In recent works, we have been studying the photophysics and binding properties of the trimethine cyanine homodimer dye BOBO-3, a DNA intercalative fluorophore that shows an important fluorescence enhancement upon binding to double-stranded DNA. During the course of studying the interactions of the dye with single-stranded homo-oligonucleotides we detected the apparition of an additional absorption band centered on 466 nm. The large hypsochromic effect and the fact that direct excitation of this band resulted in negligible fluorescence emission are characteristic properties of an H-type molecular aggregate. In this work we study the properties of this H-aggregate, and obtain by means of Principal Component Analysis the spectral shape and association constant of the complex. The H-aggregate complex shows very unique features. On one hand, the nucleotide bases cytosine or adenine are crucially involved in the formation of the aggregate. We describe here that at least six consecutive cytidine nucleosides are required to properly form the BOBO-3 H-aggregate complex. On the other hand, we demonstrate that the formation of such a stable complex prevents hybridization of the bases involved with their complementary strands. This phenomenon draws important conclusions on the anomalously high stability of the BOBO-3 H-aggregate complex. To the best of our knowledge, this is the first time such a stable H-aggregate of a dimeric cyanine dye facilitated by specific nucleotide bases in single strands has been reported.