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Nearest-neighbor model for Tm

Nearest-neighbor model for Tm. 신수용 2001.8.3. Reference. J. SantaLucia et al., Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry 1996 , 35, 3555-3562 http://jsl1.chem.wayne.edu/

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Nearest-neighbor model for Tm

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  1. Nearest-neighbor model for Tm 신수용 2001.8.3

  2. Reference • J. SantaLucia et al., Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry1996, 35, 3555-3562 • http://jsl1.chem.wayne.edu/ • A. J. Hartemink & D. K. Gifford, Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation, DNA3, 25-37, 1999 • http://www.psrg.lcs.mit.edu/~amink/ (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  3. Reference • J. G. Wetmur, Physical Chemistry of Nucleic Acid Hybridization, DNA3, 1-24, 1999. • http://www.math.tau.ac.il/~dmit/thesis/final/hm.html • H. Werntges, G. Steger, D. Riesner, & H. Fritz. (1986) Nucleic Acids Res. 14, 3773-3790. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  4. Modeling hybridization of short oligonucleotides • K-match model • Alignment model • Nearest-neighbor model (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  5. Nearest-neighbor model for Tm R : Boltzmann’s constant (1.987 cal/(K mol)) [C]] : total molar strand concentration T : Kelvin [Na+] concentrations different from 1M (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  6. Nearest-neighbor model for Tm • Self-complement : [CT]/4  [CT]/2 • The strands are not in equimolar concentration, • but one strand is present in gross excess over the other : • [CT]/4  [CT] • mismatched base pairs : “virtual stacks” (see references) (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  7. Nearest-neighbor data (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

  8. Example 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/

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