The two strands of double-helical DNA are held together mainly by hydrogen bonds between the nucleobases in opposite strands. The thermal stability of a double-helical DNA segment thus depends on the base pair composition of the DNA fragment.
In this exercise you will use a theoretical chemistry method to estimate the interaction strength between bases that form a DNA base pair. The two base pairs in DNA are the AT base pair and the GC base pair. The AT base pair is held together by hydrogen bonds between the A base and the T base. Similarly, the GC base pair is held together by hydrogen bonds between the G base and the C base.
How can we calculate interactions strengths? The strength of hydrogen bonding between nucleobases in the base pair is approximately equal to the enthalpy of the base-pairing reaction. You should remember from your introductory chemistry that the enthalpy of any reaction can be calculated from Hess's law. It states that the reaction enthalpy equals the enthalpy of products minus the enthalpy of reactants. Negative reaction enthalpy means the the reaction product is more stable than the isolated reactants.
The two basepairing reactions can be defined as:
1) A + T = AT
2) G + C = GC
The enthalpies of products and reactants can be calculated using quantum mechanics. Accurate quantum mechanical calculations can be performed only on small molecules, and several approximate methods have been developed for treatment of biochemically interesting systems. One group of approximate methods is known as the semiempirical methods. Semiempirical methods are very fast, and thus suitable for the teaching purpose. On the other hand, semiempirical methods have many known deficiencies and should be used with caution. The semiempirical method that you will be using today is called PM3, this acronym stands for Parameterized Model 3.