Studies on interactions of ruthenium(II) polypyridyl complexes [Ru(bpy)2(btip)]2+ and [Ru(dmb)2(btip)]2+ with double-stranded RNA poly(A)·poly(U) under molecular crowding conditions

Abstract

Ruthenium(II) polypyridyl complexes have emerged as excellent nucleic acid binders based on the easy-to-construct three-dimensional structures and rich photophysical and photochemical properties. However, most studies are usually performed under dilute conditions, which might be disturbed by the crowding environment of cells. Herein, two ruthenium(II) polypyridyl complexes, [Ru(bpy)2(btip)]2+ (Ru1, bpy = 2,2′-bipyridine, btip = 2-benzo[b]thien-2-yl-1H-imidazo[4,5-f]-[1,10]phenanthroline) and [Ru(dmb)2(btip)]2+ (Ru2, dmb = 4,4′-dimethyl-2,2′-bipyridine) have been synthesized and characterized. Interactions of the two complexes with double-stranded RNA poly(A)·poly(U) in dilute solution and molecular crowding environment have been studied by spectroscopic techniques and viscosity measurements, respectively. Spectral titration and viscosity experiments show that both Ru1 and Ru2 combine with poly(A)·poly(U) through an intercalative mode in both environments, and the binding affinity in crowding environment is significantly lower than that in dilute solution, but still comparatively high. Moreover, thermal denaturation experiments show that the abilities of Ru1 and Ru2 to poly(A)·poly(U) are significantly reduced under crowding condition, which are attributed to the reduced binding affinity of the complexes to poly(A)·poly(U) in crowding environment.