. From here, DNBSEQ takes a different road than Illumina.

A splint oligonucleotide, a short synthetic sequence complementary to both ends of the same single strand, hybridizes to those ends simultaneously, pulling them together into a nicked circle. DNA ligase then seals the nick, producing a stable, closed single-stranded circle. Think of it like taking a piece of string and tying its two ends together to make a loop.

Once that circle exists, rolling circle amplification takes over. A single high-fidelity polymerase travels around and around the circular template, producing a long concatemer, essentially the same sequence repeated over and over, roughly 100 to 1000 times. This concatemer naturally coils up into a compact, tangled structure: the DNA nanoball.

Why is this gentler than PCR? In PCR, each new copy is made from the previous copy, so any error introduced early in the process gets carried forward and amplified exponentially with every cycle. Rolling circle amplification instead copies the same original circular template again and again. An error introduced during one pass around the circle does not get compounded, because the next pass starts fresh from the same original template. MGI's own technical materials describe this as producing far less accumulated amplification error than PCR-based approaches, and one convenient side effect is that DNB concentration can be measured with a simple Qubit fluorometer, no expensive quantification instrument required.

Getting the nanoballs onto the chip

Once formed, DNBs are loaded onto a patterned array flow cell. Rather than letting DNA molecules land wherever they please on a randomly coated surface, these chips are etched with an orderly grid of binding sites spaced at submicron distances, each designed to hold exactly one DNB. It is a bit like an egg carton for DNA: every nanoball gets its own compartment, evenly spaced from its neighbors. This deliberate spacing helps prevent signal crosstalk between neighboring clusters, which is one of the failure modes that can plague random-cluster sequencing arrays as they get more crowded.

Reading the sequence: cPAS

The actual base calling happens through what MGI calls combinatorial probe-anchor synthesis, or cPAS. Four fluorescently labeled probes, one for each base, bind to the growing strand in a cycle. Lasers excite the fluorophores, a camera captures the resulting flash of color at every single DNB position on the chip, and proprietary software translates millions of these tiny light signals into a base call. The cycle repeats, one base at a time, across the whole flow cell simultaneously.

Where DNBSEQ sits in the platform landscape

MGI now offers a range of instruments spanning very different throughput needs, from compact benchtop systems like the E25 and G99 up through high-throughput workhorses like the G400, T7, and T20×2, the last of which is designed for genome centers running dozens of samples a day.

How does it actually stack up against Illumina, the platform most labs already know? A benchmarking study using the Korean Reference Genome compared DNBSEQ-T7 against six Illumina platforms, including the NovaSeq 6000, and found the two technologies to be broadly comparable for whole-genome sequencing accuracy (Kim et al., 2021). A separate study looking at DNA metabarcoding, sequencing COI gene amplicons from soil samples, found highly correlated results between MGI's DNBSEQ-G400RS and Illumina's NovaSeq 6000, though the MGI platform recovered a somewhat higher number of distinct taxonomic units in that particular comparison (Anslan et al., 2021).

Why this matters for malaria genomics

For a lab working on P. falciparum genomics, sequencing choices are never purely academic. Library prep cost, turnaround time, and how a platform handles an extremely AT-rich genome all factor into which sequencer ends up processing your field isolates. DNBSEQ's PCR-free amplification step is worth understanding even if your lab primarily runs Illumina, because it represents a genuinely different philosophy for how to get from a DNA sample to a finished sequence, and it is increasingly likely to show up in a collaborator's data or a published dataset you are trying to compare against your own.

Pacific Biosciences: Watching DNA Polymerase at Work

Our story begins in the early 2000s.

Scientists had already spent decades studying DNA polymerase, the remarkable enzyme responsible for copying DNA inside every living cell.

Every time a cell divides, DNA polymerase faithfully adds complementary nucleotides to a growing DNA strand.

A pairs with T.

G pairs with C.

Scientists wondered whether this natural process itself could become the sequencing instrument.

Instead of stopping DNA synthesis like Sanger sequencing, or sequencing millions of amplified DNA fragments simultaneously like second-generation sequencing, why not simply watch a single DNA polymerase molecule doing what intelligent design designed it to do?

This became the foundation of Single Molecule Real-Time sequencing, more commonly known as SMRT sequencing.

The name is actually very descriptive.

Single Molecule means that each DNA molecule is sequenced individually without requiring clusters of identical DNA molecules.

Real-Time means the sequencing instrument observes DNA synthesis as it happens.

But this immediately created another problem.

DNA polymerase is an incredibly tiny enzyme. Individual nucleotide incorporation events occur within milliseconds. Even with the world's most sensitive microscopes, how could anyone observe a single enzyme working?

This is where Pacific Biosciences introduced one of the most elegant engineering solutions in modern biotechnology.

Zero-Mode Waveguides: Shrinking the Observation Window

The answer was not to build a better microscope.

Instead, they built a smaller observation chamber.

