Binding of Intercalating and Groove-Binding Cyanine Dyes to Bacteriophage T5
Journal article, 2007
The interaction between four related cyanine dyes and bacteriophage T5 is investigated with fluorescence and absorption spectroscopy. The dyes, which differ in size, charge, and mode of DNA-binding, penetrate the capsid and bind the DNA inside. The rate of association decreases progressively with increasing dye size, from a few minutes for YO to more than 50 h for YOYO (at 37 Â°C). The relative affinity for the phage DNA is a factor of about 0.2 lower than for the same T5-DNA when free in solution. Comparison of groove-bound BOXTO-PRO and intercalating YO-PRO shows that the reduced affinity is not due to DNA extension but perhaps influenced by competition with other cationic DNA-binding agents inside the capsid. Although, the extent of dye binding to the phages decreases with increasing external ionic strength, the affinity relative to free DNA increases, which indicates a comparatively weak screening of electrostatic interactions inside the phage. The rate of binding increases with increasing ionic strength, reflecting an increase in effective pore size of the capsid as electrostatic interactions are screened and/or a faster diffusion of the dye through the DNA matrix inside the capsid as the DNA affinity is reduced. A combination of electron microscopy, light scattering, and linear dichroism show that the phages are intact after YO-PRO binding, whereas a small degree of capsid rupture cannot be excluded with BOXTO-PRO.