AVS 53rd International Symposium
    Nucleic Acids at Surfaces Topical Conference Monday Sessions
       Session DN-MoM

Paper DN-MoM2
Identifying Short DNA-Strands with Redox Markers by in situ Scanning Tunnelling Microscopy

Monday, November 13, 2006, 8:20 am, Room 2014

Session: Nucleic Acids at Surfaces I
Presenter: M. Grubb, Technical University of Denmark
Authors: M. Grubb, Technical University of Denmark
H. Wackerbarth, Technical University of Denmark
T. Albrecht, Technical University of Denmark
J. Ulstrup, Technical University of Denmark
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In situ scanning tunnelling microscopy (STM) and electrochemistry of short DNA-strands attached to Au(111)-electrodes via a mercaptohexyl linker has shown that the conformation of short single-stranded sequences depend strongly on the sample potential. Without potential control the molecules form a disordered self-assembled monolayer (SAM). Ordered domains form as the sample potential is stepped to more negative values.@footnote 1@ Mercaptohexanol (MCH) was introduced into the monolayer as a lateral spacer molecule to create a mixed DNA/MCH SAM with space for hybridisation. MCH has the same length as the linker unit and forms itself highly ordered SAMs on Au(111)-electrode surfaces, independent of the sample potential. A mixed monolayer was created by first letting a mercaptohexyl-modified single-stranded DNA adsorb to the Au(111)-surface for one hour. This was followed by washing in buffer and then letting MCH adsorb. One hour is not enough to create a complete monolayer consisting only of DNA, and this leaves space for MCH, which also replaces weakly bound DNA. The mixed monolayer showed no order, and it was not possible to distinguish DNA from MCH. This supports previous findings that DNA in disordered conformation has low contrasts in STM. Hexa-ammineruthenium (II)/(III) (RuHex) can, however, be used to identify DNA immobilised on the surface, since it binds specifically to the DNA backbone.@footnote 2@ The bound RuHex provides a high tunnelling contrast (compared to DNA), but the exact mechanism of the charge transfer process is not yet clear. Single-stranded DNA has previously been viewed as a poor charge transfer agent, but this seems to change when RuHex is bound. Studies of the nature of the charge transfer process of the DNA-bound RuHex are in progress. @FootnoteText@ @footnote 1@ H. Wackerbarth, M. Grubb, J. Zhang, A.G. Hansen, and J. Ulstrup, Angew.Chem.Int.Ed., 2004, 43, 198@footnote 2@ A.B. Steel, T.M. Herne and M.J. Tarlov, Anal.Chem. 1998, 70, 4670.