The aim of this master’s thesis was to analyse DNA-protein binding properties of nanobodies specific to guanine quadruplexes (G-quadruplexes) using the Electrophoretic Mobility Shift Assay (EMSA), Atomic Force Microscopy (AFM), Fluorescence Anisotropy and Circular Dichroism Spectroscopy (CD Spectroscopy). G-quadruplexes are non-canonical secondary structures of both DNA and RNA present predominantly in promoter regions of certain genes and in telomeres, where they serve regulatory and protective functions. G-quadruplexes are also involved in the formation and proliferation of many oncological diseases. Binding capabilities of both tested nanobodies: SG4 and its mutant SG4 R105A, were tested on canonical double strand DNA (dsDNA), on cruciform DNA and on parallel and hybrid G-quadruplex DNA. In Electrophoretic Mobility Shift Assay performed with short oligonucleotide DNA, both nanobodies displayed their expected behaviour: higher affinity towards G-quadruplexes and lower or no affinity towards cruciform and dsDNA for SG4, and low or no affinity towards any of the tested secondary structures for SG4 R105A. That was, however, not the case for EMSA performed with plasmid DNA, both supercoiled and linear, containing the same sequences as in the previous experiment. Both nanobodies showed a preference for the supercoiled version of the same plasmid as opposed to the linear version, regardless of the secondary DNA structure present. The binding of SG4 and SG4 R105A to the same set of plasmids was also analysed using Atomic Force Microscopy and either no binding or only non-specific binding was found. Additionally, interpretation of AFM pictures was made difficult by the presence of DNA aggregates and fragments and the small size of nanobodies. To measure affinity constants of SG4 and SG4 R105A toward dsDNA, cruciforms and G-quadruplexes, Fluorescence Anisotropy measurements were performed. However, due to the fluorescence properties of tested proteins and oligonucleotides, it was found to be impossible to measure a binding curve of SG4 and SG4 R105A using Fluoresce Anisotropy, and therefore to determine their corresponding affinity constants using this method. And lastly, the nanobodies’ ability to stabilize the G-quadruplex secondary structure was analysed using Circular Dichroism Spectroscopy, where both SG4 and SG4 R105A were found to not stabilize G-quadruplexes, even though SG4 showed a clear affinity towards them in EMSA experiments and in previous work.