1. Nearest-neighbor model for Tm
신수용

2. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Reference
J. SantaLucia et al., Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry 1996, 35,
A. J. Hartemink & D. K. Gifford, Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation, DNA3, 25-37, 1999
(C) 2001, SNU Biointelligence Lab, 

3. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Reference
J. G. Wetmur, Physical Chemistry of Nucleic Acid Hybridization, DNA3, 1-24, 1999.
H. Werntges, G. Steger, D. Riesner, & H. Fritz. (1986) Nucleic Acids Res. 14,
(C) 2001, SNU Biointelligence Lab, 

4. Modeling hybridization of short oligonucleotides
K-match model
Alignment model
Nearest-neighbor model
(C) 2001, SNU Biointelligence Lab, 

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, 

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, 

7. Nearest-neighbor data
(C) 2001, SNU Biointelligence Lab, 

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