AAT Bioquest

How do DNA binding dyes bind to DNA?

Posted May 18, 2020


There are 3 major types of tight binding modes between DNA binding dyes and DNA:

  1. Intercalating (e.g. Propidium iodide)
  2. Minor-groove binding (e.g. DAPI)
  3. Bis-intercalating (e.g. YOYO-1)

Some dyes can bind to DNA’s major groove or externally bind with DNA through electrostatic interaction, though the binding is not as tight as the aforementioned three modes. Multiple binding modes can occur for one dye, and the dominant binding mode may change with different dye-DNA conditions such as dye-to-DNA ratio and DNA hybridization status.

Additional resources

Propidium iodide *CAS 25535-16-4*

DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*

DiYO™-1 [equivalent to YOYO®-1] *5 mM DMSO Solution*

Wang, Y., Schellenberg, H., Walhorn, V., Toensing, K., & Anselmetti, D. (2017). Binding Mechanism of Fluorescent Dyes to DNA Characterized by Magnetic Tweezers. Materials Today: Proceedings, 4, S218–S225. doi:10.1016/j.matpr.2017.09.190

Sayed, M., Krishnamurthy, B., & Pal, H. (2016). Unraveling multiple binding modes of acridine orange to DNA using a multispectroscopic approach. Physical Chemistry Chemical Physics, 18(35), 24642–24653. doi:10.1039/c6cp03716j