Spatial and Mechanical Properties of Dilute DNA Monolayers on Gold Imaged by AFM

Abstract

Spatially distributed DNA oligomer arrays on Au(111) surfaces were created by one-step co-assembly of mixed monolayers of alkanethiol-conjugated DNA and mercaptohexanol (MCH). Tapping-mode AFM was used to visualize the distribution of DNA molecules on the surface and to study the mechanical properties of individual molecules. The DNA coating density increased nonlinearly with increasing mole fraction of DNA oligomer to MCH in the coating solution. For imaging in air, where surfaces are coated with a thin layer of water, the interaction between the AFM tip and the different structures on the monolayer varies between attractive and repulsive depending on the tapping amplitude, set-point ratio, and tip shape. It was found that both duplex and single-stranded DNA molecules extend approximately vertically upward from the surface.

The Use of an Electroactive Marker as a SERS Label in an E‐melting Mutation Discrimination Assay

“…The conditions for attachment of the probe were chosen to ensure that the probe molecules were well spaced on the surface (see below for details of coverage) so that hybridization to the target would not be sterically or electrostatically inhibited [25,26] and the remaining surface was passivated with mercaptohexanol to suppress non-specific binding to the gold [25]. The mercaptohexanol also serves to reorient the ssDNA on the surface to a more upright conformation [27,28]. Scheme 2 shows the general arrangement for the dsDNA melting experiments.…”

Structural and Optical Properties of DNA Layers Covalently Attached to Diamond Surfaces

“…The orientation of DNA in low density layers on gold substrates has been studied theoretically, 25 as well as experimentally. [26][27][28][29] One approach is to monitor the interfacial fluorescence quenching, which increases when the fluorescence dye at the distal end of DNA is brought closer to a gold substrate, while the gold electrode is biased to alternately positive and negative potentials. 26 Also atomic force microscopy (AFM) and scanning tunneling microscopy (STM) are applied to dilute, [27][28][29] as well as 'dense' DNA layers on gold.…”

“…[26][27][28][29] One approach is to monitor the interfacial fluorescence quenching, which increases when the fluorescence dye at the distal end of DNA is brought closer to a gold substrate, while the gold electrode is biased to alternately positive and negative potentials. 26 Also atomic force microscopy (AFM) and scanning tunneling microscopy (STM) are applied to dilute, [27][28][29] as well as 'dense' DNA layers on gold. 2,3 When the DNA is in a dense layer, the molecules do interact, and the conformation and orientation of the molecules can become strongly affected by these interactions.…”

DNA Biosensor Concepts Based on a Change in the DNA Persistence Length upon Hybridization

“…The physical properties of DNA change upon hybridization because the formation of the base stack causes dsDNA to be much more rigid than ssDNA [10]. This difference in rigidity can be described in terms of persistence length, which is the distance over which the DNA backbone behaves as a rigid rod [11].…”