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Aqueous Computing with DNA Hairpin-based RAM

Aqueous Computing with DNA Hairpin-based RAM. Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, and Azuma Ohuchi Hokkaido University, JST. Summarized by Ji Youn Lee. Introduction. Sequence design overhead Complete set DNA sequences  serious bottleneck

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Aqueous Computing with DNA Hairpin-based RAM

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  1. Aqueous Computing with DNA Hairpin-based RAM Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, and Azuma Ohuchi Hokkaido University, JST Summarized by Ji Youn Lee

  2. Introduction • Sequence design overhead • Complete set DNA sequences  serious bottleneck • If we can use the same sequence to solve the various problems? • Previous research • ROM: Head, Reif, Kashiwamura, Chen (ref. 1~4) • RAM: Head, Yamamura (ref. 5~7) • In this study, • Creation of RAM by exploiting the hairpin structure of DNA/construction of RAM/distinguishing of its states/writing operation

  3. DNA Hairpin-Based RAM (DNA-HRAM) • Advantages (what they say) • No need of temperature change: reaction occurs at constant temperature • Only DNA molecules are necessary (no enzymeis used ??) • Reusable

  4. Closed and Open States hairpin RAM Loop: 7 mer  67 mer Stem: 20 mer 20 mer Lead: 20 mer opener Why this strand displacement happen?

  5. Construction • Reference 11 • Figure 4 288 mer

  6. Distinguishing State • Figure 5 • Orthogonality/Specificity

  7. Retaining Bit Pattern • Writing operation • RAM + excess openers • Remaining openers have to be eliminated from the solution • Not perfect • Eliminating opener • Cover strands: same sequence as the lead (5’-biotinylated) magnet biotin cover strand opener strand

  8. Successive Operation • MISP: Maximum independent set problem B A C D A A A B C D

  9. Detection Solution • Figure 11 Longer!!

  10. Overall Discussion • RAM • Writing • Distinguishing step • Detection step

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