Biocurious is a weblog about biology, quantified.

DNA Lego

by Andre on 21 February 2006

One of the sessions this morning was called Structure by Design: Single Proteins to Nanostructure and for once, the nano reference was appropriate. The first talk described great work on designing nanoscale patterns and functional structures out of nucleic acids.

Nadrian Seeman from NYU has a long history of building with DNA and covered a lot of ground today. In its most basic form, his group’s research involves designing artificial DNA sequences that will self assemble in controlled ways. Their two most basic building units are stable asymmetric Holliday junctions and complementary overhanging sticky ends. Base pairing does the rest. They aren’t just making DNA scaffolds and passive nanopatterns though, they’re also making functional (albeit slow and fragile) nanomachines. A little over a year ago they reported a DNA nanomachine that can function as a kind of ribosome for making specific sequences of subunits (each of which is made of another helical DNA structure that they call a double cross over). Here’s a nanotech web article about there work where I got this picture of the device:

I’ve thought about trying to get into the DNA nanostructures game before and his talk was helping to motivate me until he mentioned that he “burned through” three grad students that unsuccessfully tried to make a 2D triangular pattern out of DNA until a fourth group member succeeded. That’s when I came to my senses! Future grad students beware: large groups that regularly produce high profile papers can afford to “burn through” a few students on the way. It’s not necessarily a bad situation to be in, but you should be careful. Don’t get burned.

  1. Uncle Al    4017 days ago    #

    DNA is amenable to accurate, extended, spontaneously ordering lattice formation. DNA bases can be replaced with a wide variety of complimentary chemistries that interact via hydrogen bonding or hydrophobic bonding.

    1) Why build discrete DNA constructs to do biology? Why not 2-D areal constructs for circuitry or 3-D lattices for photonics? 50-1500 nm is a very nice scale range for DNA construction

    2) William A. Little (Stanford) and excitonic high temp superconductors,

    Phys. Rev. A 134 1416 (1964)
    Phys. Rev. B 13 4766 (1976)

    Replace phonons (characterized by Debye temperature) with excitons possessing characteristic energies around 2 eV or 23,000 K. Exciton-mediated electron pairing suggests superconductor Tc’s of 500 K even under weak coupling conditions.

    Little’s structure was a conjugated polymer chain (polyene) bearing polarizable chromophore side groups. The polyene chain (e.g., polyacetylene) would be a normal metal with a single mobile electron per C-H molecular unit; electrons on separate units couple by interacting with the side groups’ (C-H to C-R) exciton field.

    When proposed in the 1970s this was safely beyond chemical synthesis. Now it can be realized as solid phase synthesis (and then maybe PCR to make buckets of the stuff) of DNA or especially peptide nucleic acids, followed by backbone modification as desirable. Biological bases would be replaced with laser dyes (coumarins are especially adaptable to hydrogen bonding requirements) or merely planar (derivatized) aromatics (hydrophobic stacking; anthraquinone and annelated vat dyes, indanthrene dyes).

    A repeated chromophore along the chain would beget a high temp supercon. A chromophore redox gradient would be a supercon diode. A Y-junction would be a supercon transistor.

    Uncle Al will kickstart the project: R is the chromophore,


    then Grubbs’ olefin metathesis to extrude H2C=CH2. This is undergrad lab synthesis. Gel permation chromatography to isolate narrow oligomer cuts. The terminal olefins go to sulfur for Au film bonding.

  2. Bill Tozier    4011 days ago    #

    Make sure you have a close look at Thom LaBean’s work with programmable self-assembled DNA lattices.

    The meshes are amazing.

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