Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. Motivation: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. The specificity of these interactions depends on the stability of intermolecular and intramolecular base pairing. While methods like deep sequencing allow to discover an ever increasing set of ncRNAs, there are no high-throughput methods available to detect their associated targets. Hence, there is an increasing need for precise computational target prediction. In order to predict base-pairing probability of any two bases in interacting nucleic acids, it is necessary to compute the interaction partition function over the whole ensemble. The partition function is a scalar value from which various thermodynamic quantities can be derived. For example, the equilibrium concentration of each complex nucleic acid species and also the melting temperature of interacting nucleic acids can be calculated based on the partition function of the complex. Results: We present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids in O(n6) time. We verify the predictive power of our algorithm by computing (i) the melting temperature for interacting RNA pairs studied in the literature and (ii) the equilibrium concentration for several variants of the OxyS-fhlA complex. In both experiments, our algorithm shows high accuracy and outperforms competitors.