CHEM 352—Biochemistry II—Spring 2025
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Nucleic Acid Chemistry
[1] Calculating Duplex Stability with Nearest-Neighbor Thermodynamics
Using the unified scale of SantaLucia (SantaLucia J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS. 95, 1460-5., Table 1, far right column), calculate the ΔGo37 for the following short DNA duplex:

5'AGTCGTGGCTAC3'
3'TCAGCACCGATG5'

Show Answer
Starting at the 5' end of the upper strand,the initiation term for an AT base pair is 1.03 kcal/mol. The dinucleotide free energies, in order, are: AG, -1.28; GT, -1.44; TC, -1.30; CG, -2.17; GT, -1.44; TG, -1.45; GG, -1.84; GC, -2.24; CT, -1.28; TA, -0.58; and AC, -1.44 kcal/mol. The initiation term at the 3' end is 0.98 for the GC base pair. The ΔGo37 is the sum of these values. For this oligonucleotide the ΔGo37 is -14.45 kcal/mol.
Interaction   ΔGo37 (kcal/mol)
init AT  1.03
AG -1.28
GT -1.44
TC -1.30
CG -2.17
GT -1.44
TG -1.45
GG -1.84
GC -2.24
CT -1.28
TA -0.58
AC -1.44
init GC  0.98
-14.45
Last updated: 05 February, 2025.
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