chapter  13

Properties of “G-Wire” DNA

WithThomas Marsh, James Vesenka

The observed properties of guanine-quadruplex “G-wire” DNA are summarized. These observations include the evaluation of the growth kinetics, along with structural and electronic properties of the dry self-assembled G4T2G4 polymer. The primary investigative tool for these studies was scanning probe microscopy. Growth kinetics studies indicate the self-assembly process is diffusion limited and provides Poisson-like distribution of G-wire lengths upon reaching equilibrium. This evidence suggests that self-assembly is driven by thermodynamic processes. The average lengths of these molecules are around 100 nm after 24 hours of growth. Longer G-wire DNA molecules (many micrometers) have been found both in flexible and crystalline forms following many months of growth. The latter structures are extremely interesting candidates for molecular templates.

Hydration layer scanning tunneling microscopy (HLSTM) of G-wires on mica was carried out under controlled humidity conditions. The HLSTM images were similar to those measured by atomic force microscopy (AFM) in dry air. The G-wire height above the mica substrate, interpreted as quadruplex diameter, and the G-wire width appeared to decrease slightly with increasing humidity. Though much of the lateral broadening is likely a result of shielding by residual cations and the lower resolving ability of HLSTM, the dependence of the DNA height and width on humidity suggests a simple explanation in terms of a hydration layer. An increased thickness of the hydration layer of up to 0.6 nm was observed.

The electrical conductivity of G-wire DNA adsorbed to the surface of mica was examined with the assistance of silicon shadow masks. Four-point probe masks were fabricated in silicon using photolithographic patterning and dry reactive ion etching. The silicon “stencils” were designed specifically for use in generating shadow-deposited metal contacts on top of G-wire DNA samples adsorbed to the atomically flat surface of mica. Two types of metal contacts were employed in these experiments: electron beam evaporated gold using a high vacuum system, and argon sputtered gold using a low vacuum scanning electron microscopy sample coating apparatus. The metal electrode patterning was characterized through AFM imaging. The conductivity of the G-wire DNA samples was analyzed using a high impedance multimeter. The lower limit of resistance of the G-wire DNA networks was determined to be in excess of 1 GΩ (sheet resistance of 105GΩ-m2) indicating from these experiments that “dry” G-wire DNA is an insulator.