A weighted insertion-deletion stacked pair thermodynamic metric for DNA codes

Thermodynamic distance functions are important components in the construction of DNA codes and DNA codewords are structural and information building blocks in biomolecular computing and other biotechnical applications that employ DNA hybridization assays. We introduce new metrics for DNA code design that capture key aspects of the nearest neighbor thermodynamic model for hybridized DNA duplexes. One version of our metric gives the maximum number of stacked pairs of hydrogen bonded nucleotide base pairs that can be present in any secondary structure in a hybridized DNA duplex without pseudoknots. We introduce the concept of (t-gap) block isomorphic subsequences to describe new string metrics that are similar to the weighted Levenshtein insertion-deletion metric. We show how our new distances can be calculated by a generalization of the folklore longest common subsequence dynamic programming algorithm. We give a Varshamov-Gilbert like lower bound on the size of some of codes using our distance functions as constraints. We also discuss software implementation of our DNA code design methods.