1. Molecular Computation by DNA Hairpin Formation
Sakamoto, Gouzu, Komiya, Kiga, Yokoyama, Yokomori and Hagiya
발표자 : 윤주영

2. SAT Problem
To find Boolean-value assignments that satisfy the given formula
CNF-SAT
CNF-SAT is form of
A clause is form of

3. Solution of CNF-SAT Literal string
conjunction of literal selected from each clause
No pair of complementary literals
-> Formula is satisfiable
Hairpin formation
One or more pair of
complementary literals

4. Algorithm for CNF-SAT Instance for Experiment Generate literal strings
Allow ssDNA molecules to form hairpins
Remove hairpin-forming molecules
Instance for Experiment
6-variable 10-clause instance
Unique solution (a,b,c,d,e,f)=(0,1,1,0,1,0)
Literal strings : 310 = 59049

5. Generate Literal Strings
DNA for each literal in clause i
Linker i-1 on left
and linker i on right
Bst XI recognize 5’-CCAWNNNNWTGG-3’
NNNN covers linker
-> Literal is form of 5’-WTGG…CCAW-3’
Bst NI site CCAGG is contained for
hairpin-removing step
30 literals were mixed in a test tube (pool 0)
Concatenated with DNA ligase
Ligation products were separated
by gel electrophoresis

6. Remove hairpin-forming molecules
Allow ssDNA molecules to form hairpins
Performed by regulating temperature
Two technique for hairpin-removing
Enzymatic digestion
Double-stranded regions of hairpin molecule become susceptible to Bst NI
Exclusive PCR
Increase population of non-hairpin molecules by PCR
DNA polymerase can’t duplicate a DNA template that forms stable hairpins
Diluted reaction mixture after each PCR cycle

7. Remove hairpin-forming molecules
Experiment result
Pool 1 (Fig 2)
Digest twice with Bst NI on pool 0 and recover remained molecule by PCR
Result : 0 satisfying string in 11 clones
Pool 2
ePCR processing of 10 cycles and one
more destructive process on pool 1
Result : 1 satisfying string in 16 clones
Pool 3 (Fig 3)
ePCR processing of 20 cycles on pool 1
Result : 6 satisfying string in 37 clones

8. Conclusion Hairpin-based computation Advantage
All clauses were processed simultaneously
In previous computations, each clauses was examined by a few laboratory steps
No negative error

9. Conclusion
Drawback
Inefficiency with respect to required amount of DNA
Lipton’s method require 2n or less molecules with n variable
Scalablity
For large instance, bias of literal strings occurs
Incompleteness of understanding of nature of hairpin molecules
Limit to available length of hairpin remains to be determined

10. Further works Unraveling nature of possible bias during PCR
Sequence design or experimental conditions that ensure hairpin formation