PacBio developed microscopic structures called Zero-Mode Waveguides, often abbreviated as ZMWs.

A ZMW is an extremely tiny hole etched into a metal film deposited on a glass chip.

These holes are far smaller than the wavelength of visible light.

Normally, light spreads throughout a sample, causing enormous background fluorescence.

Inside a ZMW, however, light cannot propagate normally.

Instead, only an incredibly thin region at the very bottom of the well becomes illuminated.

Think of shining a flashlight into an enormous room versus shining it through the eye of a needle.

Only a tiny volume becomes visible.

This tiny illuminated volume is where the magic happens.

A single DNA polymerase molecule is immobilised at the bottom of each ZMW.

The DNA template is attached to that polymerase.

Everything else remains effectively invisible.

Now scientists could watch one DNA polymerase molecule copying one DNA molecule without being overwhelmed by background fluorescence.

Fluorescent Nucleotides

Next, the polymerase needs nucleotides to build the new DNA strand.

Unlike Sanger sequencing, PacBio does not use chain-terminating nucleotides.

Instead, it uses normal nucleotides carrying fluorescent dyes.

Each of the four nucleotides has its own fluorescent colour.

A emits one colour.

T another.

G another.

C another.

Importantly, the fluorescent dye is attached to the phosphate group rather than the nucleotide base itself.

Why?

Because DNA polymerase naturally removes the phosphate groups during DNA synthesis.

When the nucleotide is incorporated, the fluorescent label is automatically cleaved away and diffuses out of the observation chamber.

The newly synthesised DNA therefore remains completely natural.

This allows the polymerase to continue synthesising DNA uninterrupted for thousands of nucleotides.

Watching DNA Being Copied

Now the sequencing reaction begins.

DNA polymerase selects the next complementary nucleotide.

As that nucleotide briefly sits inside the enzyme before incorporation, its fluorescent dye remains within the illuminated region of the ZMW.

The instrument records a short flash of coloured light.

Once incorporation occurs, the fluorescent label is released.

The light disappears.

Another nucleotide enters.

Another flash occurs.

By recording thousands of these flashes every second, the instrument reconstructs the DNA sequence one nucleotide at a time.

Unlike previous sequencing technologies, PacBio is literally watching DNA synthesis in real time.

But There Was Another Problem

Single-molecule sequencing was ground breaking.

Unfortunately, early versions were not particularly accurate.

Every sequencing technology makes occasional mistakes.

When only one molecule is observed, random errors become much more noticeable.

PacBio needed a way to improve accuracy without sacrificing long read lengths.

The solution was surprisingly clever.

Instead of reading the DNA molecule once...

they decided to read it again.

And again.

Circular Consensus Sequencing

PacBio converts each DNA fragment into a circle before sequencing.

Special DNA adapters are attached to both ends of the fragment, creating a circular molecule known as a SMRTbell template.

Because the DNA is circular, DNA polymerase simply keeps moving around the same insert multiple times.

Imagine proofreading the same sentence repeatedly.

If you read it once, you might miss a typo.

If you read it ten times, mistakes become much easier to identify.

PacBio applies exactly the same principle.

Each pass around the circular DNA generates another observation of the same sequence.

The instrument combines all these observations into a single consensus sequence.

This approach became known as Circular Consensus Sequencing (CCS).

The resulting reads are called HiFi reads because they combine long read lengths with extremely high accuracy, often exceeding 99.9%.

Today, HiFi sequencing is one of PacBio's defining strengths.

Reading More Than Just DNA Sequence

PacBio's polymerase provides another useful source of information.

DNA polymerase does not move at exactly the same speed across every DNA molecule.

Certain chemical modifications, particularly DNA methylation, cause the polymerase to hesitate slightly before incorporating the next nucleotide.

These subtle changes in incorporation timing can be measured.

Although PacBio is primarily a sequencing platform, it can also detect several DNA modifications by analysing polymerase kinetics.

The Strengths of PacBio

PacBio rapidly became one of the preferred technologies for applications requiring extremely accurate long reads.

Researchers use it for:

High-quality genome assembly
Structural variant detection
Sequencing difficult genomic regions
Full-length transcript sequencing
Haplotype phasing
Clinical research requiring highly accurate long reads

Its biggest strength is simple.

Few sequencing technologies produce reads that are simultaneously long and exceptionally accurate.

Oxford Nanopore Asked a Completely Different Question

While PacBio was perfecting fluorescent sequencing, another group of scientists was thinking very differently.

They asked:

Why copy DNA at all?

After all, DNA already contains the information.

Perhaps the molecule itself could simply be read directly.

This became the foundation of Oxford Nanopore sequencing.

Instead of watching DNA polymerase build a copy, Oxford Nanopore measures the original DNA molecule itself.

What Is a Nanopore?

A nanopore is exactly what its name suggests.

It is an extremely tiny pore only a few nanometres wide.

The pore is formed by a protein embedded within an artificial membrane.

An electrical voltage is applied across the membrane.

