1. DNA computing on surfaces
Nature 403, (2000)
Ji Yoon Park
Dept. of Biochem
Hanyang University

2. Abstract
Immobilization and manipulation of combinatorial mixtures of DNA on a support.
Candidate solution is synthesized and attached to the surface.
Successive cycles of hybridization operation and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions.
The solution to the computational problem is identified PCR to amplify the remaining molecules.
Hybridization to an addressed array.

3. I. Make: oligomer synthesis- - -
II. Attach(Immobilized):
5’HS-C6-T15-CCTTvvvvvvvvTTCG-3’
III. Mark: hybridization
IV. Destroy: Enzyme rxn(ex.EcoRI)
V. Unmark
* 문제를 만족시키지 않는 모든 strand 제거
VI. Readout:
N cycle의 마지막 단계에 해가 남게 되면,
PCR로 증폭하여 확인!
Figure 1. Overview of the surface-based approach to DNA computations.

5. The logic of the DNA computation in each cycle, leading at the end to four types of DNA molecules remaining on the surface.
The identity of those molecules that correspond to the solutions was determined by PCR.
Solution: S3 S7 S8 S9
Figure 2. Four cycles of SAT computation.

6. S3: w=0, x=0, y=1, z=1
S7: w=0, x=1, y=1, z=1
S8: w=1, x=0, y=0, z=0
S9 : w=1, x=0, y=0, z=1
y=1: (w V x V y) 만족
z=1: (w V y V z) 만족
x=0 or y=1: (x V y) 만족
w=0: (w V y) 만족
Four spots with high fluorescence intensity correspond to the four expected solutions.
DNA sequences identified in the readout step via addressed array hybridization.
Figure 3. Three-dimensional plot and histogram of the fluorescence
intensitieson a 16 element addressed array used for ‘readout’.

7. PCR amplification for “readout”
I. Template(56mer):
5’-tatttttgagcagtggctccCGAAvvvvvvvvAAGCtagctatctacaagattcag-3’
II. Primer(20mer): ’-biotin-ctgaatcttgtagatagcta-3’
5’-FAM-tatttttgagcagtggctcc-3’
III. PCR(amplification): 25 cycles
95℃ 1min,
cycles: 95℃ 30s, 40℃ 20s, 60℃ 1min

8. Hybridization to addressed array for “readout”
I. DNA array preparation
1. Gold-coated coverslip was immersed in a 0.5 mM ethanolois sol’n
for overnight
2. Coverslip was immersed in 1mM ethanolic 11-mercaptoundecanoicacid for
1hr : poly-L-lysine monolayer의 electrostatic adsorption
3. PCR amplification product(double strand: 56mer) strand separation by streptavidin-coupled magnetic beads
4. Fluorescently labelled PCR product resuspened in hybridization buffer
5. Wash & scanning

9. Number of oligonucleotide s required for scale up
1. Multiple word combinatorial mixtures
: thiol-modified group의 surface attachment
2. Single word individual oligonucleotides
- thiol-modified group의 surface attachment
- unmodified for us in the “mark” operation
- PCR primer seq
3. Ex: 36bit