In this review article we present an analysis of several aspects of four-dimensional, non-perturbative = 1 compactifications of string theory. Our study focuses on brane dynamics and their effective physics as encoded in the holomorphic couplings of the low-energy = 1 effective action, most prominently the superpotential W. This article is divided into three parts. In part one we derive the effective action of a spacetime-filling D5-brane in generic Type IIB Calabi-Yau orientifold compactifications. In the second part we invoke tools from string dualities, namely from F-theory, heterotic/F-theory duality and mirror symmetry, for a more elaborate study of the dynamics of (p,q) 7-branes and heterotic five-branes. In this context we perform exact computations of the complete perturbative effective superpotential, both due to branes and background fluxes. Finally, in the third part we present a novel geometric description of five-branes in Type IIB and heterotic M-theory Calabi-Yau compactifications via a non-Calabi-Yau threefold , that is canonically constructed from the original five-brane and the Calabi-Yau threefold Z3 via a blow-up. We use the blow-up threefold to derive open-closed Picard-Fuchs differential equations, that govern the complete effective brane and flux superpotential. In addition, we present first evidence to interpret as a flux compactification geometrically dual to the original five-brane by defining an SU(3)-structure on , that is generated dynamically by the five-brane backreaction.