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

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

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

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

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

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

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

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

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

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