DNA Nanofabrication: A New Method of Construction
DNA nanofabrication functions on quite an intuitive premise — to use DNA a building material to build nanoscale constructs.
On of the main goals of DNA nano-technology is to build self-assembling objects of ever increasing complexity. It seems like other-wordly bizarre magic at first — how do you “program” DNA into creating these complex structures?
The answer is surprisingly simple: DNA base pairing.
We often discuss DNA in the context of its role in the Central Dogma — with it’s role as an information repository for the genetic code. We’re going to ignore all of that in this article and focus on something entirely different!
There are 3 key properties of DNA which allow this mechanism to function:
- Double-stranded DNA ladder with anti-parallel strands (i.e. DNA strands running in opposite directions)
- Right-handed twist with 10.5 bpt
- Complementary base pairing of purine & pyrimidine bases via Hydrogen bonding (A-T, C-G)
Base per turn: The given number of base pairs within one helical turn
Genesis
The field was borne out of a slightly odd idea from crystallographer, Ned Seeman. Inspired by a woodcut by MC Eshcer, he postulated that the fish in the image with 3 orthogonal axes, arranged periodically in 3D were analogous to molecules in a crystalline structure. In fact, these fish could be replaced by DNA Holliday Junctions, with their contacts being programmed by through the specificity of its sticky ends.
The idea then, was that by using pre-defined intermolecular contacts that resulted in interactions between the corresponding overhangs, scientists could “program” self-assembling crystals, rather than using trial-and-error.
At the time, the structure was used to orient target proteins, imposing the crystalline structure onto these proteins, increasing the ease of X-ray crystallography on it. However, in the decades since, the field has continued to blossom into exploring the potential complexities and permutations of this incredible technology.
Experimentation
To take it one step further, DNA origami works by using long template strand — the scaffold — and shorter oligonucleotide segments — staple strands. The mechanism uses the scaffold as a backbone, onto which oligonucleotides can base-pair & hybridise, causing it to fold in specific sections. Adjacent DNA helices are joint through Holliday junctions, resulting in the parallel array of these helices.
Incredibly, the structures achieved are often also the most stable, as the predictability of complementary base-pairing & its programmability means that the scaffold & DNA strands are likely to self — assemble into its lowest energy state.
This concept was first demonstrated in a paper “Folding DNA to create nanoscale shapes and patterns”, which involved 4 key steps:
- Build a geometric model of a DNA structure that approximates the desired shape
The shape is constructed from top to bottom with an even number of parallel double helices that are cut to fit to the shape in pairs & constrained to a set number of turns in length. At the same time, they’re held together by an array of crossovers which dictate the positions at which staple strands along one helix cross-over to an adjacent one!
2. Folding a single long scaffold strand back and forth in a pattern so it makes up one of the two strands in every helix
3. Designing complementary “sample strands”
The geometric model is inputted as a “lists” of DNA lengths, along with the DNA sequence of the actual scaffold used into a computer programme. In turn, it outputs the complements for the scaffold and creates the appropriate crossovers in these strands.
4. Readjusting configuration
Due to the crossovers created & the asymmetrical nature of the double helix, the twist of the scaffold crossovers are recalibrated & their position is changed to minimise strain, recomputing staple sequences accordingly.
Scaffold strands can also act as molecular breadboards, allowing us to engineer surface features onto scaffold strands, that manifest in bumps, enabling the patterning of 2-D structures like this!
To combine these different 2D-shapes together, scientists used “extended staples” that connected these shapes along their edges, by merging and breaking original staples along their edges.
To create assemble square lattices meanwhile, we’ve realised that we can underwind DNA (creating additional helical turns per base pairs in a counter-clockwise direction) by 10.67 bp. Consequently, the global structure compensates for this with a clockwise supertwist.
Up to this point, the structures we’ve built have remained relatively simple and small. If we do plan on approaching the end-goal of building increasingly complex self-assembling structures, we have to consider the question: How do we build larger structures?
One answer is constructing wireframes with a high strength to weight ratio (a material’s strength divided by its density)
Take a look at this 3-D wire-framed Icosahedron.
Each strut — a linear rod — is made up of a 6-helix DNA nanotube. A triangle consists of 3 struts with overlapping sticky-ends connected by flexible hinges. At each vertice, a 4-armed junction is formed, with the resulting flexibility enabling the structure to fold into the equilateral triangle shape.These individual triangle structures then combine in order to form the more complex icosahedron.
Another interesting example are floating compression structures.
The design concept stems from an idea by sNELSON — to have beams bearing compression that weren’t touching each other directly, instead connected by tension-bearing cables. Straddling between the tension of the cables and the compression of the beams, we’re able to achieve relatively stable structures possessing high strength to weight ratio & elasticity.
Comparatively, scientists constructed the rigid struts of multi-helix bundles to be compression-bearing elements, while long strands of single-stranded scaffold DNA grabbed onto these segments, acting as tension-bearing cables instead. Ultimately, this formed
Rigid struts of multi-helix bundles (??) are used as compression-bearing elements, while long sections of single-stranded scaffold DNA act as tension-bearing cables, creating these complex 3D structures.
Another interesting strategy used is to create curved helices. Up to this point, DNA helices have been largely straight, so this offers a really interesting means of reconfiguration! It’s really simple — we just need 1 DNA strand to contain less base pairs than the other. Mechanically, this means that both strands will be under tension, with the longer strand experiencing compression and the shorter one being stretched out. To relieve this tension, the DNA helix will bend, and has been shown to bend up to 180degrees, comparable to DNA helices around a histones in a nucleosome! The only difference is nature’s mechanism relied on protein-DNA interactions, while this relies on equally pliableDNA base pairing interactions.
Conclusion
While still relatively nascent, DNA nanofabrication presents itself as an incredibly interesting way for us to engineer biology, as we continue to strive towards the formation of increasingly complex self-assembling structures!
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Hey, I’m Sarrah Rose! A 17 year old deeply passionate in utilising Synthetic Biology & Artificial Intelligence to solve major problems in the world today. If you enjoyed this article or would just like to chat, I’d love to hear from you:
