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Real Value Representation for DNA Computing

Real Value Representation for DNA Computing. 2001.9.14 신수용. Reference. John SantaLucia, Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics”, Proc. Natl. Acad. Sci. USA, Vol. 956, pp.1460-1465, Biochemistry. Unified parameters for Tm.

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Real Value Representation for DNA Computing

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  1. Real Value Representation for DNA Computing 2001.9.14 신수용

  2. Reference • John SantaLucia, Jr., “A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics”, Proc. Natl. Acad. Sci. USA, Vol. 956, pp.1460-1465, Biochemistry (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  3. Unified parameters for Tm (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  4. Unified parameters for Tm • H순으로 • CG/GC(-10.6) > GC/CG(-9.8) > CA/GT(-8.5) > GT/CA(-8.4) > GA/CT(-8.2) > GG/CC(-8.0) > AA/TT(-7.9) > CT/GA(-7.8) > TA/AT(-7.2) = AT/TA • S순으로 • CG/GC (-27.2) > GC/CG (-24.4) > CA/GT (-22.7) > GT/CA (-22.4) > GA/CT (-22.2) = AA/TT > TA/AT (-21.3) > CT/GA (-21.0) > AT/TA (-20.4) > GG/CC (-19.9) (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  5. NN model for Tm • H는 클수록 S는 작을수록 Tm이 올라간다. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  6. Example (다른 data 사용) GCTAGC at 0.1mM H = 2(-11.1) + 2(-6.1) + (-6.3) = -40.7 kcal/mol S = 2(-28.4) + 2(-16.1) + (-18.5) – 5.9 –1.4 = -114.8eu (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  7. GC% method for Tm • 50 mer 이상의 oligomer (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  8. Representation (NN + GC%) • NN에서는 H가 중요한 요소. • GC%에서는 GC%와 길이가 중요한 요소. • 정리하면 H가 클수록, GC%가 많을수록, 길이가 길수록Tm이 상승함. • 기본적으로 큰 숫자에 큰 Tm을 할당 (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  9. Representation • 길이는 해결이 쉬운 편. • H와 GC%는 아래의 방법 사용 • Tm을 높이기 위해서는 CG/GC, GC/CG, CA/GT, GT/CA를 주로 사용 • Ex) CGCAC • Tm을 낮추기 위해서는 GA/CT, AA/TT, CT/GA, TA/AT, AT/TA를 주로 사용. • Ex) ATAGGA (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  10. Conclusion • Vertex sequence • NN + GC%을 이용한 일정 온도 • Weight sequence in Edge sequence • GC%을 이용해서 가중치 반영 (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

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