A computational chemist has calculated the interaction energy between two DNA si

Question

A computational chemist has calculated the interaction energy between two DNA single strands in the gas phase. An ab initio quantum mechanical approach was used instead of the semiempirical method. This time 14-nucleotide long GC-rich polyanions are used instead of individiual nucleobases. Knowing that he has to compare his data with aqueous phase thermodynamic results, he carefully evaluates contributions from internal vibrations and scales all electrostatic interactions between two molecules down 80-fold (to account for the dielectric constant of water). When comparing his theoretical results with the enthalpy data obtained by his colleague, who is the world leader in calorimetric measurements of DNA duplexes, he notices that the computational data are rubbish: his results predict that the dsDNA is unstable while experiment clearly shows that the enthalpy of association is favorable.

Provide a possible explanation why the computational enthalpies might be wrong in this scenario.

Explanation / Answer

Hydrogen bonds are formed within bases and with the surrounding water molecules. This accounts for the stability of the duplex dsDNA molecule. In addition, stacking of the bases also gives stability. Since DNA contains all the 4 bases, not only GC, the combination of the 4 bases gives stability in size and structure.

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