DNA DESIGNER CRYSTALS -- 3D TRIANGLE, DODECAMER, 16MER

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We have prepared three types of DNA crystals. The first one is called triangle. The space group is R3. Resolution we got is about 5A. The second one is dodecamer DNA crystal. The space group is C2. The resolution we can get for it is about 3A. The third one is 16mer DNA crystal. The space group is P43. The resolution is about 3.1A. Our group has designed a variety of DNA motifs expected to form 3D lattices. Ultimately, the applications of 3D DNA lattices include providing scaffolding that is capable of binding and orienting a variety of species. Crystals of macromolecules and notoriously difficult to grow, and the process of crystallization relies heavily on pure luck. DNA cages could act as a host to these molecules, aligning them in a periodic fashion necessary for X-ray analysis. The 3D designs pursued in our laboratory are predicated on Watson-Crick complementarities. In order to confirm the formation of 3D DNA lattices, we purify the strands corresponding to those designs and self-assemble them into the desired motifs. It will attempt to form crystalline lattices with the DNA motifs. When crystals appear, they will be characterized by X-ray diffraction methods. Derivatized crystals will be prepared, and the structures solved when the resolution is high enough to warrant such studies. A 3D triangle was made in this work involved incorporating DX molecules to replace the double helices. Crystals of this motif were grown using a combination of vapor diffusion and a heating protocol. They ranged from 100 to 200um in length. A two-tile version of the 3D DX triangle has been designed and the AFM evidence supports its formation. So far, we have completed the DLS characterization of the melting behaviors of the aggregates so as to determine proper temperature ranges and preferred lattice periodicities and to establish a relationship between the melting temperatures established by the DLS and the proper temperature at which to attempt crystallization. In our lab we also tried HPLC purification followed by gel purification. The improved resolution on some simple version encourages us to apply HPLC purification on this motif. Also followed Dr. Sherman¿¿¿¿¿"s suggestion, we modified the motif design to make sure the structure is in less strain. Hopefully, during this course, we would have crystals from this new modification.