Patterning nanocrystals using DNA

Abstract

One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases selfassembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-2 branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA "trimer." This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 µm, and collecting atomic force microscopy (AFM) images up to 30 µm. We found the lattices' requirement of divalent magnesium cations to stabilize Holliday junctions to be incompatible with the stability of charge-stabilized gold nanoparticles used for the experiments here, and gold particles added indiscriminately to the lattice surface through non-specific binding. Redesigning the lattices to avoid magnesium may improve results.

Circular DNA Logic Gates with Strand Displacement

“…Here, the lengths of the two designed thiolated oligonucleotides were 59 bases, including long poly-T tails. This was because, if the length was shorter than 50-mer, it would be hard to discriminate among discrete AuNP/DNA conjugates by agarose gel. − After adding input strands 2F-1 and 2C-1 (anchored to AuNPs), the exposed toehold region on DNA ring A allowed for its specific removal of the two original short DNA strands and migration with the fully complementary input strands. Thus, when DNA displacement was completed, a pair of AuNPs were attached to each DNA ring.…”

“…17,18 However, in the presence of Mg 2þ , AuNPs tend to aggregate in a disorganized manner. 31 To avoid this, 0.5Â TBE buffer was applied, with 100 mM NaCl. Monoconjugated AuNP/ DNA particles were prepared by incubating 5 nm AuNPs and 5 0 -thiolated ssDNA together overnight.…”

“…In recent years, a method of DNA self-assembly has been developed using TAE/Mg 2+ buffer. , However, in the presence of Mg 2+ , AuNPs tend to aggregate in a disorganized manner . To avoid this, 0.5× TBE buffer was applied, with 100 mM NaCl.…”