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Hybridization
Melting
I-2. λ- and Synthetic- dsDNA
A. NATRAL Lambda dsDNA (1) Isolated from E. coli λ (cI857 S7) (2) Length: 48,502 base pairs ~16.5 μm (3) TM-AFM height: ~0.68 nm on air [experimentally known: 0.6 ± 0.2 nm, Antognozzi, M. D. et. al., J. Single Mol. 3, 105 (2002). ]
•
250nm x 250nm 500nm x 500nm
p(2x2 w/o outer arms)≈0.90
Demonstration of full addressability utilizing biotinlated loop-strands • ~70% of all 2x2 NMs are correctly addressed protein
• Three strand families: loop-strand, shells & arms
One step-annealing (high temp.) for 2x1 NM • cross-tile participation ratio of NxM NM, p(NxM) = (total # of tiles participating in NxM NM) divided by (total # of tiles) • p(2x1)≈0.81 Two step-annealing (high temp. for 1st and low temp. for 2nd step) for 2x2 NM • p(2x2 w/ outer arms)≈0.75
80nm x 80nm
Park, Ahn, Reif, and LaBean: Publication in preparation (2005)
• Four step-annealing for 4x4 NM
• 4x4 NM consisting of 16 fully addressable cross-10.5 2nm 0.34 nm 3.4 nm ~36 °
(b) Why DNA in NanoBioTechnology?
[1] Self-assembly: Massive and Parallel [2] Structuring Property with programmability: Molecular-scale building blocks with molecular-level recognition [3] Diverse attachment chemistry: Nanomaterial arrays (ex. nanoparticle, nanowires, CNT) with molecular level precision
Experimentally observed angles
Number of diagonal square 4 5 6 Diameter (D) : nm Width (W) : nm Intrinsic Angle ( θ) : Degree 36 30 26
40 48 57
62 76 89
200nm x 200nm
Significances of the Original Research Accomplishments
• Construction of Unique DNA motifs: 3HB and
• • •
cross-tile (also known as 4x4 tile) Demonstration of fixed-size & fully-addressable DNA nanomatrices Fabrication of silver nanowires templated on artificially designed 1D DNA nanostructures Construction of one of thinnest (~15 nm) metallic nanowires templated on DNA
I-5. NanoMatrix (NM)
• Stepwise assembly • Finite-size DNA nanostructure: Size
controllable • Templates for desired nanomaterial arrays: Fully addressable • ‘NxN’ NM
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Self-assembled DNA Nanostructures & DNA-templated Silver Nanowires
Sung Ha Park Department of Physics Duke University April, 13, 2005
a’
30nm x 30nm
a B. SYNTHETIC dsDNA (1) Unit length: 50 base pairs ~16.2 nm (2) CG concentration: 46% (3) After assembly: ~10 μm (4) TM-AFM height: ~1.13 nm under buffer [experimentally known: 1.2 ± 0.2 nm]
Gold nanoparticle (~5nm) attachment to Nanogrids using thiolated loop strands at the end of 3’
[5] Two tiles (A and B tiles): 1D Nanotrack
[6] Two tiles (A and B tiles): 1D Barbed wire
Thanks To:
• Members in DNA Nanotechnolgy Group in •
•
Computer Science: M. Yamamoto, H. Li, S.J. Ahn, P. Yin, L. Peng, and N. Johnson Members in Electronic Nanostructures Group in Physics: M. Prior, A. Makarovski H. Yan (ASU) and J. Liu (Duke, Chem)
2um x 2um
Courtesy: M. Yamamoto
[4] Two tiles (A and B tiles): 2D Nanogrid (Fully corrugated design)
150x150nm
Park, Yin, Reif, LaBean, and Yan: Nano Lett., in press (2005)
• p(4x4)≈0.20 which corresponds [p(1x2)]8≈ [0.81]8 ≈0.19
NxN NM
[1] Three distinct conditions (i) N = 2n, with n = 1, 2, 3 …, (ii) Utilizing two different cross- A and B tiles, and (iii) Using minimum number of the complementary sticky-ends sets. [2] For NxN NM; (i) total # of annealing steps: ntotal-step= [2 + 2(m - 1)] and (ii) total number of minimum required stick-ends strands,
3 HB

r
helix
≈18 x pdsDNA (50nm)≈0.9μm
* Rothemund, Ekani-Nkodo, Papadakis, Kumar, Fygenson, and Winfree: JACS, 126, 16344 (2004) Park, Barish, Li, Reif, Finkelstein, Yan, and LaBean: Nano Lett., in press (2005)
1D-3HB: Individual unit tiles with a length of ~16.5 nm (designed ~17.0nm) can be seen clearly (circled in blue)
I-4. Cross-tiles (also known as 4×4)
[1] One tile (A tile):1D Nanoribbon
2D-3HB: Upward-facing stripes sagging slightly lower to the substrate: (height of upward-facing stripes is ~2.5 nm and that of downward-facing stripes is 2.3 nm)
Gleb Finkelstein, Supervisor (Physics) Thomas H. LaBean, Co-supervisor (Computer Science) John H. Reif (Computer Science) Henry S. Greenside (Physics) Glenn S. Edwards (Physics)
So, Pnanoribbon ≈ 100μm
[2] One tile (A tile): 2D Nanogrid
Park, Yan, Reif, LaBean, and Finkelstein: Nanotechnology, 15, S525-S527 (2004)