This creates a flow of ions through the nanopore, producing a steady electrical current.

Initially, the current remains constant.

Then DNA enters the pore.

Everything changes.

DNA Interrupts the Electrical Current

DNA carries a negative charge because of its phosphate backbone.

When a DNA molecule enters the nanopore, it partially blocks the movement of ions.

The electrical current immediately changes.

Importantly, different combinations of DNA bases obstruct the pore differently.

The nanopore is actually sensing several neighbouring bases simultaneously rather than one nucleotide at a time.

Each group of bases produces its own characteristic electrical signature.

The sequencing instrument continuously records these tiny changes in current thousands of times every second.

Controlling the Speed

At first glance this sounds simple.

But there was another problem.

DNA moves far too quickly.

If allowed to pass freely through the nanopore, the molecule would move so rapidly that meaningful measurements would be impossible.

Oxford Nanopore solved this using another biological enzyme.

A specialised motor protein grabs the DNA and feeds it through the nanopore one small step at a time.

This slows DNA movement sufficiently for the electrical signal to be measured accurately.

Without the motor protein, nanopore sequencing would not work.

Turning Electrical Signals into DNA Sequence

Unlike PacBio, Oxford Nanopore never observes fluorescent light.

Instead, it records one long electrical signal.

The challenge becomes interpreting that signal.

Sophisticated machine learning algorithms analyse the changing current and determine which DNA bases most likely produced each electrical pattern.

This computational process is known as basecalling.

As sequencing chemistry and artificial intelligence have improved, nanopore sequencing accuracy has increased dramatically.

Reading Native DNA and RNA

One of Oxford Nanopore's biggest advantages is that the DNA molecule does not need to be copied.

The original molecule passes directly through the nanopore.

This means researchers can sequence native DNA.

Even more remarkably, Oxford Nanopore can also sequence native RNA directly.

Most sequencing technologies require RNA to be converted into complementary DNA (cDNA) before sequencing.

Nanopore sequencing can often bypass this step entirely.

Detecting DNA Modifications

Because Oxford Nanopore measures the physical properties of the DNA molecule itself, chemical modifications alter the electrical current.

This means methylated DNA produces a different signal from unmethylated DNA.

Researchers can therefore identify many DNA modifications directly during sequencing without requiring additional chemical treatments.

This has made nanopore sequencing particularly valuable for epigenetics research.

Ultra-Long Reads

Perhaps the most famous feature of Oxford Nanopore sequencing is its read length.

In theory, the nanopore does not limit how long a DNA molecule can be.

As long as high-quality DNA can be extracted without breaking, the molecule can continue passing through the pore.

Researchers have generated sequencing reads exceeding one million base pairs in length.

These ultra-long reads are invaluable for assembling highly repetitive genomes that were previously impossible to resolve.

The Strengths of Oxford Nanopore

Oxford Nanopore has carved out a unique position in DNA sequencing.

Its major strengths include:

Ultra-long sequencing reads
Direct sequencing of native DNA
Direct sequencing of native RNA
Detection of DNA modifications
Portable sequencing instruments
Real-time data generation

Perhaps its most recognisable instrument is the MinION, a pocket-sized sequencer small enough to fit in the palm of your hand.

Researchers have used it in remote rainforests, during infectious disease outbreaks, aboard the International Space Station, and in field hospitals where traditional sequencing laboratories simply do not exist.

PacBio vs Oxford Nanopore

Although both technologies generate long reads, they solve the sequencing problem in fundamentally different ways.

PacBio watches DNA polymerase synthesise a new DNA strand.

Oxford Nanopore measures the original DNA molecule passing through a nanopore.

PacBio relies on fluorescent light.

Oxford Nanopore relies on electrical current.

PacBio obtains exceptional accuracy by repeatedly sequencing the same circular DNA molecule to generate HiFi consensus reads.

Oxford Nanopore achieves extraordinary read lengths because the DNA molecule itself passes continuously through the nanopore.

PacBio is generally preferred when the highest possible sequence accuracy is required.

Oxford Nanopore is often preferred when ultra-long reads, portability, direct RNA sequencing, or epigenetic analysis are the primary goals.

Neither technology is universally better.

Each was designed to solve a different problem.

The Future of Long-Read Sequencing

For many years, scientists believed they had to choose between long reads and accurate reads.

Today, that distinction is becoming less clear.

PacBio continues to improve the accuracy and throughput of HiFi sequencing.

Oxford Nanopore continues to improve its nanopore chemistry, pore design, motor proteins, and machine learning basecalling algorithms.

Both technologies are becoming faster, more accurate, and more affordable every year.

Together, they are allowing scientists to study regions of the genome that were previously inaccessible, discover structural variants that short-read sequencing often misses, characterise complex epigenetic modifications, assemble complete genomes with unprecedented accuracy, and even sequence DNA outside traditional laboratories.

The story of long-read sequencing reminds us that there is often more than one solution to the same scientific problem.

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