DNA Origami Boosts Rapid Test Sensitivity: Diagnostics Breakthrough!

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What if we could increase rapid test’s sensitivity 125 times? Today, we see how: with DNA origami!

Let’s dive right in.

Better Diagnostics with DNA Origami

You know what’s convenient? A rapid test. We all learnt it in 2020, when they confirmed our paranoia: that running nose was, indeed, COVID. These simple paper-based devices are examples of lateral flow essays. They can detect a target substance (usually a protein or an hormone) without the need for expensive equipment, so they are simple, cheap, and fast. This makes them perfect for use in diagnostics at home, at the point of care, and in the lab. But they have a problem: they’re not always sensitive enough.

How Rapid Tests Work, Simplified

Here is a simple breakdown of how a rapid test works, being for COVID or a pregnancy test:

1. You apply the sample to one end of a test strip, sometimes with an additional buffer.

2. The sample flows through a pad with labeled antibodies. If the target is present, the antibodies will bind to it!

3. The sample moves to the test line. If present, the target-antibodies complex will get captured by immobilized antibodies, forming a visible line.

4. Further down the strip, a control line capture any excess labeled antibodies, confirming that the test ran properly.

Easy peasy. But there is the problem: these tests are simply unable to detect important, low-abundance biomarkers. Think:

• Cardiac troponin I (cTnI): A key indicator for cardiovascular diseases.

• Neurofilament light chain (NfL): A marker for neurodegenerative diseases.

And detecting low amounts of biomarkers is important for early diagnosis! For these, methods like ELISA or PCR are used, but they are a lot more time-consuming and expensive.

But why the low sensitivity? Simple: multiple detection antibodies are bound to a single label. Fewer labels equals a weaker signal: hence the low sensitivity!

So, to summarize. Rapid tests: fast, cheap, convenient. Also, not sensitive enough.

DNA Origami for the Save

The authors of today’s paper decided to address this gap, using my favorite technique: DNA origami.

DNA origami is the most used method to create DNA nanostructures. A long single-stranded DNA (ssDNA) scaffold is folded into shape using short “staple” DNA strands, creating amazing structures at the nanoscale! DNA origami allows to place molecules with nanoscale precision: antibodies, fluorophores, nanoparticles, anything you want. Just slap some ssDNA on and you’re done.

The team focused on this ability to massively amplify signal output in lateral flow essay test: up to 125-fold enhancement! But let’s start from the beginning.

The authors used a six-helix bundle (6HB) DNA origami structure, almost 500 nm long and 8 nm in diameter. This 6HB acts a molecular scaffold, with:

1. Two Binding Domains:

   On both ends, the DNA structure has 3 ssDNA overhangs, for a total of six hybridization sites. These are used to attach antibodies or analyte-binding oligonucleotides!

2. Central Amplification Domain:

   The central part of the structure contains up to 180 single stranded overhangs! Each one of them can bind to signal-generating units, like:

   • DNA-fluorophores conjugates

   • DA-AuNPs (40 nm gold nanoparticles)

This modularity allows the team to tune the recognition and signal domains independently. This makes it easy to swap target or detection system!

Implementing in Rapid Tests

The team implemented this innovative amplification system into a conventional lateral flow assays setup:

1. Sample containing the target biomarker is added.

2. A detection antibody, modified with a DNA oligo, binds the analyte.

3. The 6HB DNA origami binds the DNA-tagged antibody via complementary overhangs.

4. Signal oligonucleotides or labeled DNA–AuNPs hybridize to the central domain.

5. The origami-analyte complex flows and binds to the capture antibody on the test line.

The authors also fine-tuned the ratios of 6HB:antibody:label and determined that low excesses of labels worked best, keeping costs low (more on that later!).

Results: 125x Fluorescence Increase!

So, we now arrive at the best part: did it work? Well, judge for yourself.

After the classic agarose gel + electron microscopy characterization (6HB are always funny, they are just so long and thin), the researchers tested the performance of their system. And the results were stunning.

1. Fluorescent Readout:

   They compared the performance of the DNA origami system with standard fluorophore-labeled antibodies. There was no contest: the DNA origami system showed up to 125-fold increase in fluorescence! And the limit of detection was reduced to 35 ng/L, making it clinically relevant!

2. Colorimetric Readout (Gold Nanoparticles):

   The researchers also used a test based on gold nanoparticles, which are convenient because the color change can be detected with the naked eye.
   Here, the limit of detection increase 55 times, and there was a clear, distinguishable band after just 10 minutes!

The researchers tested their system on the biomarkers for cTnI and NfL in different medium:

• Saliva

• Serum

• Synthetic matrix (PBS + BSA)

Their results were consistent across these 3, showing the robustness and versatility of the DNA-origami addition.

Final Thoughts: Promises and Price!

Such a great work! DNA nanotech is super cool, but there are still very few commercial applications, especially when it comes to life science. So it’s great to see a solution leveraging DNA origami’s capacity for precision positioning to create an impactful solution.

And one that is economically viable, in addition. The authors calculated that the DNA origami only adds a cent to the cost of the materials. It might even make the tests cheaper: the biggest cost is the antibodies, and this solution minimizes that.

I enjoyed this paper! But don’t take my word for it: go and read it for yourself here!

Thank you for making it this far! What do you think about this paper? Do you have other ideas for use of DNA origami? Reply and let me know!

More Room:

• Designer DNA origami crystals: DNA crystals are super cool. How to make them even cooler? Make them dynamic, of course. This study presents a DNA origami-based unary system that self-assembles into crystals and shifts between phases using external DNA and ion triggers, enabling precise, controllable nanomaterial fabrication.

• Making DNA G-Wires: G quadruplex are interesting 3D DNA structures, formed using 4 Gs. They have electrical properties and high stability, but until today it was hard to make long strands. This study presents an optimized method for forming long G-quadruplex DNA nanowires (G-wires) from short guanine-rich strands. By fine-tuning conditions, the team achieved micrometer-scale G-wires. Interesting for nanoelectronics maybe?

• AlphaFold for DNA? I love AI-based protein design. Is the time to bring it to DNA nanotech? This paper shows how AlphaFold 3 can improve the design of complex DNA nanostructures by predicting difficult structural elements. Instead of relying on trial-and-error, the authors demonstrate a more efficient modeling approach, helping advance applications in nanomedicine, biosensing, and nanotechnology. Are RNA structures next?

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