ANALYSIS OF SYNTHETIC DNAS AND DNA-PROTAMINE COMPLEXES WITH THE SCANNING TUNNELING MICROSCOPE

Three duplex DNAs 22, 47, and 100 base-pairs in length have been image d with the scanning tunneling microscope (STM) after deposition on hig hly oriented pyrolytic graphite (HOPG). Images of the 47 base-pair (bp ) molecules are resolved sufficiently to identify the two phosphodiest er strands, the direction of helical coiling (this molecule contains t hree turns of left-handed helix), and single-stranded ends. Length mea surements indicate that all three DNA sequences have adopted an ''A-li ke'' conformation. DNA-protamine complexes were also prepared and imag ed under similar conditions. Length measurements of the complexes demo nstrate that the binding of bull protamine 1 to the 47-mer stabilizes the DNA in a B conformation and prevents the B to A transition that ha s been shown to occur as the DNA molecules dehydrate on the surface. M easurements of the diameter of the complex (3 nm) were also obtained a nd were found to be only slightly larger than the DNA molecule. This o bservation is consistent with the binding of the protamine molecule in side one of the grooves.