Auto-orientation of G-wire DNA on mica

Abstract

Scanning probe microscopy was used to examine the orientation of Tet1.5 quadruplex DNA polymers, a.k.a. "G-wires", after adsorption onto freshly cleaved Phyllosilicate micas. The G-wires appear to have a preferential orientation at 60• intervals after thorough rinsing and slow drying. The angles the G-wires made with the fast scan direction of the SPM probe were measured and the frequency-angle information was quantitatively characterized by an empirical correlation coefficient. Careful measurements indicate the Tet1.5 G-wires orient along the b lattice vector of mica, the next nearest neighbor potassium vacancy. A model is proposed to explain this auto-orientation affect due to alignment of the G-wires' phosphate backbone through magnesium tether cations. Pairs of adjacent, parallel phosphate groups of the G-wires (0.95 nm apart) appear to align with the next nearest neighbor potassium vacancy sites of mica (0.90 nm apart). This behavior is not observed in solution. The potential for using the auto-orientation phenomena in the development of high-density biomolecular nano-electronic devices is explored.

A stable G‐quartet binds to a huntingtin protein fragment containing expanded polyglutamine tracks

“…The primary and secondary structure of DNA are not affected by adsorption onto mica, although the tertiary structure is known to be affected by ionic concentration (Lyubchenko and Shlyakhtenko, 1997; Dingley et al, 2005). The presence of divalent cations is essential for binding DNA to mica (Vesenka et al, 1992), and these cations are known to cause alignment of quadruplex DNA along the hexagonal atomic structure of mica surface (Vesenka et al, 2007). The orientation of the G‐wires can also be seen in Figure 7c because of the presence of Ca 2+ in the reaction buffer.…”

“…The rafts seen in Figure 7d also have a height of 0.5 6 0.1 nm (cross-section not shown). Because the G-wires appear oriented on the surface of mica, because of an interaction among the G-wires, mica, and a tethering ion found in the buffer (Vesenka et al, 2007), the G-wires probably lay down first, and the Htn protein is assembled over and around them.…”

Long‐range assembly of DNA into nanofibers and highly ordered networks

“…Their unique geometries and properties open up otherwise inaccessible structural options and new functionalities to DNA architectures. For example, guanine‐rich sequences have been shown to assemble into G‐wires, extended 1D stacks of G‐quadruplexes100,101; similarly, long‐range assembly of cytosine‐rich i‐motif‐forming sequences has been reported 102. More complex constructs based on alternate DNA base pairing are an area of interest 103,104.…”

Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

“…Similar phenomena are also reported at high concentration of DNA in solution, [32][33][34] as well as on surfaces. [35][36][37] DNA aggregation has been extensively studied theoretically from the perspective of DNA-DNA interactions, including electrostatic interactions, pair interactions, hard core, van der Waals, and hydration interactions. [38] The common denominator of these processes is associated with large DNA densities obtained either due to modulations of the solvent activity or upon confinement of DNA into a limited space.…”