Biologically, G-quadruplexes (G4s) are single-stranded structures that fold back on themselves, and are formed by DNA or RNA molecules in which one guanine base from each chain associate via cyclic Hoogsteen hydrogen bonding to form planar G-tetrad. Two or more of these tetrads can hydrophobically stack on top of one another to form G4 which are further stabilized by the presence of a mandatory monovalent cation centered between the planes. RNA Helicase Associated with AU-rich element (RHAU) is a member of the ATP-dependent DExH/D family of the RNA helicases that can bind and resolve G4 structures. To gain insight into the structural basis of G4 recognition by RHAU, a series of G4s were characterized using biophysical techniques including UV-Visible spectroscopy, electrophoretic mobility shift assays, dynamic light scattering, circular dichroism, small angle x-ray scattering and nuclear magnetic resonance spectroscopy. The mRNA for the Pituitary homeobox 1 (PITX1) protein was chosen as a model system to investigate G4 structures as it possesses three distinct G4 forming sequences in its 3ʹ- untranslated region (UTR) that interact with RHAU (Q1: PITX11371-1400, Q2: PITX11901-1930, and Q3: PITX12044-2079). First, Q2 was studied and demonstrated to adopt a parallel G4 orientation that can interact with the N-terminal domain of RHAU via its G-tetrad face. Interestingly, the DNA counterpart of Q2 adopted a different hybrid-type G4 structure with mixed parallel and antiparallel strands which was unable to interact with RHAU. Next, Q3 from PITX1 mRNA was studied as it contains long loops of 6 nucleotides to investigate the potential impact of interrupting loops on both the G4 structure and interaction with proteins/small molecules. Scrambling of only specific loop sequences impacted the global fold of Q3 while retaining a parallel G4 conformation. Disruption of the global fold through loop scrambling was shown to impact binding affinity of RHAU and a small molecule ligand that selectively interacts with the G-tetrad faces of parallel G4s. Taken together, the data in this thesis provides a biochemical and structural starting point for understanding the recognition of RNA G4s by binding partners.