DNA Origami Design Processes

DNA Origami

• A field of structural DNA nanotechnology, started ~30 years ago, with pioneering research using DNA junctions and lattices
• A key advancement was the invention of DNA origami in 2006
• The origami method folds a long single-stranded DNA scaffold strand into a customized shape using short synthetic staples to bind the structure.

Design of Scaffolded DNA Origami

• Five phases involve two manual design steps and three program passes
  • Generation of a block diagram: A diagram is created to represent the intended structure, showing bases and turns
  • Generation of a folding path: Defines the order of the folding process for the origami structure
  • The following processes are also involved in specific phases, (listed below)

Design of Staple Strands

• Staple design lengths and turns are calculated for specified sections
• Data is calculated and summarized for different sections of the design

Refinement of Helical Domain Lengths

• Crossovers along the edges of the shape are adjusted to minimize strain
• Twist computations of scaffold crossovers change to minimize strain. Staple sequences then recalculated

Breaking and merging of strands

• The illustration shows how strands are adjusted

One-pot Reaction

• A method involves ~200-250 staple and remainder strands + scaffold annealed from 95°C to 20°C in a PCR machine for ~2 hours
• AFM (atomic force microscopy) imaging displays the final results

Design of Three-Dimensional DNA Origami

• Illustrative image of the process

caDNAno Software

• Slice panel: displays the x-y cross-section view of the honeycomb helix lattice, with helices represented as circles
• Path panel: tool for nucleotide-level editing of the scaffold and staple-path connectivity
• Render panel: shows a real-time, 3D cylinder model, visualized during the shape construction

Further Scaffold Design

• Short stretches of the scaffold are inserted into the panel as helices
• The path panel edits tools create continuous paths for scaffolds

Staple Paths

• Staple paths are created for scaffold areas based on an algorithm that follows crossover spacing rules
• Editing for satisfactory arrangement using "Add Sequence" tool and user-defined DNA
• Exportable 3D model with double helices as cylinders

Role of DNA Origami in Cancer Therapy

• DNA origami as a biocompatible drug delivery system (Qiao Jiang, et al 2012)
• Doxorubicin-loaded origami structures effectively internalized into tumor cells. (Qian Zhang, et al 2014)
• M13 DNA, triangle, tube, and square DNA origami structures characterized as potentially useful for carriers

DNA Origami as Drug Delivery Vehicle

• DNA origami nanostructures as biocompatible carriers for drugs. (Qiao Jiang, et al 2012)
• Triangle origami displays optimal tumor accumulation; others also studied. (Qian Zhang, et al 2014)

Biodistribution in Tumor Model

• M13 DNA and three DNA origami shapes with equivalent quantum dots incorporated
• Triangle origami showed optimal tumor accumulation
• Fluorescence signals (Triangle > Square > Tube)
• Fluorescence signals for free QD and QD-M13 DNA were weak within tumor sites

Additional Applications

• DNA structures for siRNA (small interfering RNA) delivery and CpG-triggered immunostimulation
• Rectangular DNA origami coated with virus capsid proteins for delivery of proteins
• Virus-inspired membrane-encapsulated spherical DNA origami for reducing immune activation, increasing bioavailability.
• DNA origami ion channels for cell membrane insertion.

Conclusion

• Transition from platonic structures to nano-objects with predefined tasks is fast using DNA origami
• DNA-based nanostructures are advantageous in therapeutics and other applications due to biocompatibility and biodegradability.
• Modularity allows precise control over object size, shape, and positions of modifications
• Superior adjustable properties enable straightforward characterization(labeling/bioimaging), targeting, and releasing features for delivery.

###Other Notable Points

• drug loading and distribution methods: DOX (doxorubicin) within tissues, origami loading and accumulation in tumor sites, drug release surrounding blood vessels

Explore the intricate world of DNA origami and learn about the design processes involved in creating customized structures. This quiz covers the phases of scaffolded DNA origami, including scaffold design, staple strand design, and refinement of helical domains. Test your understanding of this innovative field of structural DNA nanotechnology.