DNA contour length
Based on X-ray crystallography, B-form DNA has a helical rise of 3.38 Å/bp, and therefore our 560 bp DNA would be expected to have a contour length of 189 nm instead of the 159 ± 24 nm length that we measured in the absence of protein. This result was doublechecked by using an AFM calibration standard with a 500 nm ± 1% period, comparable to the image size. Possible physical reasons for the shortening could be associated with the immobilization of DNA on the mica substrate. In the presence of NiCl2 and Tris, the average helical rise is 2.97 ± 5% Å/bp.39 Shortening of 500 bp DNA by about 10 nm occurs in the presence of Mg2+ or Mn2+ due to partial conformational transition from B-DNA to A-DNA upon drying.40 The drying process, phosphate-cation interactions on the mica surface, and cations that bridge two parts of the DNA backbone40 may contribute to shortening.