DNA Nanobiotechnology Flashcards
Main 6 nanoproblems
-Viscosity (Surface area of 1 cm3 of a single cube compared to 1 cm3 of 1nm cubes has 10,000,000x more SA so more friction. Modelling a small bacteria in water use a robot in syrup)
-Diffusion (diffusion is not effective over 30 micrometres so something that far is unreachable for a 1 micron bead, limiting and enabling)
-Power stroke (asymmetry needed (screws are best) as shown in the model bacteria in syrup )
-Stickiness (intermolecular forces can be huge and the relative size of friction increases, Surface area of 1 cm3 of a single cube compared to 1 cm3 of 1nm cubes has 10,000,000x more SA)
-Brownian motion (constant buffeting everything unpredictably in all directions)
-Pertinent design (devices that work above 1 micrometre in size may not if made smaller)
-Need to consider that different forces are dominant on nano scale: electrostatic forces and an der Waals (ex. ants can hold a tiny drop of water in hands cause surface tension dominates. Humans can’t since gravity dominates.)
What is DNA nanotechnology
The use of DNA (a polymer in the nano scale in size; along with viruses, proteins, actin bundles, etc) to solve problems in biomedicine and research.
Can utilise the fact we can transcribe DNA in vitro and read the sequences
Nanotechnology is 1nm – 100 nm
Examples of nanotechnology in biological processes
All dependent on Brownian motion (random movement for small particles due to collision with other small molecules) is prevalent and is the basis of lots of biological processes (can find out forces driving interactions by changing temperature or chemical interface with PTM in chemical computing):
Molecular recognition/all interations (ex. antibody binding, Watson-Crick base pairing, etc. increasing velocity of all particles drives weak binding since it brings them together)
Chemical computing (an experimental computer that relies on chemistry instead of hardware to store and move data, for example working much like a brain or bodies)
Biomineralisation to control where silica is deposited, or potassium/calcium phosphate is deposited in bones (through diffusion. Also ions aggregate and are nucleation sites for bone formation)
Protein gel/collagen formation (collide and aggregate into networks)
Virus particle formation
self assembly (self- hybridisation of DNA for example) as energy of sticky forces must dominate Brownian motion
Conformational transitions (since the proteins aren’t stiff;)
Describe why DNA can be applied in technology
Can exploit lots of the properties DNA have for use in technology:
Sticky: has sticky ends so can apply to beads (silica, etc) to conjugate chemical groups on. Due to complementary Watson-Crick base pairing)
Nucleus of cell where DNA is acts as a mechanosensor and is limiting when cell tries to squeeze between things (why cancer cells have a less stiff nucleus to aid metastasis)
DNA in rod cells rearranges its organisation to aid eyesight and increases sensitivity (ex. evolutionary aids see predators)
DNA aids NETtosis in neutrophils. DNA is expelled and forms extracellular structures (NETs) that trap pathogens to immobilise.
Due to the nano scale, different forces are dominant. Electrostatic forces and Van der Waals are dominant on nano scale (ex. ants can hold a tiny drop of water in hands cause surface tension dominates. Humans can’t since gravity dominates.)
How to make DNA for use in biotechnology
Manipulate chemistry of DNA can cause large changes:
RNA (one less oxide on its ribose sugar compared to deoxyribose sugar) is a lot more flexible and can create more shapes (ex. tRNA) than DNA (stable and long-lasting) so can utilise it’s more properties too.
Stiffness: Single strand of DNA is less stiff than double strand
Uses of different nanotechnologies outside biotechnology
-DNA:
Store data by assigning code meaning to A, T, G, and C and their strings and construct DNA. Too much data in the world and computer chips aren’t sufficient to store all. Have already encoded a play by Shakespeare and the Watson Crick paper discovering the shape of DNA onto DNA.
Benefit of DNA over current technology for computer data storage (discs and USB drives): quicker production time, and by orders of magnitude better in storage time (before degrading), amount of data that can be storge in a unit space, and
DNA hairpin loop with a fluorophore on both ends. When in hairpin the 2 are close enough that FRET occurs, so one absorbs light and emits it at larger wavelength/lower energy which the other absorbs and emits light at an even larger wavelength/lower energy. When denatured and separate, the emission of the first is detected and the second is not stimulated.
Use to signal changes in pH, heat (thermometer) and ionic interactions
-Nanotechnology as Particles:
Sunscreen: titanium oxide nanoparticles block UV. Previously used a dye that penetrates skin
Quantum dots (ex. conjugate with Ab, nucleic acid, etc to use as fluorescent probe for in vivo imaging)
MRI contrast agents (iron nanoparticles)
How DNA constructs are formed
-In top-down assembly manipulate and produce DNA cut down from larger DNA constructs:
Method: Electron beam lithography to etch designs onto materials then use light (UV or X-ray) to copy that design onto other materials (faster than electrons) before placing on specific DNA strands in the specific areas.
Atomic force microscopy to use a small sharp tip to ‘write’ nanoscale features
Different areas will bind different things
Result: Can make template/scaffold for DNA origami for strands will attach to specific surface patterns
AFM to image DNA origami or physically move them
Cons: Expensive large machines needed (in a very clean room with suit. machine in clean, vacuum area that people don’t enter)
Pros: Cheap
-In bottom-up assembly (potentially hard to scale up), use small biomolecule building blocks (nucleotides, etc) to create DNA constructs.
Uses: Make 3D and 2D constructs with specific shapes (alphabet, cubes, etc). In a beaker add DNA (scaffold strands) and staples (short DNA strands) and self-assembly occurs. (ex. cube for drug delivery).
Can image shapes with atomic force microscopy (run ruler over shape and it measures the dips. Image the shape row by row) or with cryo-EM (free constructs and see images of the different orientations. Use computer to group those similar and find average of each orientation. Join images together to construct the full 3D shape to atomic resolution)
Cons: May be hard to scale up (good for initial testing)
Pros: Cheaper, self-assembly based, can easily order DNA staples and sequences online nowadays (before had to design and construct each inddividual strand)
Natural biology that can be exploited for nanotechnology
Viral capsid as nanotemplate: hollow protein shell that can be loaded with drugs or other materials to be a nanocapsule/nanocarrier
