Initiating Conformation Transitions of Individual YOYO-Intercalated DNA Molecules with Optical Trapping

Abstract

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 ∼2.7 kbp (pUC19) to ∼105 kbp (T5). With atomic force microscopy, individual YOYO-intercalated λ-DNA condensates (∼48.5 kbp) were shown to exhibit a toroidal structure that ranged in diameter from 100 to 150 nm with a maximum height of ∼6 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.