Characteristic differences in the X-ray photoelectron spectrum between B-DNA and M-DNA monolayers on gold

Duplex DNA monolayers were self-assembled on gold through a disulfide linkage and both B- and M-DNA conformations were studied using X-ray photoelectron spectroscopy (XPS). The film thickness, density, elemental composition and ratios for samples were analyzed and compared. The DNA surface coverage, calculated from both XPS and electrochemical measurements, was approximately 1.2 × 1013 molecules/cm2 for B-DNA. All samples showed distinct peaks for C 1s, O 1s, N 1s, P 2p and S 2p as expected for a thiol-linked DNA. On addition of Zn2+ to form M-DNA the C 1s, P 2p and S 2p showed only small changes while both the N 1s and O 1s spectra changed considerably. This result is consistent with Zn2+ interacting with oxygen on the phosphate backbone as well as replacing the imino protons of thymine (T) and guanine (G) in M-DNA. Analysis of the Zn 2p spectra also demonstrated that the concentration of Zn2+ present under M-DNA conditions is consistent with Zn2+ binding to both the phosphate backbone as well as replacing the imino protons of T or G in each base pair. After the M-DNA monolayer is washed with a buffer containing only Na+ the Zn2+ bound to the phosphate backbone is removed while the Zn2+ bound internally still remains.