Interaction between DNA and a Si(111) substrate with steps observed by noncontact atomic force microscopy

Toyoko Arai, Masahiko Tomitori, Masato Saito and Eiichi Tamiya

School of materials science
Japan Advanced Institute of Science and Technology

DNA sustained on a Si(111) substrate are observed by a noncontact atomic force microscope (nc-AFM) operated in a UHV. The substrate is cleaned in the nc-AFM chamber to exhibit a 7x7 reconstruction of Si(111) with bi-atomic steps, 0.31 nm high; the step distribution is roughly determined by a vicinal cut angle of the substrate, where the terrace width is roughly 100 nm. The milli-Q solution containing pBR322 plasmid DNA digested by Cla I is dropped on it in a nitrogen atmosphere of a glove box, which is directly connected into the introduction chamber of the nc-AFM chamber. The molecule has a 4361bp. Interestingly, we have found that the DNA are stretched by being pinned at the steps of the substrate; both ends of the digested DNA, which looks folding, are preferentially pinned at a crossing of two steps on the Si(111) substrate with a double height, 0.62 nm.