Frank Lee
HYBRIDIZATION CONTINUED
Strands A and B are two strands in a proposed computation. You must make sure that A does not stick to itself, stick to B, or any other combination. (See diagrams)
A and B are only acceptable if A, A’, B, and B’ do not stick to themselves.
Set up a binary table:
A B C D A’ B’ C’
A 0 1 0 0 1 0
Etc…
D’ A 1 is put in the table if the two strands
B
C
1
D
A’ 1
B’
1
C’
1
D’ 1
1
1 stick to each other. The only strands that should stick to each other are the complements (A sticks to A’). After you have filled out the table, you’re looking for the max clique of the table – the most strands you can keep that will not stick to each other. This problem is NP complete.
Should you remove the horizontal strand or the vertical strand when you run into a problem? This is up to you. A good algorithm is to check to see which strand causes the most problems – the one that sticks in the most bad places. Also, if the strand sticks to itself, is should automatically be thrown out.
There is no method in DNA computing that does not use Hybridization. Hybridization is what allows DNA strands to be used as a Universal Turing Machine.
“STICKER MODEL” (Adleman, et al)
Create a “memory” strand that is able to encode a string of bits. Design “stickers” that attach themselves to only one specific “bit” location each.
0 … bit L L+1 L+2 … K
...ATCGG|TCATA|GCACT...
...TAGCC|-----|CGTGA...
...ATCGG|TCATA|GCACT...
1 0 1
Operations: Combine 2 test tubes, separate contents of 1 tube using any bit, set any bit, clear any bit
See handout for more details

Frank Lee
Algorithm:
-is it complete? (unambiguous, all possible inputs)
-is it correct? (right answer)
-what resources does it need? (time & space || lab operations & quantity of DNA) time * processors = work work = time/processor