1. Fitness measures for DNA Computing
신수용

2. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
H-measure
Simple hamming distance including position shift.
Compared the sequences with their complement sequences.
Compared the sequences with another sequences.
ATGCATGC
TCGATACG
fitness = 5 (0  fitness  8)
shift
(C) 2001, SNU Biointelligence Lab, 

3. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
H-measure
If unplanned duplex
Do not permit 6 continuous base pairing
Do not permit more than L/4 base pairing (?) including bulge configuration
(C) 2001, SNU Biointelligence Lab, 

4. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
H-measure
Compare the vertex sequence with edge sequence to make planned duplex.
Mismatch hybridization
Shifted mismatch
Internal loop
Compare the vertex sequences with another vertex sequences.
Compare the edge sequences with another edge sequences. (if including weight sequences)
(C) 2001, SNU Biointelligence Lab, 

5. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Self-complementary
To make secondary structure using one strand.
Hairpin
>= 5 mer
>= 6 mer
(C) 2001, SNU Biointelligence Lab, 

6. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
GC contents
User-define GC portion
Default value = 50%
(C) 2001, SNU Biointelligence Lab, 

7. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Similarity
Simple hamming distance including position shift.
Compared the sequences with sequences (not complementary sequences)
ATGCATGC
ACCAATCG
fitness = 3 (0  fitness  8)
(C) 2001, SNU Biointelligence Lab, 

8. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Continuity
If the same base appears continuously, a reaction is not well controllable since the structure of DNA will become unstable.
Allow only three same base appears continuously.
Is it correct?
(C) 2001, SNU Biointelligence Lab, 

9. Melting Temperature (Tm)
Wallace method
Less than 13mer
Nearest Neighbor method
Between 13mer and 50mer
L : sequence length
R : Boltzmann’s constant (1.987 cal/(K mol))
[C]] : total molar strand concentration
T : Kelvin
(C) 2001, SNU Biointelligence Lab, 

10. Melting Temperature (Tm)
[Na+] concentrations different from 1M
Self-complement : [CT]/4  [CT]/2
(C) 2001, SNU Biointelligence Lab, 

11. Melting Temperature (Tm)
(C) 2001, SNU Biointelligence Lab, 

12. Melting Temperature (Tm)
GC% method
More than 50mer
(C) 2001, SNU Biointelligence Lab, 

13. Completely complementary at 3’-end
If there exist the point where some bases at 3’-end of each DNA sequence is completely complementary, the unexpected extension would occur.
Already considered in H-measure
(C) 2001, SNU Biointelligence Lab, 

14. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
PCR primer
GC portions is 50~60%
G or C do not appear continuously.
Valid when GC portion method is used to represent the weights.
(C) 2001, SNU Biointelligence Lab, 

15. Weight representation for TSP
Length representation [Narayanan&Zorbalas-98]
Weight is represented by sequence length
GC content method
Weight is represented by GC portion using GA.
How can we detect the solutions?
Concentration control method [Matsuura et al.-01]
Weight is represented by concentration of molecules.
k : constant
(C) 2001, SNU Biointelligence Lab, 

16. Weight representation
Tm method
Weight is represented by melting temperature
Vertex sequence : similar Tm
What is proper Tm of vertex sequence?
What is proper Tm of edge link sequence?
Edge link is decide by vertex, but the Tm will be different.
Weight sequence : Tm is decided by weights
What is base Tm? (Tm which represents weight ZERO)
What is proper rate of Tm? (to represent weight difference)
(C) 2001, SNU Biointelligence Lab, 

17. Weight representation
Tm method (some drawbacks)
Scaling problem. (bounded by 100C)
Different Tm calculation methods based on length
New method?
(C) 2001, SNU Biointelligence Lab, 

18. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Evaluation function
How can we decide the weight of fitness measure?
Multi-objective optimization problem!
Effective methods?
(C) 2001, SNU Biointelligence Lab,