Investigation of the NIR cyanine dye MHI-36 shows binding affinity to charged amino acids. This cyanine dye showed aggregation and dimer formation at higher dye concentration (2.0x10-3 M) induced by lysine. When dye concentration decreased to 1.0x10-4M no strong aggregate formation was viewed. Dye shows strong binding and selectivity properties towards charged amino acids lysine and arginine, compared to neutral leucine. It’s believed the positively charged presence was able to break and disrupt the conjugated π- π bonds at lower dye concentration. Computational work showed intramolecular aggregation of the phenyl groups on the dye. These aggregates are believed to create electron rich environment suitable for lysine interaction.