Construction of Tetrahedral Photonic Bandgap Crystal:

Demonstrating Three-Dimensional Self-Assembly using DNA Linkage

Principle Investigator: Peter V. Schwartz, Cal Poly Physics Department

This project is truly multidisciplinary, involving faculty on Cal Poly campus from physics, chemistry, biology, and material science, and is done in collaboration with the UCSB Materials Engineering and Chemical Engineering Departments.ÝÝ All work is done by undergraduates.Ý During the summer, five students conducted this DNA related research: Jackson Crews (Physics), Antoine Calvez (Physics, AERO), Phil Rogers (Physics), Alistair Wood (Physics), Mike Yeung (EE).Ý A sixth student, James Kwok On Lau (MATE) worked with our collaborator, David Pine at UCSB.

Technical Background:

Short strands of DNA (10ñ20 bases) are used as nanoscopic, selective VelcroÆ to guide the self-assembly of nanostructures in solution because DNA strands only bond (hybridize) to other DNA strands if they have a complementary sequence.Ý A three-component system is used in our studies (see Figure 1); where a linker is hybridized to two separate surface-bound DNA strands in order to achieve aggregation of microspheres.Ý

Figure 1.Ý A schematic of the three-component system used in our studies.Ý The green square and the red cycle represent the fluorescence labels used to quantify the DNA coverage and hybridization efficieny described in the ìProgressî section.Ý Many thousands of identical DNA strands are on each microsphere.

We have successfully achieved DNA attachment to single polystyrene microspheres and subsequent controllable aggregation of these microspheres by means of DNA hybridization (Figure 2).

Figure 2.Ý Micrographs of aggregation of microspheres via DNA hybridization.Ý Left: no linker present results in no aggregation.Ý Right: linker present results in aggregation.

Progress:

Quantifying DNA surface coverage.Ý In more recent work, we are quantifying the DNA coverage (amount of DNA bonded to the microsphere), and the subsequent hybridization efficiency (the percentage of bonded DNA that attach to freely-floating DNA strands via hybridization) through measurements using fluorescent-labeled DNA.Ý The concentration of DNA in solution is also measured using light absorption techniques in order to confirm measurements.Ý Figure 3 and Figure 4 show the schemes we have used to quantify the DNA coverage and the hybridization efficiency, respectively.Ý Quantification of the DNA coverage and hybridization efficiency has allowed us to optimize the procedure we use to aggregate microspheres.Ý We

have found that the surface density of DNA bonded to the beads can be controlled by the concentration of DNA in solution and the pH of the reaction.Ý We have also found that the hybridization efficiency decreases at higher DNA surface coverage.Ý We have also designed and constructed an improved observation cuvette to do fluorescence spectroscopy on our opaque suspensions of microspheres (Figure 5), and plan on repeating our measurements with improved accuracy.

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ÝÝ Figure 4.Ý Scheme to measure linker DNA hybridization on surface-bound DNA.

Improving Specificity of BondingÝ

Although our preliminary results are very encouraging, we are taking an additional step to investigate how to produce pure aggregates and how to anneal out imperfections and impurities.Ý We have introduced into the experiment an impurity in the form of ìrandom strand beadsî ñ microspheres covered with a DNA sequence that is not complementary to anything else in suspension.Ý The random strand beads are also a different color, so that they can be identified.Ý Our efforts are focused on eliminating random strand beads from the aggregates made from hybridized beads.Ý We have discovered that lowering salt concentration and providing gentle agitation during hybridization can improve the size and purity of the aggregates.Ý A large aggregate made of yellow microspheres is shown in Figure 6.Ý The random strand beads are white and are largely absent from the aggregate.Ý Using fluorescence microscopy, we can identify the minority impurities inside the aggregate.Ý We have designed and built a heating stage that fits on optical and fluorescence microscopes, and have begun preliminary annealing experiments (Figure 7).Ý We will observe aggregates during future annealing experiments and hope to be able to expel impurity beads through heating.

Investigating a new Substance

An aggregate of DNA-linked microspheres is a new substance with unique properties.Ý We have been able to make macroscopic samples of microsphere aggregate and future experiments will quantify the visco-elastic properties as well as the dependence on temperature.