1. DNA Computing on Surfaces
Anne Condon, Computer Science, UBC
Robert Corn, Chemistry, U. Wisconsin
Max Lagally, Materials Science, U. Wisconsin
Lloyd Smith, Chemistry, U. Wisconsin

2. Goals Encode information in DNA strands
(Adleman, Science 266:1994)
Encode information in DNA strands
Compute on many strands in parallel: chemical manipulations = logical operations

3. “…the number of of operations per second … would exceed that of current supercomputers by a thousandfold…remarkable energy efficiency… information density a dramatic improvement over existing storage media
Len Adleman, Science 266:1994

4. “for certain intrinsically complex problems…where
existing electronic computers are very inefficient and
where massively parallel searches can be organized to
take advantage of the operations that molecular biology
currently provides, molecular computation might
compete with electronic computation in the near term”

5. Outline Background DNA Computing on Surfaces Conclusions
What is computation? What is DNA?
DNA computation
Research on DNA computation
in the biotech industry
in the solution of combinatorial problems
Models
Experiments

6. What is Computation? (very simple view)
Input: string over finite alphabet
Process: determine if input satisfies
some property
Output: yes or no

7. Satisfy a Property: Binary Inputs
Output: 1
and
set the output of
a circuit to 1 1 or 1
and
not
Input: 1 1

8. Satisfy a Property: Non-binary InputsC
Output:
Set the output of a
generalized circuit to
a given value G T G A G C G

9. Simple Parallel Computation
Input: set of strings
Process: independently for each input,
determine if it satisfies a
common circuit
Output: indicate whether there exists an
input satisfying the circuit

10. What is DNA?

11. “DNA Computation:” Affymetrix Arrays
Input: strings over {A,C,G,T}, (represented as the corresponding single-stranded DNA)
Photolithography used to synthesize and array DNA strands on a planar surface

12. “DNA Computation:” Affymetrix Arrays
Process: e.g. for each input, test if it approximately matches a given string
(i.e. hybridizes to Watson-Crick complement of given string)

13. “DNA Computation:” Affymetrix Arrays
Output: fluorescence detection

14. Adleman’s Hamiltonian Path Experiment
Input: generate random paths
Process:
Output: “yes” iff path remains 2 1 3
select paths from S to T
select paths with 7 nodes
select paths entering all
nodes at least once 5 4 T

15. Generate Random Paths
Associate DNA strands with nodes and edges
Join edge strands in test tube to form double-stranded “paths” (hybridization, ligation)
Wash to form single-stranded paths 2 3 4 5

16. Adleman’s Experiment: Select Paths That Enter Node 2
Attach strand associated with node 2 to beads and introduce to test tube
The paths that enter node 2 hybridize to strands on the beads
Remove beads; wash and detach desired paths

17. Biomolecular Computation Research
“Classical” DNA/RNA computation
(e.g. search-and-prune)
O(1)-biostep computation
(e.g. self-assembly of 3-D DNA molecules)

18. Biomolecular Computation Research
Splicing-based computation
Non-computational applications
(e.g. exquisite detection, DNA2DNA computation, DNA nanotechnology, DNA tags)

19. DNA Computing on Surfaces

20. DNA Computing on Surfaces
Advantages over “solution phase” chemistry:
Disadvantages:
Facile purification steps
Reduced interference between strands
Easily automated
Loss of information density (2D)
Lower surface hybridization efficiency
Slower surface enzyme kinetics

21. DNA Surface Model: Input
DNA strands representing the set {0,1}^n are synthesized and subsequently immobilized on a surface in a non-addressed fashion

22. Encoding of Binary Information in DNA Strands
Word Bit
A strand is comprised of words. Each word is a short DNA strand (16mer) representing one or more bits. 1 2 3 4 . 1 2 3 4 A C T .

23. DNA Word Design Problem
Requirements of a “DNA code”:
Success in specific hybridization between a DNA code word and its Watson-crick complement
Few false positive signals
Virtually all designs enforce combinatorial constraints on the code words
Applications:
Information storage, retrieval for DNA computing
Molecular bar codes for chemical libraries
On last bullet, mention that combinatorial design can provide a promising set that can then be pruned using experimental methods

24. What combinatorial constraints are placed on DNA Codes?
Hamming: distance between two code words should be large
Reverse complement: distance between a word and the reverse complement of another word should be large
Also: frame shift, distinct sub-words, forbidden sub-words, …

25. Work on DNA code design
Seeman (1990): de novo design of sequences for nucleic acid structural engineering
Brenner (1997): sorting polynucleotides using DNA tags
Shoemaker et al. (1996): analysis of yeast deletion mutants using a parallel molecular bar-coding strategy
Many other examples in DNA computing

26. Word Design Example

27. DNA Surface Model: Process
MARK strands in which bit j = 0 (or 1):
hybridize with Watson-Crick complements of word
containing bit j, followed by polymerization
DESTROY
UNMARK

28. DNA Surface Model: Process
MARK strands in which bit j = 0 (or 1)
DESTROY unmarked strands:
exonuclease degradation
UNMARK

29. DNA Surface Model: Process
MARK strands in which bit j = 0 (or 1):
hybridize with Watson-Crick complements of word
containing bit j, followed by polymerization

30. DNA Surface Model: Process
MARK strands in which bit j = 0 (or 1)
DESTROY unmarked strands
UNMARK strands:
wash in distilled water

31. DNA Surface Model: Output
Detect remaining strands (if any)
by detaching strands from surface and
amplifying using PCR (polymerase chain
reaction).

32. Computational Power of DNA Surface Model
Theorem: Any CNFSAT formula of size m can be computed using O(m) mark, unmark and destroy operations.
Theorem: Any circuit of size m can be computed using O(m) mark, unmark, destroy, and append operations.

33. Surface DNA Computation: the Satisfiability Problem
Input: 16 strands
Process:
Output: exactly those strands that satisfy
the circuit remain on the surface.
and
MARK if bit z = 1
MARK if bit w = 1
MARK if bit y = 0
DESTROY
UNMARK
MARK if bit w = 0 … or or or or
not
not
not z w y x

34. DNA Computing on Surfaces: Experiments
Students: Tony Frutos, Susan Gillmor,
Zhen Guo, Qinghua Liu,
Andy Thiel, Liman Wang

35. MARK Operation: 4-Base Mismatch Word Design

36. Repeated MARK, DESTROY, UNMARK Operations

37. Append (DNA Ligase) . Hybridize with Cb . Hybridize with Cab, Wb
. Ligate; Wash;
Hybridize with Cb.

38. Two-Word Mark and Destroy
A. Mark C1a, C1b, C2b
B. Ligate; Melt single words
C. Destroy; Unmark; Mark C1a, C1b, C2b.

39. Surface Attachment Chemistry

41. Word Readout Strategy PCR amplify words remaining on surface
Detect PCR products on single word readout arrays

42. 4-Variable SAT Demo Synthesize; Attach Mark Destroy Umark Readout
Cycle

44. Conclusions
DNA computing has expanded the notion of what is computation
Solid-phase chemistry is a promising approach to DNA computing
DNA computing will require greatly improved DNA surface attachment chemistries and control of chemical and enzymatic processes
New research problems in combinatorics, complexity theory and algorithms

45. Open Problem: DNA Strand Engineering
Given a DNA strand, there are polynomial-time algorithms that predict the secondary structure of the strand.
Inverse Problem: find an efficient algorithm that, given a desired secondary structure, generates a strand with that structure.