In this study, electrospray ionization mass spectrometry (ESI·I\tIS) was Llsed to investigate the binding interactions of ten flavonoid aglycones and ten flavonoid glycosides with DNA duplexes. Relative binding affinities of the flavonoids toward DNA duplexes were estimated based on the fraction of bound DNA. The results revealed that the 4'-OH group of flavonoid aglycones was essential for their DNA-binding properties. Flavonoid glycosides with sugar chain linked on ring A or ring B showed enhanced binding toward the duplexes over their aglycone counterparts, whereas glycosylation of the flavonol quercetin on ring C exhibited a less pronounced effect. The aglycone skeletons and other hydroxyl substitutions on the aglycone also have an effect on the fractions of bound DNA. Upon collision-induced dissociation, the complexes containing flavonoid aglycones underwent the predominant ejection of a neutral ligand molecule, suggesting an intercalative DNA-binding mode. . These drugs may bind to certain DNA sequences, prevent the specific recognition of these sequences with their trans-acting factors, and interfere with the replication or transcription of certain genes, and thus exert their pharmacological activities [2]. Among the various organic molecules, natural products have attracted considerable interest given that many clinical anticancer drugs are natural products (or their derivatives) and most of them exert their effects by acting on DNA [1]. In this context, studies of the binding of natural products with DNA are helpful for better understanding the molecular basis of their bioac· tivities as well as providing useful guidance for further deSign of more efficient anticancer drugs [1, 3-7J.As an important class of natural products, flavonoids have received considerable attention because of their health benefits and chemopreventive properties [8]. Flavonoids consist of a diverse group of compounds derived from 2-phenolchromotome and can be categorized into several subgroups according to the structure (Table 1). Flavonoid aglycones and their modified forms are widely found in the roots, stalks, and fruits of many natural plants and act as the major functional components in many herb medicines [8,9]. Many studies have demonstrated that flavonoids possess a wide range of biological activities, such as anticancer, antiviral, antibacterial, antiOXidants, and anti~inflammatory effects [8J. These biological activities are considered to be related to their interaction with several enzymes in the human body as well as their notable antioxidant activity [8, 1OJ. Meanwhile, the binding of flavonoids to nucleic acid structures has also been recognized as one important mechanism of their actions [11-19[. The noncovalent interactions between flavonoids and DNA have been elucidated using several solution-phase techniques including absorption [20,21], fluorescence [21], linear dichroism [22], and nuclear magnetic resonance [23J spectroscopies, as well as electrochemical [24] and surface plasmon resonance [25] techniques. Ho...