DNA Origami Design Processes
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Questions and Answers

What was the first three-dimensional DNA origami structure designed?

  • A sphere with a diameter of 30 nm
  • A cube with a side length of approximately 40 nm (correct)
  • A tetrahedron with each edge measuring 40 nm
  • A pyramid with a base of 50 nm

    • Which feature of the caDNAno program allows for visualization of the DNA origami shape in three dimensions?

  • Slice panel
  • Path panel
  • Auto-staple button
  • Render model (correct)

    • What is one of the main challenges in constructing three-dimensional DNA origami?

  • Minimizing the size to below 20 nm
  • Designing structures that are only two-dimensional
  • Ensuring staple strands hold the structure at correct angles (correct)
  • The requirement for complex scaffolding materials

    • In cancer therapy, how are DNA origami structures used?

    <p>As a biocompatible drug carrier system</p> Signup and view all the answers

    Which DNA origami shape was found to have optimal tumor passive targeting accumulation?

    <p>Triangle DNA origami</p> Signup and view all the answers

    What is doxorubicin primarily used for in the context of DNA origami?

    <p>Chemotherapy drug delivery</p> Signup and view all the answers

    What is the main purpose of staple strands in DNA origami?

    <p>They hold the scaffold strand in its designed position.</p> Signup and view all the answers

    What was incorporated into M13 DNA and three DNA origami shapes in the breast tumor model study?

    <p>Quantum dots</p> Signup and view all the answers

    How long was the annealing process conducted in a PCR machine?

    <p>Approximately 2 hours</p> Signup and view all the answers

    In the design of DNA origami, which phase involves adjusting crossovers to minimize strain?

    <p>Refinement of the helical domain lengths</p> Signup and view all the answers

    Which of the following best describes the folding path in DNA origami?

    <p>It represents the sequence of moves the scaffold strand follows to form the shape.</p> Signup and view all the answers

    What is the typical length of a scaffold strand used in DNA origami?

    <p>7,243 nucleotides long</p> Signup and view all the answers

    How are the staple strands designed to interact with the scaffold strand?

    <p>They are complementary to the scaffold strand sequences.</p> Signup and view all the answers

    What happens during the breaking and merging of strands phase?

    <p>The stability of the structure is improved or its flexibility is enhanced.</p> Signup and view all the answers

    What role did Ned Seeman play in the development of DNA nanotechnology?

    <p>He conducted groundbreaking research on DNA junctions and lattices.</p> Signup and view all the answers

    What does the honeycomb crystal lattice represent in the design process?

    <p>The spatial arrangement of the scaffold strand.</p> Signup and view all the answers

    What primary benefit does DOX/origami offer in drug delivery within tumor regions?

    <p>It enables controlled drug release in the tumor region.</p> Signup and view all the answers

    Which characteristic of DNA origami makes it advantageous over other nanosized systems?

    <p>Intrinsic biocompatibility and biodegradability.</p> Signup and view all the answers

    Where was the accumulation of doxorubicin observed in the treated groups?

    <p>At the tumor sites primarily surrounding blood vessels.</p> Signup and view all the answers

    Which application is NOT mentioned for DNA structures?

    <p>Triggering selective apoptosis in mitochondria.</p> Signup and view all the answers

    What is a significant challenge that DOX/origami helps to overcome during drug delivery?

    <p>Rapid nonspecific distribution of doxorubicin.</p> Signup and view all the answers

    How has the development of DNA origami structures impacted health sciences?

    <p>Led to significant advancements in drug delivery systems.</p> Signup and view all the answers

    What feature of DNA nanostructures facilitates their characterization?

    <p>Precise control of modifications at a nanometer scale.</p> Signup and view all the answers

    Which property of DNA origami allows it to enhance pharmacokinetic bioavailability?

    <p>Incorporation of virus-inspired design elements.</p> Signup and view all the answers

    Study Notes

    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

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    Related Documents

    DNA Origami PDF

    Description

    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.

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