MOLECULAr PROGRAMMINg. Luca Cardelli Microsoft Research Lab Tutorial
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1 MOLECULAr PROGRAMMINg Luca Cardelli Microsoft Research Lab Tutorial
2 Smaller and Smaller Dec. 23, John Bardeen and Walter Brattain show the first working transistor. September Jack Kilby builds the first integrated circuit. Jan 30, Intel and Micron announce 25nm NAND flash. Dec. 24, Working transistor made of a single molecule. The race is on for molecular scale integrated circuits. Observation of molecular orbital gating. Nature, 2009; 462 (7276): 1039 Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotechnology 4, (2009).
3 Building The Smallest Things How do we build structures that are by definition smaller than your tools? Basic answer: you can t. Structures (and tools) should build themselves! By programmed self-assembly.
4 Molecular IKEA Nature can self-assemble. Can we? Dear IKEA, please send me a chest of drawers that assembles itself. We need a magical material where the pieces are pre-programmed to fit into to each other. Add water At the molecular scale many such materials exist; let s pick one
5 DNA GC Base Pair Guanine-Cytosine TA Base Pair Thymine-Adenine Interactive DNA Tutorial ( Sequence of Base Pairs (GACT alphabet)
6 ssdna Double-stranded DNA Single-stranded DNA has an orientation Each strand spells a GACT sequence The two strands have opposite orientations
7 Robust, and Long DNA in each human cell: o 3 billion base pairs o 2 meters long, 2nm thick o folded into a 6µm ball o 750 MegaBytes A huge amount for a cell o Every time a cell replicates it has to copy 2 meters of DNA reliably. o To get a feeling for the scale disparity, compute: DNA in human body o 10 trillion cells o 133 Astronomical Units long o 7.5 OctaBytes DNA in human population o 20 million light years long DNA wrapping into chromosomes Andromeda Galaxy 2.5 million light years
8 Zipping Along DNA can support structural and computational complexity. DNA replication in real time In Humans: 50 nucleotides/second Whole genome in a few hours (with parallel processing) In Bacteria: 1000 nucleotides/second (higher error rate) DNA transcription in real time RNA polymerase II: base/second Drew Berry
9 Nanoscale Engineering Sensing o Reacting to forces o Binding to molecules Actuating o Releasing molecules o Producing forces Constructing o Chassis o Growth Computing o Signal Processing o Decision Making Constructing Sensing Computing Actuating Nucleic Acids (DNA/RNA) can do all this, and interface to biological structures.
10 Hybridization
11 Sensing Computing Constructing Actuating Hybridization Tricks
12 Sensing Computing Constructing Actuating Constructing
13 Crosslinking
14 Crosslinking
15 Crosslinking
16 Crosslinking
17 Crosslinking In nature, crosslinking is deadly (blocks DNA replication). In engineering, crosslinking is the key to using DNA as a construction material.
18 DNA Tiling 4 sticky ends crosslinking
19 2D DNA Lattices Chengde Mao Purdue University, USA N-point Stars
20 3D DNA Structures Ned Seeman NYU 3D Cyrstal AndrewTuberfield Oxford Tetrahedron
21 CADnano
22 CADnano William Shih Harvard S.M. Douglas, H. Dietz, T. Liedl, B. Högberg, F. Graf and W. M. Shih Self-assembly of DNA into nanoscale three-dimensional shapes, Nature (2009)
23 DNA Origami Folding long (7000bp) naturally occurring (viral) ssdna By lots of short staple strands that constrain it PWK Rothemund, Nature 440, 297 (2006) Black: long viral strand Color: short staple strands
24 DNA Origami Paul Rothemund s Disc with three holes (2006) This means we can already selfassemble meso-scale structures. Paul W K Rothemund California Institute of Technology
25 DNA Circuit Boards DNA-wrapped nanotubes European Nanoelectronics Initiative Advisory Council "What we are really making are tiny DNA circuit boards that will be used to assemble other components." --Greg Wallraff, IBM
26 Sensing Computing Constructing Actuating Sensing
27 Aptamers Artificially eveloved DNA molecules that stick to anything you like (highly selectively).
28 Pathogen Spotlights DNA aptamer binds to: o A) a pathogen o B) a molecule our immune system already hates and immediately removes (eats) along with anything attached to it Result: instant immunity o Mice poisoned with Anthrax plus aptamer (100% survival) o Mice poinsoned with Anthrax (not so good) Kary Mullis (incidentally, also Nobel prize for inventing the Polymerase Chain Reaction)
29 Sensing Computing Constructing Actuating Computing
30 Rules of the Game Short complementary segments hybridize reversibly Long complementary segments hybridize irreversibly
31 DNA Strand Displacement Short strand (toehold): reversible binding Long strand (body): irreversible binding Input Output Gate Random collision/ breakup Random walk Entropy gain
