Molecular Computation by DNA Hairpin Formation

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 • 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