Analyzing Thermodynamics of DNA Spaces

Encoding information using DNA words is an essential part in DNA computing. These DNA words should hybridize only as desired otherwise false negatives and/or false positives may result. Therefore, words should be chosen properly to encode problem instances. Several features affect the hybridization property and some of these are the word content, the free energy, and melting temperature. This paper presents a study of DNA spaces from which DNA words are chosen for problem solving. A DNA space is the collection of all possible DNA words of a specific length. Full DNA spaces of lengths that range from 5 to 11 and samples of longer lengths were analyzed. The analysis focuses on the free energy, melting temperature, entropy, and enthalpy values. The ability of prediction of these features for large spaces helps researchers estimate the number of good DNA words that might be used for encoding. Results show that the distribution of the free energy approximates a normal distribution.