Morphology of 15-mer Duplexes Tethered to Au(111) Probed Using Scanning Probe Microscopy
The long-range film structure of 15 base pair, thiol-derivatized duplexes tethered through single 3' and 5' linkages to a Au(111) surface is measured via scanning probe microscopy. Film morphology of the 3' linked duplexes differs from that of its 5' counterpart as observed by scanning probe microscopy in contact mode under buffer solution. No structural features are distinguished in a film formed with the 5' linked duplexes as measured with either a bare silicon nitride or chemically modified probe. However, a distinct pattern in the film structure of the 3' linked duplexes is measured with a chemically modified, hydrophobic tip. Small changes in linker orientation can greatly affect DNA film structure, and a hypothesis for the self-assembly mechanism of the 3' linked duplexes is presented. Factors such as linker placement and composition must be considered in comparing DNA microarrays formed with different tethering methods.
© 2001 American Chemical Society. Received 2 April 2001. Published online 18 August 2001. Published in print 1 September 2001. E.M.S. and M.S. thank the National Science Foundation (PECASE, NSF No. 9703345), Occidental College, and the Howard Hughes Medical Institute through the Undergraduate Biological Sciences Education Program for generous financial support. J.K.B., E.M.B., and M.G.H. are grateful to the NIH for financial support (GM61077). In addition, we are grateful to Dr. William Royea and Professor Nathan Lewis of Caltech for the application of gold overlayers to the SPM tips required for derivatization.