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DNA Computing and Robotics Using DNAymes :

DNA Computing and Robotics Using DNAymes :. Milan N. Stojanovic NSF Center for Molecular Cybernetics Department of Medicine Columbia University. Engineering (Science?), Fun, and Applications. Joyce 1995, 1997. Introduction to deoxyribozymes:. Single stranded DNA (or RNA). Complementary.

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DNA Computing and Robotics Using DNAymes :

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

  2. Joyce 1995, 1997 Introduction to deoxyribozymes: Single stranded DNA (or RNA) Complementary

  3. Before we give examples of gates, a reminder: 1 is an increase in fluorescence, 0 no such increase!

  4. A bit more about FRET: Cleavage

  5. 250000 200000 150000 FU 100000 50000 0 0 100 200 300 400 t (min) Catalytic Molecular Beacons as Sensor Gates Detector Stojanovic et al., ChemBioChem 2001 Stojanovic et al., J. Am. Chem. Soc. 2002 Joyce 1995, Breaker 1999, Tyagi, Kramer 1996

  6. Introduction to deoxyribozymes II: Joyce 1995, 1997

  7. …and we can combine them with stem loops: S

  8. …into a two-state switch: Detector gate or sensor or YES gate or …

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

  10. i3 Complete set of switches: NOT Gate: AND Gate: ANDANDNOT:

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

  12. 200000 150000 100000 FU 50000 0 0 100 200 300 t(min) NOT Gates – Inverters: Stojanovic et al., J. Am. Chem. Soc. 2002

  13. FU t(min) Dual Input Molecular Computation Elements: AND Gate

  14. Triple Input Elements: ANDANDNOT (INHIBIT)

  15. Triple Input Elements: ANDAND Harvey Lederman

  16. Before we give examples of gates, a reminder: 1 is an increase in fluorescence, 0 no such increase!

  17. A + X = O 0 1 0 0 1 2 1 01 00 01 00 00 01 10 GR GR GR i1 i2 Let’s add A (0 or 1) and X (0 or 1) and get O (0 or 1, or 2):

  18. Is it possible to have serial circuits? (Upstream enzyme) (downstream enzyme)

  19. Intergate Communication : Ligase-Cleavase Stanka Semova, Dmitry Kolpashchikov

  20. XOR IA O IB Ligase-cleaves XOR circuit: JACS 2005

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

  22. 10 01 2 1 Implement addition with gates: Stojanovic & Stefanovic, J. Am. Chem. Soc. 2003

  23. 1 Now, a twist: 1 is an increase in fluorescence, 0 no such increase!

  24. Segments required d1 d2 d3 d4 d5 d6 d7 d8 d9 Here is 7-segment display: J. Macdonald, Columbia University

  25. Binary inputs Non general Display output A1 A0 + X1 X0 1+1: 0 1 + 0 1 = 1+2: 0 1 + 1 0 = 2+1: 1 0 + 0 1 = 2+2: 1 0 + 1 0 = More arithmetical operations: Test by constructing simple 2+2-bit adder Expected display Adder result “hard-wired” into decoder Designate 4 oligonucleotides as binary inputs J. Macdonald, Columbia University

  26. Adding 2+2 with visual display: • Determine logic gates required, and layout in wells (via Microsoft Excel) • Very simple logic gate arrangement required: • 4 YES gates • 2 AND gates • Fully constructible from reagents in freezer • Tested with all input combinations…. J. Macdonald, Columbia University

  27. Adding 2+2 with visual display: (A1A0 + X1X0 display) 01+01= 01+10= 10+01= 10+10= Binary inputs: No inputs Perfect digital behavior Constructed & tested in a single day Fluorescence reader ~20-30mins 7-segment Display B&W imager within ~1hr Color photograph ~5hrs (1+1=2) Arithmetic (2+1=3) (1+2=3) (2+2=4) Background J. Macdonald, Columbia University; DNA 13, 2007

  28. 2x2 multiplier with visual display: (A1A0× X1X0 display) Gate arrangement 19 gates required J. Macdonald, Columbia University

  29. 2x2 multiplier with visual display: (A1A0× X1X0 display) Color photography Binary inputs: 01 × 01 = 01 × 10 = 01 × 11 = 10 × 01 = 10 × 10 = 7-segment Display Arithmetic (1×1=1) (1×2=2) (1×3=3) (2×1=2) (2×2=4) Binary inputs: 10 × 11 = 11 × 01 = 11 × 10 = 11 × 11 = (00 × 00) 7-segment Display Arithmetic (2×3=6) (3×1=3) (3×2=6) (3×3=9) no input control J. Macdonald, Columbia University

  30. Implementation of tic-tac-toe playing algorithm with deoxiribozymes: Molecular Array of YES and ANDANDNOT Gates (MAYA) Stojanovic, Stefanovic, Nat. Biotech. 2003

  31. MAYA vs. Milan: Losing Game

  32. MAYA vs. Milan: losing game Mg2+ From Sci. Am. 2008

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

  34. The Simplest Moving Primitive:

  35. But, what about multivalent design? => Molecular Spider [Pei et. al JACS, 2006] R Pei, S Taylor, D Stefanovic, S Rudchenko, T Mitchell, M Stojanovic, Behavior of Poly- catalytic Assemblies in a Substrate-displaying Matrix, Journal of the American Chemical Society, vol. 128, no. 39, pp. 12693-12699, 2006.

  36. Molecular Spider [Pei et. al JACS, 2006] Molecular spider performing biased random walk. Diffusion of a multi-pedal DNA walker (spider) on a 2D substrate. The legs form duplexes - double stranded links - to the complementary strands in the surface. One of the duplexes is cleaved and the leg explores the surrounding surface forming another duplex at another position. If the leg binds to a position already visited, its stay there is brief as it 'remembers' the process; for new positions, the cleavage takes longer. By repeating this process the walker moves along the surface independently. At the end of the track the walker binds to uncleavable DNA strands and stops. 

  37. Molecular Spider [Pei et. al JACS, 2006] • Molecular spider performing biased random walk. • Diffusion of a multi-pedal DNA walker (spider) on a 2D substrate. • Body of spider is a molecule of streptavidin, and • The 4 legs are DNAzyme molecules attached to the body. • The spiders crawls a surface by attaching and detaching from RNA substrates via DNAzyme. • Leg attachment occurs via DNA-RNA hybridization while the detachment is via the catalytic restriction of the RNA stator by the DNAzyme followed by spontaneous denaturation from short strands due to entropic effects. • Once a leg detaches from a substrate it binds (with high probability) to a new substrate and the process continues. • The spider is biased towards binding unvisited substrates.

  38. Molecular Spider [Pei et. al JACS, 2006] Molecular spider performing biased random walk. Diffusion of a multi-pedal DNA walker (spider) on a 2D substrate.

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

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

  41. Programming Spider Walking Paths

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

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