Hairpin Completion Distance Lower Bound

Abstract

Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into $S\cdot S'$ where $S'$ is the reverse complement of a prefix of $S$. Similarly, a left hairpin completion operation transforms a string $S$ into $S'\cdot S$ where $S'$ is the reverse complement of a suffix of $S$. The hairpin completion distance from $S$ to $T$ is the minimum number of hairpin completion operations needed to transform $S$ into $T$. Recently Boneh et al. showed an $O(n^2)$ time algorithm for finding the hairpin completion distance between two strings of length at most $n$. In this paper we show that for any $\varepsilon>0$ there is no $O(n^{2-\varepsilon})$-time algorithm for the hairpin completion distance problem unless the Strong Exponential Time Hypothesis (SETH) is false. Thus, under SETH, the time complexity of the hairpin completion distance problem is quadratic, up to sub-polynomial factors.