peng yin - massachusetts institute of technologycba.mit.edu/events/13.03.scifab/yin.pdfa b d c b a c...
TRANSCRIPT
Nano-assembly
Peng Yin
Department of Systems Biology, Harvard Medical School
Wyss Institute for Biologically Inspired Engineering, Harvard University
March 7th, 2013
The Science of Digital Fabrication Workshop
A B
D C
B
A
C D
Digital fabrication with DNA
Same color denotes complementary segments
Simple Robust Designable
N.C. Seeman, J. Theor. Biol., 1982
DNA nano-structures
1D tubes
3-helix bundle
TX-tube
6-helix bundle
4x4 tube DX tube
single-strandDX-like tubes
(Liu, Park, Reif & LaBean 04)
(He, Chen, Liu,Ribbe & Mao 05)
(Park, Barish, Li, Reif,Finkelstein,Yan & LaBean 05)
(Rothemund, Ekani-Nkodo, Papadakis, Kumar,
Fygenson & Winfree 04)
…(Mathieu, Liao, Kopatsch,Wang, Mao & Seeman 05)
Chiral DX tube
(Mitchell, Harris, Malo, Bath &Turberfield 04)
(Yan, Park, Finkelstein,Reif & LaBean 03)
1D ribbons
(Schulman, Winfree, 06)
Zigzag ribbonNano-trackRhombus ribbon
…
(Mao, Sun & Seeman, 1999)
(Park, Yin, Liu, Reif LaBean & Yan 05)
TX ribbon
(Li, Park, Reif, LaBean, Yan 03)
3D
(Shih, Quispe & Joyce 04)
(Goodman, Schaap, Tardin, Erben, Berry, Schmidt & Turberfield 05)
TetrahedronOctahedron
…
Algorithmic latticeSierpinsky triangle Counting/copying
(Rothemund, Papadakis& Winfree 04)
(Barish, Rothemund & Winfree 05)
Barcode lattice
(Yan, LaBean, Feng & Reif 03)
…
triangle lattice
2D latticesDX lattice TX lattice 4x4 lattices
hexagonal lattice 3 point-star lattices symmetry lattice
Rhombus lattice
(Mao, Sun & Seeman 99)
(Winfree, Liu, Wenzler & Seeman 98)
(LaBean, Yan, Kopatsch, Liu, Winfree, Reif, & Seeman 00)
(Liu, Wang, Deng, Walulu & Mao 04) (He, Tian, Chen, Deng,
Ribbe & Mao 05)
(He, Chen, Liu,Ribbe & Mao 05)
HJ lattice
(Malo, Mitchell, Venien-Bryan, Harris,Wille,
Sherratt & Turberfield 05)
(Reishus, Shaw, Brun,Chelyapov & Adleman 05)
DDX lattice
(Chelyapov, Brun, Gopalkrishnan, Reishus, Shaw & Adleman 04)
(Yan, Park, Finkelstein,Reif & LaBean 03)
(Rothemund 05)
SAO lattice
(Rothemund 06)
Origami
(Rothemund 06)
Rapid prototyping with
DNA bricks
Y. Ke, L. Ong, W. Shih, P. Yin, Science, 338:1177-1183, 2012 Yin lab @ Harvard
Building 3D structures with DNA bricks
Y. Ke, L. Ong, W. Shih, P. Yin, Science, 338:1177-1183, 2012 Yin lab @ Harvard
Yin lab @ Harvard
Scaling up
Hierarchical assembly
Yan lab @ ASU
Zhao Zhao , Yan Liu *, and Hao Yan * Nano Lett., 2011
100 nm
NanoAssembler: iterative, solid phase synthesis of geometry
Slide credit: Charles Fracchia Gershenfeld lab @ MIT
Scaffolds for functional materials
Fluorescent barcodes for multiplexed imaging
Lin, Jungmann, Leifer, Li, Levner, Church, Shih* & Yin*, Nature Chemistry 4:832 (2012)
Fluorophores
Church, Shih, Yin labs @ Harvard
Fluorophores
SM Douglas, I Bachelet, GM Church (2012) Science. 335:831
DNA “nanorobot” for targeted delivery
Proteins
Church lab @ Harvard
Proteins
Anton Kuzyk et al, Nature 483, 311, 2012
Chiral gold arrays for “Carving light”
Liedl lab @ LMU
Gold particles
Gold particles
DNA to
inorganic
3D nano-printing with DNA bricks
Scaffolds for functional materials Digital fab of inorganic nano-structures
Scaling up
Digital fabrication of functional nano-structures with DNA
Digital fabrication by nature: Genome for a whale
Digital fabrication by us: Genome for a computer?
“Grow” a computer using DNA?
ATGGTGAGCAAGGGCGCCGAGCTGTTCACCGGCATCGTGCCCATCCTGATCGAGCTGAATGGCGATGTGAATGGCCACAAGTTCAGCGTGAGCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCTGTGCCCTGGCCCACCCTGGTGACCACCCTGAGCTACGGCGTGCAGTGCTTCTCACGCTACCCCGATCACATGAAGCAGCACGACTTCTTCAAGAGCGCCATGCCTGAGGGCTACATCCAGGAGCGCACCATCTTCTTCGAGGATGACGGCAACTACAAGTCGCGCGCCGAGGTGAAGTTCGAGGGCGATACCCTGGTGAATCGCATCGAGCTGACCGGCACCGATTTCAAGGAGGATGGCAACATCCTGGGCAATAAGATGGAGTACAACTACAACGCCCACAATGTGTACATCATGACCGACAAGGCCAAGAATGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGATGGCAGCGTGCAGCTGGCCGACCACTACCAGCAGAATACCCCCATCGGCGATGGCCCTGTGCTGCTGCCCGATAACCACTACCTGTCCACCCAGAGCGCCCTGTCCAAGGACCCCAACGAGAAGCGCGATCACATGATCTACTTCGGCTTCGTGACCGCCGCCGCCATCACCCACGGCATGGATGAGCTGTAC
Acknowledgements
molecular-systems.net
Wyss Institute for Biologically Inspired Engineering
Office of Naval ResearchYoung Investigator Program Award
& Biomat. and Bionanotech. Program
National Institute of Health Director’s New Innovator Award
NIGMS
Defense Advanced Research Projects Agency
Young Faculty AwardLiving Foundries
National Science FoundationFaculty CAREER Award
CISE
Army Research OfficeBiochemistry
Molecular Systems Lab at Harvard