ATOMIC-FORCE MICROSCOPY OF SUPERCOILED DNA-STRUCTURE ON MICA

Atomic force microscopy (AFM) has been used to investigate supercoiled DNA structure. In AFM imaging, the deformation of DNA structure in th e adsorption process onto the mica surface is a serious problem. To in vestigate the structure of supercoiled DNA in solution by AFM, the met hod by which DNA is fixed on the substrate without any deformation of the structure should be developed. In this paper, it is made c:lear th at the structure of supercoiled DNA on mica is dependent on the method of treatment of the mica substrate. We prepared four kinds of mica su rfaces; which were (1) no treatment (freshly cleaved) mica, treated wi th (2) spermine, (3) spermidine and (4) 3-aminopropyltriethoxysilane. Tile values of roughness of the mica treated with spermine and spermid ine were 0.18 and 0.19 nm, respectively, while that of the mica treate d with 3-aminopropyltriethoxy silane was 0.38 nm. Supercoiled DNA mole cules (pUC19) were fixed in the shape of open circles on the freshly c leaved mica surface, whereas supercoiled DNA molecules on the mica tre ated with spermine or spermidine interwound tightly. We could, moreove r, observe the clockwise handedness of the supercoiled DNA with AFM us ing the mica treated with spermine as substrate. The apparent length o f DNA in the supercoil was shorter than that in open circular DNA. It was made clear by analysis of the differences of these measured length s that the superhelix winding angle and the value of writhe of pUC19 w ere 61 degrees and 10.2, respectively. (C) 1998 Elsevier Science B.V.