DNA Computing and Robotics:

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DNA Computing and Robotics

• Engineering (Science?), Fun, and Applications

Milan N. Stojanovic NSF Center for Molecular
Cybernetics Department of Medicine Columbia
University
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Suppose we have a set of primitives
Sensor primitives
Computing primitives
Moving primitives
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Recipe for Computing Primitives
2. Take Nucleic acid catalysts,
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Logic Gates YES (Detector or Sensor Gate)
Stojanovic et al., ChemBioChem 2001 Stojanovic
et al., J. Am. Chem. Soc. 2002
Joyce 1995, Breaker 1999, Tyagi, Kramer 1996
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Switching Primitives (Logic Gates)
NOT
AND
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Some demonstrations of molecular computing
A. Full adder (Lederman et. al, Biochem. 2006)
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Implementation of Naughts-and-Crosses Playing
Algorithm with Deoxiribozymes Molecular Array
of YES and ANDANDNOT Gates (MAYA)
Stojanovic, Stefanovic, Nat. Biotech. 2003
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MAYA vs. Milan Losing Game
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The Simplest Moving Primitive
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But, what about multivalent design?
Pei et. al JACS, 2006
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AFM Images of Spider at Starting Point
Kyle Lund, Hao Yan, video now with Nadine Dabby,
Erik Winfree
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AFM images of Spider on Lanes of Substrates
Kyle Lund, Hao Yan
Video with Nadine Dabby, Erik Winfree
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Center for Molecular Cybernetics Phase II?
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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)
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Acknowledgments

• Postdocs Steven Taylor, Renjun Pei, Dmitry
  Kolpashchikov, Joanne Macdonald
• Techs 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

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