32 Failed Strand Displacement What if the input does not match the gate?
33 Failed Strand Displacement
34 Failed Strand Displacement
35 Failed Strand Displacement?
36 Failed Strand Displacement
37 Failed Strand Displacement
38 Failed Strand Displacement Hence an incorrect binding will undo o That s why toeholds must bind reversibly Matching depends on the long segment only o Strand displacement succeeds iff the whole long segment matches o The address space is determined by the size of the long segment, which is unbounded (not by the size of the toehold) o The toehold is just a cache of the address
39 What does DNA Compute? Electronics has electrons o All electrons are the same: you can only count them o Few electrons = False; lots of electrons = True o But Boolean Logic is only a necessary evil to build symbolic computation DNA computing has symbols (DNA words) o DNA words are not all the same o Symbolic computation on abstract signals can be done directly o Signals are presented concurrently (in a soup) o No requirement to do Boolean Logic Then, what are our gates (if not Boolean?) o Theory of Concurrency o Process Algebra as the Boolean Algebra of DNA Computing
40 Signals A signal is the representation of an abstract event o E.g. generated by a sensor o E.g. accepted by an effector o We are not limited to true/false 3-domain signals o x h : hystory (ignore) o x t : toehold (binding) o x b : body (recognition) Signals (single stranded DNA) are prepared by (artificial) DNA synthesis
41 Gates Double-stranded structures with free toeholds Gates are prepared by self-assembly from singlestranded DNA that is synthesized
42 Fork Gate x y + z x y + 0 transform x to y (transducer) x x + y linear production of y (catalyst) x x + x exponential production of x (amplifier)
43 Fork Gate This is the Fork Gate structure
44 Fork Gate
45 Fork Gate
46 Fork Gate
47 Fork Gate
48 Fork Gate
49 Fork Gate
50 Fork Gate
51 Fork Gate
52 Fork Gate
53 Fork Gate
54 Fork Gate This is Waste
55 x + y z Join Gate
56 Join Gate This is the Join Gate structure
57 Join Gate
58 Join Gate
59 Join Gate
60 Join Gate
61 Join Gate
62 Join Gate
63 Join Gate
64 Join Gate
65 Join Gate
66 Join Gate
67 Join Gate
68 Join Gate
69 Join Gate
70 Join Gate
71 Join Gate This is Waste
72 Strand Algebra Join + Fork + Populations = Petri Nets Join Fork
73 Gate Design Verification Active garbage o The active join residuals slow down the performance of following joins. o Add a garbage collector to remove the active residuals. Interference between gates o The join garbage collector interferes with the fork gate. o Modify the fork gate to remove the interference. What else could go wrong? o Endless possibilities. o Prove that the fork/join gate structures correctly implement fork/join in all larger circuits.
74 Sensing Computing Constructing Actuating Actuating
75 Hybridization Chain Reaction
76 Polymerization Motor Rickettsia (spotted fever)
77 Sensing Computing Constructing Actuating Curing
78 A Doctor in Each Cell
79 DNA Compilation
80 Compilers Language Design #1 Language Design #2 Language Design #3 Boolean Networks Petri Nets Monolithic Compilers Language Implementation #1 Language Implementation #2 Language Implementation #3
81 Intermediate Languages Boolean Networks Petri Nets Front End Back End Intermediate Language Strand Algebra The algebra of fork and join gates
82 Front Ends Boolean Networks Petri Nets Front End Circuit Design Intermediate Language Strand Algebra Intermediate Language #2
83 Back Ends Intermediate Language Strand Algebra Back End Gate Design 4-domain Signals 3-domain Signals 2-domain Signals Device Design
84 The Actual Tutorial (The Back End Work)
85 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: the program directive sample directive plot sum(<_ T^ xb>); sum(<_ T^ yb>); sum(<_ T^ zb>) def scaling = 1000 def bind = /(float_of_int scaling) (* /nm/s *) (* =3*10^5 /M/s *) def unbind = (* /s *) new T@bind,unbind def F1x2(N,Xb,Yb,Zb) = new a ( N * T^:[Xb T^]<Yb>:[a T^]<Zb> N * <T^ a T^> ) ( F1x2(10*scaling,xb,yb,zb) (1*scaling)* <xh T^ xb> )
86 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: the structures x y + z gate x input
87 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: the reactions x input y output z output
88 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: the reaction graph x input y output z output
89 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: the behavior x input y output z output
90 Gates to Structures Visual DSD (Andrew Phillips) o A tool for exploring, e.g., gate designs Fork gate: check Ok, I want this
91 Structures to Sequences Input Structure Output Sequences Ok, I want these
92 Sequences to DNA Oligonucleotide Synthesis Your Chance to Win a Nintendo Wii
93 Experiments
94 How are they Actually Done? Postdoc Faculty
95 Web Order
96 Wait 24 Hours
97 DNA by Mail
98 Spec Sheet
99 Add Water
100 Put DNA into Gel Polyacrylamide gel electrophoresis (PAGE) Sorts DNA strands by length
101 Wait 6 Hours
102 Get DNA out of Gel Find DNA with ultraviolet light. Cut it out. too long just right too short
103 Wait 12 Hours
104 Mix DNA Up Screaming for robotic automation
105 Spectrofluorometer Fluorescence is your print statement Windows XP
106 Go To Lunch
107 Execution Trace
108 Core Dump
109 Repeat
110 Health and Safety Don t try this at home o (Although you could) Latex gloves, UV glasses o Fear the Gel (acrylamide) o Fear the Light (UV) Otherwise safe o No smells o No fires o No biohazards o No life forms Most complex machines: o Gel machine o Fluorometer o Atomic force microscope Most dangerous activity: o Replacing the light bulb in the fluorometer (hot; may explode) Not wearing glasses Not wearing gloves
111 Acknowledgments Illustrations o John Reif, Duke o Ned Seeman, NYU o Erik Winfree, Caltech o Bernard Yurke, Boise State o Wikipedia o YouTube David Soloveichik
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