Theory of Melting and the Optical Properties of Gold/DNA Nanocomposites

We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in temperature for larger particles, and much sharper than that of an isolated DNA link. All these features are in agreement with available experiments. The aggregate is modeled as a cluster of gold nanoparticles on a periodic lattice connected by DNA bonds, and the extinction coefficient is computed using the discrete dipole approximation. Melting takes place as an increasing number of these bonds break with increasing temperature. The melting temperature corresponds approximately to the bond percolation threshold.Comment: 5 pages, 4 figure. To be published in Phys. Rev.

Structure Formation, Melting, and the Optical Properties of Gold/DNA Nanocomposites: Effects of Relaxation Time

We present a model for structure formation, melting, and optical properties of gold/DNA nanocomposites. These composites consist of a collection of gold nanoparticles (of radius 50 nm or less) which are bound together by links made up of DNA strands. In our structural model, the nanocomposite forms from a series of Monte Carlo steps, each involving reaction-limited cluster-cluster aggregation (RLCA) followed by dehybridization of the DNA links. These links form with a probability $p_{eff}$ which depends on temperature and particle radius $a$. The final structure depends on the number of monomers (i. e. gold nanoparticles) $N_m$, $T$, and the relaxation time. At low temperature, the model results in an RLCA cluster. But after a long enough relaxation time, the nanocomposite reduces to a compact, non-fractal cluster. We calculate the optical properties of the resulting aggregates using the Discrete Dipole Approximation. Despite the restructuring, the melting transition (as seen in the extinction coefficient at wavelength 520 nm) remains sharp, and the melting temperature $T_M$ increases with increasing $a$ as found in our previous percolation model. However, restructuring increases the corresponding link fraction at melting to a value well above the percolation threshold. Our calculated extinction cross section agrees qualitatively with experiments on gold/DNA composites. It also shows a characteristic ``rebound effect,'' resulting from incomplete relaxation, which has also been seen in some experiments. We discuss briefly how our results relate to a possible sol-gel transition in these aggregates.Comment: 12 pages, 10 figure

Density functional study of Aun_n (n=2-20) clusters: lowest-energy structures and electronic properties

We have investigated the lowest-energy structures and electronic properties of the Au$_n$(n=2-20) clusters based on density functional theory (DFT) with local density approximation. The small Au$_n$ clusters adopt planar structures up to n=6. Tabular cage structures are preferred in the range of n=10-14 and a structural transition from tabular cage-like structure to compact near-spherical structure is found around n=15. The most stable configurations obtained for Au$_{13}$ and Au$_{19}$ clusters are amorphous instead of icosahedral or fcc-like, while the electronic density of states sensitively depend on the cluster geometry. Dramatic odd-even alternative behaviors are obtained in the relative stability, HOMO-LUMO gaps and ionization potentials of gold clusters. The size evolution of electronic properties is discussed and the theoretical ionization potentials of Au$_n$ clusters compare well with experiments.Comment: 6 pages, 7 figure

Computer-aided design of nano-filter construction using DNA self-assembly

Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules

The sequence-specific cellular uptake of spherical nucleic acid nanoparticle conjugates

The sequence-dependent cellular uptake of spherical nucleic acid nanoparticle conjugates (SNAs) is investigated. This process occurs by interaction with class A scavenger receptors (SR-A) and caveolae-mediated endocytosis. It is known that linear poly(guanine) (poly G) is a natural ligand for SR-A, and it has been proposed that interaction of poly G with SR-A is dependent on the formation of G-quadruplexes. Since G-rich oligonucleotides are known to interact strongly with SR-A, it is hypothesized that SNAs with higher G contents would be able to enter cells in larger amounts than SNAs composed of other nucleotides, and as such, cellular internalization of SNAs is measured as a function of constituent oligonucleotide sequence. Indeed, SNAs with enriched G content show the highest cellular uptake. Using this hypothesis, a small molecule (camptothecin) is chemically conjugated with SNAs to create drug-SNA conjugates and it is observed that poly G SNAs deliver the most camptothecin to cells and have the highest cytotoxicity in cancer cells. Our data elucidate important design considerations for enhancing the intracellular delivery of spherical nucleic acids

Multivesicular assemblies as real-world testbeds for embryogenic evolutionary systems

Embryogenic evolution emulates in silico cell-like entities to get more powerful methods for complex evolutionary tasks. As simulations have to abstract from the biological model, implicit information hidden in its physics is lost. Here, we propose to use cell-like entities as a real-world in vitro testbed. In analogy to evolutionary robotics, where solutions evolved in simulations may be tested in real-world on macroscale, the proposed vesicular testbed would do the same for the embryogenic evolutionary tasks on mesoscale. As a first step towards a vesicular testbed emulating growth, cell division, and cell differentiation, we present a modified vesicle production method, providing custom-tailored chemical cargo, and present a novel self-assembly procedure to provide vesicle aggregates of programmable composition

Towards tailored communication networks in assemblies of artificial cells

Living Technology is researching novel IT making strong use of programmable chemical systems. These chemical systems shall finally converge to artificial cells resulting in evolvable complex information systems. We focus on procedural manageability and information processing capabilities of such information systems. Here, we present a novel resource-saving formation, processing, and examination procedure to generate and handle single compartments representing preliminary stages of artificial cells. Its potential is exemplified by testing the influence of different glycerophospholipids on the stability of the compartments. We discuss how the procedure could be used both in evolutionary optimization of self-assembling amphiphilic systems and in engineering tailored communication networks enabling life-like information processing in multicompartment aggregates of programmable composition and spatial configuration