1. Three Dimensional DNA Structures in Computing
N. Jonoska, S. A. Karl, M. Saito
4th DNAC
Summarized by Lee, In-hee

2. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
Introduction
Solution to two NP-complete problems
Satisfiability(SAT) problem
3-vertex-colorability problem
© 2001, SNU BioIntelligence Lab,

3. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
SAT problem
SAT is equivalent to the “contact network” problem
Contact network
Source s and target t
Each edge is labeled with x or x’
Edge is connected if and only if the value of the variable assigns 1 to the edge
© 2001, SNU BioIntelligence Lab,

4. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
SAT problem
© 2001, SNU BioIntelligence Lab,

5. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
SAT problem
Vertex
Source
Target
Edge
Contains a restriction enzyme site
Different enzyme for each variable and its negation
Cap
Binds to overhang of each enzyme site
© 2001, SNU BioIntelligence Lab,

6. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
SAT Problem
Solution
Combine vertex, edge, source, target in a single tube
Hybridize and ligate
Remove partial graphs by exonuclease
For each variable x
Divide into two tubes
Add x=0 enzyme to first tube, x = 1 enzyme to second one
Add cap to both tube, and hybridize and ligate
Combine the tubes in single tube
Detect solution by PCR
© 2001, SNU BioIntelligence Lab,

7. © 2001, SNU BioIntelligence Lab, http://bi.snu.ac.kr/
SAT Problem
© 2001, SNU BioIntelligence Lab,

8. 3-vertex-colorability Problem
For given graph, paint each adjacent vertex with different colors, using only 3 colors.
Vertex
Edge
© 2001, SNU BioIntelligence Lab,

9. 3-vertex-colorability Problem
Solution
Combine all vertex, edge in a single tube
Hybridize and ligate
Remove partial graph by exonuclease
Remove larger graph by gel electrophoresis
© 2001, SNU BioIntelligence Lab,