Abstract
Atomic-Force Microscopy (AFM) has become an effective tool in the three dimensional characterization of biological systems and is capable of Angstrom sensitivity in the vertical dimension. One unresolved dilemma is that the observed height (diameter) of B-DNA being about 10Å, is less than half its x-ray diffraction value. In this paper we attempt to determine the source of this discrepancy by comparing plasmid DNA co-deposited with a novel form of DNA called “G-wires” (Figure 1). G-wires are formed by G-rich sequences. They are composed of G-4 DNA, a quadruple helical structure. X-ray data of G-4 DNA gives a diameter of 27Å, comparable to that expected for B-DNA (20 to 25Å). In the AFM these structures have a significantly greater height (av. = 22 Å) compared to double stranded (av. = 7 Å) or supercoiled B-DNA (av. = 14 Å) (Figure 2). Thus, the apparent height of nucleic acids in the AFM is dependent upon their innate structural characteristics.