Aqueous Computing with DNA Hairpin-based RAM

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Aqueous Computing with DNA Hairpin-based RAM
Naoto Takahashi, Atsushi Kameda, Masahito
Yamamoto, and Azuma Ohuchi Hokkaido University,
JST
Summarized by Ji Youn Lee
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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. 14)
• RAM Head, Yamamura (ref. 57)
• In this study,
• Creation of RAM by exploiting the hairpin
  structure of DNA/construction of
  RAM/distinguishing of its states/writing operation

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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

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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?
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Construction

• Reference 11
• Figure 4

288 mer
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Distinguishing State

• Figure 5
• Orthogonality/Specificity

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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
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Successive Operation

• MISP Maximum independent set problem

B
A
C
D
A
A
A
B
C
D
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Detection Solution

• Figure 11

Longer!!
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Overall Discussion

• RAM
• Writing
• Distinguishing step
• Detection step