Structural and folding patterns of promoter regions (c-MYC, BCL) and telomeric (TTAGGG repeats) G-Quadruplexes were explored and their interactions with small molecules were tested. EAO-108 and MHI-21, symmetric heptamethine cyanines, were identified to exhibit strong interaction with the telomeric G-Quadruplex (mixed hybrid-1), while promoter region G-Quadruplexes were discriminated against. ZK-26 binds strongly to the c-MYC derivative and it is capable of discriminating between (3+1) hybrid-1 and -2 telomeric G-Quadruplexes with an initial binding preference towards the latter. To aid future binding studies, a novel labeling method is also described in this work.