Fitness measures for DNA Computing 2001.8.24 신수용

(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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/

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

(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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/

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, http://bi.snu.ac.kr/

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

Melting Temperature (Tm) (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Melting Temperature (Tm) GC% method More than 50mer (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/

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, http://bi.snu.ac.kr/

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, http://bi.snu.ac.kr/

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, http://bi.snu.ac.kr/

(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, http://bi.snu.ac.kr/