The miniaturization, top-down ‘‘sizeshrinking’’

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

• Beads are immobilized on array of discrete optical traps

• Optical tweezers to move the traps closer to trigger DNA hybridization

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.