DNA Box : 3D DNA Nanotechnology

Chemistry World is reporting that Danish researchers have made a nano-sized box out of DNA that can be locked or opened in response to ‘keys’ made from short strands of DNA. By changing the nature or number of these keys, it should be possible to use the boxes as sensors, drug delivery systems or even molecular computers.

To make the box shape, the team took a long, circular single strand of DNA from a virus that infects bacteria called bacteriophage M13. This M13 sequence is a cheap source of single-stranded DNA and is convenient size for building with. To turn this ring of DNA into a box, the team used a computer to work out exactly the right combination of short strands of complementary DNA which could ‘staple’ the appropriate areas of the ring together to get the desired box shape. When they mixed the M13 strand with the 220 short ‘staple strands’ and heated them up for an hour, the boxes neatly self-assembled.

Kjems reveals that the group have already had some success with putting cargo inside the boxes, including enzymes and quantum dots. ‘It’s quite big (about 30nm) inside – it could fit virus particles or quite big enzymes and other macromolecules.’ In terms of applications, Kjems can foresee three main purposes for the box: ‘One is as a calculator or logic gate; the second is for controlled release, for example of drugs, in response to external stimuli; and the last is as a sensor – where the thing you are sensing causes the box to open or close and give a readout.’

The DNA origami technique is quite straightforward, Mao comments, so could be applied to all sorts of similar structures. The fact that the box can be easily opened and closed also makes it ideal for moving guest molecules around. ‘I’m really looking forward to seeing what the group do next,’ he adds.

MIT Technology Review also has coverage.

Deoxyribose sugar cubes: Because complementary regions of DNA like to pair up, researchers were able to design a long strand of DNA that, combined with many tiny DNA staples, would automatically assemble itself into a nano-sized box. This technique is known as DNA origami. Here, the boxes were imaged using cryo-electron tomography to confirm their cubelike structures and hollow interior.
Credit: : Ebbe S. Andersen, Aarhus University

21 pages of supplemental information from the Journal Nature article.

The abstract in the journal Nature. [Nature 459, 73-76 (7 May 2009) | doi:10.1038/nature07971; Received 9 November 2008; Accepted 6 March 2009]
Self-assembly of a nanoscale DNA box with a controllable lid

The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach1. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 36 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.


The DNA origami design software program with documentation and tutorials is
available here: http://www.cdna.dk/origami/.

0 thoughts on “DNA Box : 3D DNA Nanotechnology”

  1. “Whether Israel attacks is in the end their choice.”

    If someone’s intent to kill you and all you hold dear is implacable, do you really have a choice?

    The US national interest would be against such an attack, as it will cost us dearly and decrease US security.” JPS

    Beyond the immediate cost of an attack on Iran, please explain how Iran gaining nukes is not a greater decrease in US Security?
    To do that, logically you must:

    Explain upon what premise you postulate that should Iran gain nukes it will not provide them to a radical Islamic terrorist group(s)?

    Also, upon what premise you postulate that if Iran did give nukes to terrorists, those terrorists would not use them against us?

    If you cannot do so, then logic compels you to agree that you have no rational basis for your opinion and acknowledge that your position is based in either willful denial or wishful thinking (another form of denial).

    If you cannot articulate why Iran is not a threat given their active support for terrorists and stated objectives and then Iran gains nukes, gives them to terrorists and they successfully use them, you are culpable in their use.

    Opinions matter because nations act on them and we all bear the responsibility for what we advocate.

  2. I wounder what would happen to all those Iranian centrifuges, if a bomb going off above gave them a sudden kinetic shock, even if the explosion itself doesn’t penetrate?

    Assuming they are storing a lot of kinetic energy, might they violently disintegrate?

    Even if only a few of them were to disintegrate, they are in close proximity and probably not adequately shielded from each other. Might it not trigger a (non-nuclear) chain reaction as shrapnel from one triggers another to disintegrate, etc?

    (Why do mouse-traps and ping-pong balls suddenly come to mind?)

    Or am I over-estimating how much kinetic energy is stored in them, versus how strongly built they are? Probably…

  3. Whether Israel attacks is in the end their choice. The US national interest would be against such an attack, as it will cost us dearly and decrease US security. Israel is not the fifty-first state.

    What to do?


  4. I believe Stratfor is the most reliable and credible source on geopolitical issues, and they don’t believe Israel will attack Iran.

    Israel has completely blown any chance of maintaining the element of surprise for an attack on Iran.

    Since the success of the Israeli attack on Iraq’s reactor depended greatly on the element of surprise, and because Iran is much more fortified than Iraq was, the odds are pretty low that Israel will go through with it.


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