Initiating conformation transitions of individual YOYO-intercalated DNA molecules with optical trapping

This letter reports that the commonly used DNA intercalator dye YOYO-1 can act as a condensing agent under moderately acidic pH conditions (pH 5.7) for DNA molecules ranging in size from similar to2.7 kbp (pUC19) to similar to105 kbp (T5). With atomic force microscopy, individual YOYO-intercalated lambda-DNA condensates (similar to48.5 kbp) were shown to exhibit a toroidal structure that ranged in diameter from 100 to 150 nm with a maximum height of similar to6 nm. Once these molecules are compacted, optical trapping can be used to initiate the conformational transitions of such single, condensed DNA molecules with excellent time resolution.