Oligonucleotide from SARS virus was selected as a target molecule in the paper. The noncovalent complexes of ginsenosides with the target molecule were investigated by electrospray ionization mass spectrometry. The effects of experimental conditions were examined firstly on the formation of noncovalent complexes. Based on the optimized experimental conditions, the interaction of different ginsenosides with the target molecule was researched, finding that the interaction orders are relative with the structure of aglycons, the length and terminal sugar types of saccharide chains in the ginsenosides. There are certain rules for the interaction between the ginsenosides and DNA target molecule. For different type ginsenosides, the interaction intensity takes the orders 20-S-protopanaxatriol＞20-S-protopanaxadiol, and panaxatriol ginsenosides＞panaxadiol ginsenosides. For the ginsenosides with the same type aglycone, tri-saccharide chain＞di-saccharide chain＞tetra-saccharide chain and single-saccharide chain＞panaxatriol. For the ginsenosides with the same tetra-saccharide chain, the ginsenosides with smaller molecule masses＞the ginsenosides with larger molecule masses. For some ginsenoside isomers with the same saccharide chain sequence, Rb2 with xylose(fur) terminal＞Rc with xylose(pyr) terminal, that is furanose form＞pyranose form. The above results are helpful for the elucidation of bio-activities and structure relationship of ginsenosides.

Key words: single-strand oligonucleotide, ginsenoside, non-covalent complex, effect factor, electrospray ionization mass spectrometry