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Molecular Computation by DNA Hairpin Formation

This study explores the use of DNA hairpin formation as a computational mechanism to solve CNF-SAT problems. Focusing on the algorithm for generating literal strings, it describes how single-stranded DNA can form hairpins that are crucial for the computation process. Using a 6-variable, 10-clause CNF-SAT instance, the researchers applied different techniques to remove hairpin-forming molecules and analyzed the outcomes through gel electrophoresis and enzymatic digestion. The findings underline the efficiency and parallel processing of all clauses, along with addressing drawbacks like DNA quantity and bias.

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Molecular Computation by DNA Hairpin Formation

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  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

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