DNA Computing and Robotics:

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Presentation transcript:

DNA Computing and Robotics: Engineering (Science?), Fun, and Applications Milan N. Stojanovic NSF Center for Molecular Cybernetics Department of Medicine Columbia University

Suppose we have a set of primitives: Sensor primitives: Computing primitives: Moving primitives:

Recipe for Computing Primitives: Beacons (Tyagi and Kramer) 1. Take Recognition Regions, 2. Take Nucleic acid catalysts, Phosphodiesterase (Joyce) E S Ligase (Szostak) E S1 S2 3. And combine (for computing elements, at least) them in: Cf. modular design (e.g. Breaker…)

Logic Gates: YES (Detector or Sensor Gate) 50000 100000 150000 200000 250000 100 200 300 400 t (min) FU Stojanovic et al., ChemBioChem 2001 Stojanovic et al., J. Am. Chem. Soc. 2002 Joyce 1995, Breaker 1999, Tyagi, Kramer 1996

Switching Primitives (Logic Gates): NOT AND Three-input Gates

Some demonstrations of molecular computing: A. Full adder (Lederman et. al, Biochem. 2006) B. Maya-II (Macdonald et al. Nano Lett. 2006) 11 × 01 = 11 × 10 = 11 × 11 = (3×1=3) (3×2=6) (3×3=9) 01 × 01 = (1×1=1) 01 × 10 = (1×2=2) C. DNA Calculator (Macdonald) D. AND Hub with Beads (Rudchenko) (Yashin et al. JACS ~2007)

Implementation of Naughts-and-Crosses Playing Algorithm with Deoxiribozymes: Molecular Array of YES and ANDANDNOT Gates (MAYA) Stojanovic, Stefanovic, Nat. Biotech. 2003

MAYA vs. Milan: Losing Game

The Simplest Moving Primitive:

But, what about multivalent design? Pei et. al JACS, 2006

AFM Images of Spider at Starting Point Kyle Lund, Hao Yan, video now: with Nadine Dabby, Erik Winfree

AFM images of Spider on Lanes of Substrates Kyle Lund, Hao Yan Video with: Nadine Dabby, Erik Winfree

Center for Molecular Cybernetics Phase II?

Center Members & Friends Erik Winfree (CS) Hao Yan (CHE) Niles Pierce (ApM) Paul Krapivsky (Phys) Sergei Rudchenko (BPh) Nils Walter (CHE) Milan Mrksich (CHE) Darko Stefanovic (CS/EE) Milan Stojanovic (MEDSci) Nadrian Seeman (CHE) Henry Hess (CHE/MATS) William Shih (CHE) Srboljub Mijailovich (ME) Natasha Yonoska (MATH) Satoshi Murata (CS/ME) Friedrich Simmel (P-CHE) Vojislav Stojkovic (CS) Qiao Lin (ME) Paul Rothemund (CHE/CS) CHE 0533096 CHE 0533096 Chemical Bonding Center NSF (CHE-0533096)

Acknowledgments: Postdocs: Steven Taylor, Renjun Pei, Dmitry Kolpashchikov, Joanne Macdonald Tech’s: Stanka Semova, Erik Green, Payal Pallavi, Ma Li High Shool Program: Harvey Lederman, Yang Lee, Marko Sutovic, Kiran Pendri, Wengho Lu, Kirill Lebedov, Srikanth Damera, George Lederman, Kaitlin Kyi. Tiffany Elizabeth Mitchell Collaborators: Sergei Rudchenko (HSS), Ruslan Yashin Darko Stefanovic (UNM), Mark Olah Nils Walter (UM, Ann Arbor), Tony Manzo, Chamaree De Silva Vincent Butler (Columbia) Milan Mrksich (Chicago), Haim Tsubery Erik Winfree (Caltech), Georg Seelig, Nadine Dabby Hao Yan (ASU), Kyle Lund Current funding NSF (ITR, 3xEMT, and CBC), JDRF, NIH (NCI-R21) Lymphoma and Leukemia Society Scholarship Previously: NASA, NSF QuBIC, NSF Biophotonics, NIH (NIBIB), Searle

Potential practical applications: 1. Cell-death by Boolean Calculations: 2. Glucose-triggered movement of catalytic nanoassemblies: