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

2. Cell and Microbial Engineering Laboratory DNA Computing 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. Cell and Microbial Engineering Laboratory DNA Computing 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 enzyme is used ??)  Reusable

4. Cell and Microbial Engineering Laboratory DNA Computing 4  Closed and Open States Lead: 20 mer Stem: 20 mer20 mer Loop: 7 mer  67 mer opener hairpin RAM Why this strand displacement happen?

5. Cell and Microbial Engineering Laboratory DNA Computing 5  Construction Reference 11 Figure 4 288 mer

6. Cell and Microbial Engineering Laboratory DNA Computing 6  Distinguishing State Figure 5 Orthogonality/Specificity

7. Cell and Microbial Engineering Laboratory DNA Computing 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) biotin magnet cover strand opener strand

8. Cell and Microbial Engineering Laboratory DNA Computing 8  Successive Operation MISP: Maximum independent set problem A B C D AAA BCD

9. Cell and Microbial Engineering Laboratory DNA Computing 9  Detection Solution Figure 11 Longer!!

10. Cell and Microbial Engineering Laboratory DNA Computing 10  Overall Discussion RAM Writing Distinguishing step Detection step