The miniaturization, top-down ‘‘sizeshrinking’’


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The miniaturization, top-down ‘‘sizeshrinking’’

  • The miniaturization, top-down ‘‘sizeshrinking’’

    • microelectronics technology
    • pushing down the limits of size and
    • compactness of components and devices
  • The nanofabrication and nanomanipulation bottom-up

    • molecular nanotechnology
    • of novel nanolevel materials and methods
    • (e.g., near-field scanning microscopies) to
    • electrical devices built on carbon nanotubes
    • optical devices like optical sieves (69).
  • The supramolecular self-organization approach

    • complexity through self-processing,
    • self-fabrication by controlled assembly & hierarchical growth
    • connected operational systems


An example of a reciprocal exchange: Two DNA helices are connected by sharing two DNA strands (Seeman, 2001)

  • An example of a reciprocal exchange: Two DNA helices are connected by sharing two DNA strands (Seeman, 2001)



Size: Ø of 1nm for ssDNA and Ø 2nm for dsDNA

  • Size: Ø of 1nm for ssDNA and Ø 2nm for dsDNA

  • Chemical stability and robustness

  • Production costs for synthesis are low

  • Self-assembly properties







Specific and reversible aggregation of micro-beads grafted with oligonucleotides

  • Specific and reversible aggregation of micro-beads grafted with oligonucleotides

  • The key to reversibility is preventing the particles from falling into their van der Waals well at close distances



Trick is: create a Uminimum well outside UvdW well

  • Trick is: create a Uminimum well outside UvdW well

  • Balancing finely Urep and Udna

  • Limiting the number of base-pair bonds between two cDNAs





Beads are immobilized on array of discrete optical traps



Micro-beads manipulated with optical tweezers

  • Micro-beads manipulated with optical tweezers

  • Two types of DNA hybrids: “flexi” and “rigid”



For identical Tm (43.7¤C), “rigid” spacer gives stronger U well

  • For identical Tm (43.7¤C), “rigid” spacer gives stronger U well



DNA density of 14000 molecules / sphere lead to unstructured aggregates

  • DNA density of 14000 molecules / sphere lead to unstructured aggregates

  • DNA density of 3700 molecules / sphere lead to self-assembled crystallites





Any type of ss or dsDNA secondary structure can be exploited to create geometric shapes by self-assembly

  • Any type of ss or dsDNA secondary structure can be exploited to create geometric shapes by self-assembly

  • Typically, junctions and sticky-ends are exploited for this purpose





























Molecular Electronics:

  • Molecular Electronics:

    • Layout of molecular electronic circuit components on DNA tiling arrays.
  • DNA Chips:

    • ultra compact annealing arrays.
  • X-ray Crystallography:

    • Capture proteins in regular 3D DNA arrays.
  • Molecular Robotics:

    • Manipulation of molecules using molecular motor devices arranged on DNA tiling arrays.
















In nano-electronics designs: possibility to self-assemble proteins on DNA grid

  • In nano-electronics designs: possibility to self-assemble proteins on DNA grid

  • Nano-electronics components







Tiling Self-assembly can:

  • Tiling Self-assembly can:

    • Provide arbitrarily complex assemblies using only a small number of component tiles.
    • Execute computation, using tiles that specify individual steps of the computation.
  • Computation by DNA tiling lattices:

    • Fist proposed by Winfree (1998)
    • First experimentally demonstrated by Mao, et al (2000) and N.C. Seeman (2000).




DNA computing (Adleman, 1994)

  • DNA computing (Adleman, 1994)

  • Theory of tilings (Grunbaum and Sheppard, 1986)

  • DNA nanotechnology (Seeman, 2003).





Only tiles with binding strength > 2 bonds will bind

  • Only tiles with binding strength > 2 bonds will bind



Ultra Scale: each ”processor” is a molecule.

  • Ultra Scale: each ”processor” is a molecule.

  • Massively Parallel: number of elements could be 1018 to 1020

  • High Speed: perhaps 1015 operations per second.

  • Low Energy:

    • example calculation ~10-19 Joules/op.
    • electronic computers ~10-9 Joules/op.
  • Existing Biotechnology: well tested recombinant DNA techniques.



Many Laboratory Steps Required:

  • Many Laboratory Steps Required:

    • is very much reduced by Self-Assembly !
  • Error Control is Difficult:

    • may use a number of methods for error-resilient Self-Assembly


Bounds on error rates of self-assembly reactions:

  • Bounds on error rates of self-assembly reactions:

    • No complete studies yet.
    • Non-computational assemblies appear to be less error-prone.
  • Methods that may Minimize Errors in self-assembly:

    • Annealing Temperature Variation.
    • Improved Sequence Specificity of DNA Annealing.
    • Step-wise Assembly versus Free Assembly.
    • Use of DNA Lattices as a Reactive Substrate for Error Repair.



























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