Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Rationalizing the Outcome of One-Pot DNA Nano-Assemblies
Here we present a fully addressable four-ring DNA nanonetwork composed of tripodal oligonucleotide building blocks and show that with a set of unique oligonucleotide building blocks, based on orthogonal sequence design, it is possible to assemble non-repetitive networks with high information density. Our DNA based assembly system is focused on building fully addressable networks, using the smallest practical units of DNA, i.e. one turn of the double helix (1, 2). Having addressable structures is a prerequisite for controlled positioning of functional units, being components for energy transfer or chemical reaction centers. Huge progress has been made in the past decade using DNA as a building block for nanoscale fabrication (3). The nanoscale fabrication relies solely on self-assembly of carefully designed DNA molecules with the free energy of hybridization as the underlying driving force. With extra consideration taken to the design of base sequences, a desired structure can be created in a one-pot, one-step assembly reaction. In our study we address a fundamental problem with DNA nanofabrication based on a one-step assembly process, i.e. the reaction yield. The total yield of DNA assemblies in one-pot reactions can be described in terms of the yield of one hybridization reaction, raised to the power of total number of events. We therefore look for and suggest alternative assembly strategies, one of which being a fixation strategy based on click chemistry, creating robust units for a modular build-up approach (4).
Erik P. Lundberg1*
1Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.