Antioxidants are essential to good health. Flavonoids are powerful
antioxidants, and prevent DNA damage. The antioxidative protections are
related to their binding modes to a DNA duplex and complexation with
free radicals in vivo. Recently we reported the interaction of
flavonoids with DNA in vitro (Kanakis et al., J. Biomol. Struct. Dyn.
22, 719-724, 2005), where polyphenol different binding modes were
discussed. The aim of this study was to examine the interaction of
transfer RNA with quercetin (que), kaempferol (kae), and delphinidin
(del) in aqueous solution at physiological conditions and to make a
comparison with the corresponding pigment-DNA adducts. Constant tRNA
concentration (6.25 mM) and various drug/RNA( phosphate) molar ratios of
1/48 to 1/8 were used. FTIR and UV-visible difference spectroscopic
methods have been applied to determine the drug binding mode, the
binding constants, and the effects of drug complexation on the stability
and conformation of tRNA duplex. Both intercalative and external binding
modes were observed. Structural analysis showed que, kae, and a del
intercalate tRNA duplex with minor external binding to the major or
minor groove and the backbone phosphate group with overall binding
constants K-que = 4.80 x 10(4) M-1, K-kae = 4.65 x 10(4) M-1, and K-del
= 9.47 x 10(4) M-1. The stability of adduct formation is in the order of
del > que > kae. A comparison with flavonoids-DNA adducts showed both
intercalation and external bindings with the stability order K-que =
7.25 x 10(4) M-1, K-kae = 3.60 x 10(4) M-1, and K-del = 1.66 x 10(4)
M-1. Low flavonoid concentration induces helical stabilization, whereas
high pigment content causes helix opening. A partial B- to A-DNA
transition occurs at high drug concentration, while tRNA remains in the
A-family structure