Programming Molecules Anne Condon U. British Columbia 100 nm Paul Rothemund, 2006
Programming Molecules Anne Condon, U. British Columbia
Programming Molecules | outline motivation principles experimental successes C G theory A T open questions closing thoughts
Programming Molecules | principles sequence secondary structure folding pathway C G A T
Programming Molecules | principles C G T C G secondary structure: set of A-T T C G T or C-G pairs of a sequence (or C G A G sequences) A A T roughly speaking, the more A base pairs, the more stable (low energy) the structure C C C C G A G A A A G T T T T G G
Programming Molecules | principles B A secondary structure: set of A-T or C-G pairs of a sequence (or sequences) C D roughly speaking, the more base pairs, the more stable (low energy) the structure A B C D
Programming Molecules | principles folding pathway : a sequence of secondary structures that strands assume as they change from one structure to another folding is a stochastic process; at each step one base pair forms or breaks folding process is biased to favour low energy barrier pathways Kinefold Web Server
Programming Molecules | principles folding pathway : a sequence of secondary structures that strands assume as they change from one structure to another folding is a stochastic process; at each step one base pair forms or breaks folding process is biased to favour low energy barrier pathways Kinefold Web Server
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles toehold-mediated DNA strand displacement (DSD) Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles from chemical reactions to DSDs ⇌ B A ( ) ( ) waste byproduct auxiliary reactant transformer molecules Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles from chemical reactions to DSDs ⇌ C + D A + B this is a little tricky: C and D should be produced only if both A and B are present transformer molecules are needed Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles from chemical reactions to DSDs ⇌ C + D A + B this is a little tricky: C and D should be produced only if both A and B are present transformer molecules are needed Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles from chemical reactions to DSDs ⇌ C + D A + B this is a little tricky: C and D should be produced only if both A and B are present transformer molecules are needed Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles from chemical reactions to DSDs ⇌ C + D A + B this is a little tricky: C and D should be produced only if both A and B are present transformer molecules are needed Soloveichik, Seelig, Winfree PNAS 2010
⇋ Programming Molecules | principles from chemical reactions to DSDs 0 1 ⇋ 1 1 also doable if long domains (rather than toeholds) represent species Soloveichik, Seelig, Winfree PNAS 2010
⇋ Programming Molecules | principles from chemical reactions to DSDs Soloveichik, Seelig, Winfree PNAS 2010
⇋ Programming Molecules | principles from chemical reactions to DSDs from chemical reactions to DSDs Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | principles sequence secondary structures folding pathways C DSD’s are an energy-efficient (low- G A T barrier) way to convert one DNA species (type of molecule) to another from a programming perspective, this is a way to change the value of a variable
Programming Molecules | experimental successes tiles (double-crossover molecules) adhere to a growing assembly if glue strengths (sticky end lengths) are sufficiently strong A B C D Fu and Seeman, Biochemistry, 1993
Programming Molecules | experimental successes tiles (double-crossover molecules) adhere to a growing assembly if glue strengths (sticky end lengths) are sufficiently strong A B C D Fu and Seeman, Biochemistry, 1993
Programming Molecules | experimental successes DNA self assembly Winfree et al., Nature, 1998; Rothemund et al., Nature, 2004
Programming Molecules | experimental successes 3D structures Dietz, Douglas & Shih, Science, 2009
Programming Molecules | experimental successes DNA origami 100 nm • Short “staple” strands bring pieces of a long strand together, folding the long strand into a desired shape Dietz, Douglas & Shih, Science, 2009
Programming Molecules | experimental successes DNA walkers fuel walker has two “feet” Rothemund, Science 2004
Programming Molecules | experimental successes DNA walkers fuel fuel walker has two “feet” Rothemund, Science 2004
Programming Molecules | experimental successes DNA walkers fuel Rothemund, Science 2004
Programming Molecules | experimental successes DNA walkers fuel Rothemund, Science 2004
Programming Molecules | experimental successes DNA walkers fuel Rothemund, Science 2004
Programming Molecules | experimental successes circuit simulation A B C D E F Seelig et al., Science 2006
Programming Molecules | theory motivation principles experimental successes C G theory A T open questions closing thoughts
Programming Molecules | theory principles for describing, programming and analyzing DNA at different levels of abstraction new questions about the power and limits of (molecular) computing systems
Programming Molecules | theory case study: circuit simulation principles for describing, programming and analyzing DNA at different levels of abstraction new questions about the power and limits of (molecular) computing systems
Programming Molecules | theory case study: circuit simulation (1) express circuit as chemical reaction network (CRN) A A + B ⟶ C C B D ⟶ F D F E ⟶ F E Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | theory case study: circuit simulation (2) compile CRN into DSDs toehold-mediated (3) design DSD domain sequences Soloveichik, Seelig, Winfree PNAS 2010
Programming Molecules | theory case study: circuit simulation (1) (1) express circuit as CRN (2) compile CRN into DSD (3) design DSD domain sequences (4) plus more... debug, identify (2,3) systematic errors, develop error- correcting techniques ...
Programming Molecules | theory principles for describing, programming and analyzing DNA at different levels of abstraction new questions about the power and limits of (molecular) computing systems
Programming Molecules | theory can we write “volume-efficient” DNA programs? analogous to memory/space-efficient algorithms for example ... can we design a DSD that counts for 2^n steps using poly(n) strands/bases? (all of the previous examples use a number of strands that grows polynomially with the number of steps)
Programming Molecules | theory put another way... CRN and DSD programs can in principle do universal computations in an energy-efficient manner but CRN’s and DSD’s typically use a number of molecules that is proportional to the number of reactions. can DSD’s recycle strands to minimize volume?
Strand Recycling Example 3-bit Gray counter 0 0 0 0 0 1 0 1 1 0 1 0 1 1 0 1 1 1 1 0 1 1 0 0 Condon et al., DNA 2011
Strand Recycling Example deterministic CRN 3-bit Gray counter – The counter state is represented 0 0 0 by three of six signal molecules: 0 0 1 b3 b2 b1 (b=0,1) 0 1 1 – Initially the state is 03 02 01 0 1 0 1 1 0 1 1 1 1 0 1 1 0 0 Condon et al., DNA 2011
Strand Recycling Example deterministic CRN 3-bit Gray counter 0 0 0 0 0 1 0 1 1 0 1 0 1 1 0 1 1 1 1 0 1 1 0 0 Condon et al., DNA 2011
Strand Recycling Example deterministic CRN 3-bit Gray counter (1) 0 1 ⇋ 1 1 (2) 0 2 + 11 ⇋ 1 2 + 11 0 0 0 (3) 0 3 + 12 + 01 ⇋ 1 3 + 12 + 01 0 0 1 0 1 1 0 1 0 1 1 0 – The counter proceeds as a random 1 1 1 walk through the states in Gray code 1 0 1 order 1 0 0 Condon et al., DNA 2011
Strand Recycling Example deterministic CRN 3-bit Gray counter (1) 0 1 ⇋ 1 1 (2) 0 2 + 11 ⇋ 1 2 + 11 0 0 0 (1-for) (3) 0 3 + 12 + 01 ⇋ 1 3 + 12 + 01 0 0 1 (2-for) 0 1 1 (1-rev) 0 1 0 (3-for) 1 1 0 – The (atomic) reactions ensure that (1-for) 1 1 1 exactly one of 0i and 1i are present (2-rev) at any given time 1 0 1 (1-rev) 1 0 0 Condon et al., DNA 2011
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