We have investigated the interactions and structures of various guanine-rich oligonucleotides that are covalently linked by a BODIPY dye at the 5′ end. HPLC was used to purify and separate different complexes. A single predominant complex is collected for BODIPY-modified d(T₁₀) and d(G₁₀), while two major complexes are collected at different retention times for the BODIPY-modified d(CGCGT₄CGCG) and d(T₂G₄T₂G₄) in the HPLC chromatograms during sample preparation. Distinct nonresonant holes in the satellite hole spectra allow us to distinguish different conformational structures with the same BODIPY–oligonucleotide sequence. In addition, our satellite hole results indicate that the coupling between the BODIPY and the thymine residues in the G-rich sequences can affect the yield of the G-rich aggregation. Furthermore, the appearance of new bands in the absorption spectra resulting from BODIPY aggregates may be a useful diagnostic of various G-rich structures at room temperature. This is because the BODIPY aggregates are driven by the association of G-rich sequences.