Marsh Research Group - Biochemistry, Nanochemistry, Materials Science
Background. Research in the Marsh group is focused on the self-assembly of guanine-rich DNA's into higher order structures for development of nanoscale devices. The use of DNA in the development novel biomaterials is of great interest in the rapidly growing field of nanotechnology. Potential applications for DNA nanostructures include the development molecular sensors, switches, molecular scaffolding, and molecular wires (see links). Nature has provided a number of useful characteristics in DNA that make it an attractive material for these applications. Nucleic acids have the capacity to self-assemble into complex structures under relatively mild conditions. Formation of a specific structure may be programmed into the DNA sequence and oligonucleotides may be synthesized with modifications through facile automated or manual chemical methods. Much of the published work on the development of DNA nanotechnology has taken advantage of what nature employs for information storage and processing, the Watson and Crick (W/C) base pairs G:C and A:T of double helical DNA (B-DNA, Figure 1 A). Other DNA morphologies, in particular quadruple helical DNA, may also perform in a similar or superior way to B-DNA in certain nanotechnology applications.
Figure 1. Comparison of B-DNA and G-DNA structures.
A molecule of DNA comprised of multiple guanine repeats in its sequence may form a quadruple helical structure generally known as G-DNA (Figure 1 B). In contrast to the A:T , G:C interactions that direct the self-assembly of double stranded B-DNA, a guanine-rich nucleic acid will self-assemble into a quadruple helix due to guanines H-bonding to other guanines forming a G-quartet. G-DNAs come in several varieties depending on the number of molecules it's made of and the conditions used to make it (pH, concentration, coordinating cation, temperature). Short molecules of single stranded nucleic acid called guanine-rich oligonucleotides (GROs) can self-assemble into much larger structures known as supramolecular polymers. This is the material we work with to create self-assembled nanostructures. The principle building block material for our work is the 10-mer oligonucleotide (d(G 4 T 2 G 4 )) that self-assembles into linear filaments called G-wires. These structures may be visualized by a high-resolution scanning probe microscopy (SPM) technique known as TappingMode -Atomic Force Microscopy (Figure 2) (go to Veeco Metrology for more information, http://www.veeco.com/). We can grow G-wires using a variety of buffer and temperature conditions and have observed these structures using a variety of substrates and SPM techniques.
Figure 2 . A) A very simplistic model for self-assembly of the Tet1.5 oligonucleotide into long G-wires. Arrows represent the sequence d(G 4 T 2 G 4 ) and the quadrilaterals are G-quartets. B) TM-AFM image of G4-DNA filaments. Scale bar = 50 nm. (adapted from Marsh et al 1995)
At this point the really big question we want to answer is can the Tet 1.5 oligonucleotide be utilized as a nucleic acid molecular scaffold? Of course we say yes to this or at least we think so. The usefulness of G-wires as a molecular scaffold depends upon the ability to attach other things to it such as a nanoparticle. There are many examples of nanoparticles arranged on DNA scaffolds and how this is done can be divided into three main strategies:
1. Oligonucleotide mediated
2. Functional group mediated