Kinetics of DNA and RNA Hybridization in Serum and Serum-SDS

Cancer is recognized as a serious health challenge both in the United States and throughout the world. While early detection and diagnosis of cancer leads to decreased mortality rates, current screening methods require significant time and costly equipment. Recently, increased levels of certain micro-ribonucleic acids (miRNAs) in the blood have been linked to the presence of cancer. While blood-based biomarkers have been used for years in cancer detection, studies analyzing trace amounts of miRNAs in blood and serum samples are just the beginning. Recent developments in deoxyribonucleic acid (DNA) nanotechnology and DNA computing have shown that it is possible to construct nucleic-acid-based chemical networks that accept miRNAs as inputs, perform Boolean logic functions on those inputs, and generate as an output a large number of DNA strands that can be readily detected. Since miRNAs occur in blood in low abundance, these networks would allow for amplification without using polymerase chain reaction. In this study, we report initial progress in the development of a DNA-based cross-catalytic network engineered to amplify specific cancer-related miRNAs. Subcomponents of the DNA network were tested individually, and their operation in serum, as well as a mixture of serum with sodium dodecyl sulfate, is demonstrated. Preliminary simulations of the full cross-catalytic network indicate successful operation

Cavity Resonant Mode in a Metal Film Perforated with Two-Dimensional Triangular Lattice Hole Arrays

The transmission property of metallic films with two-dimensional hole arrays is studied experimentally and numerically. For a triangular lattice subwavelength hole array in a 150 nm thick Ag film, both cavity resonance and planar surface modes are identified as the sources of enhanced optical transmissions. Semi-analytical models are developed for calculating the dispersion relation of the cavity resonant mode. They agree well with the experimental results and full-wave numerical calculations. Strong interaction between the cavity resonant mode and surface modes is also observed

Synthesis and Functionalization of Small Silver Nanoparticles

Metal nanoparticles in general exhibit interesting properties due to their small sizes. This response shows up as an intense absorption band in the visible region making metallic nanoparticles ideal probes for medical imaging as well as for countless other applications. Functionalizing metallic nanoparticles with DNA enables targeted labeling, controlled by their base sequence. Another purpose of functionalization is to attach the nanoparticle to a DNA substrate allowing controlled bottom up engineering of nanoscale devices. Gold or gold-encapsulated silver is usually used for these purposes instead of bare silver due to the ease with which silver is oxidized although silver nanoparticles show more intense plasmon resonance. The functionalization of silver with DNA is difficult because their surfaces are easily oxidized. The goal of this experiment was to attach thiolated DNA strands to bare 5-10 nm silver nanoparticles proving that it can indeed be done without extensive modification of the functionalization procedure. In order for this to be accomplished silver nanoparticles were synthesized using two different methods: a UV light directed growth method and a sodium borohydride/sodium citrate buffered reduction method. The first method resulted in nanoparticles in the 10-15 nm range while the second resulted in smaller particles (5-10 nm). DNA was then attached to purified particles using a process that has previously been applied to gold nanoparticles. The functionalization was verified using UV-Vis spectroscopy (to measure changes in the Plasmon peak and concentration) and the stability of the final product in a 0.3 M sodium chloride solution. Several samples have exhibited minimal peak shifts and minimal concentration loss indicating that little or no silver was oxidized in the functionalization process. These samples also remained stable as the sodium chloride concentration was slowly brought up to 0.3 M. Control samples precipitated out of solution almost immediately upon the addition of sodium chloride. Successful functionalization of silver nanoparticles opens up the way for the addition of functionalized silver particles and their inherent optical properties onto DNA heterostructures where they can then be used as seeds for directed growth of nanowires or nanoprisms. This will be accomplished by adding target strands to the DNA structure that are complimentary to the sequence bound to the nanoparticles which then hybridize with the strands on the nanoparticle resulting the incorporation of the nanoparticle into the DNA heterostructure

Atomic Force Microscopy of DNA Self-Assembled Nanostructures for Device Applications

DNA nanotechnology, which relies on Watson-Crick hybridization, is a versatile selfassembly process whereby a variety of complex nanostructures can be fabricated with sublithographic features.[1] Adopting this technology, 1012 identical devices can be synthesized to have hundreds of components with 1nm resolution. Example nanostructures include: 1) DNA motifs [2], 2) two-dimensional DNA crystals [3], and DNA origami [4]. Currently, this technology is being adopted towards electronic, optical, and opto-electronic devices.[5

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkagefrom only one target DNA strand, catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gelelectrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules

Availability: A Metric for Nucleic Acid Strand Displacement Systems

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks

DNA-Mediated Excitonic Upconversion FRET Switching

Excitonics is a rapidly expanding field of nanophotonics in which the harvesting of photons, ensuing creation and transport of excitons via Förster resonant energy transfer (FRET), and subsequent charge separation or photon emission has led to the demonstration of excitonic wires, switches, Boolean logic and light harvesting antennas for many applications. FRET funnels excitons down an energy gradient resulting in energy loss with each step along the pathway. Conversely, excitonic energy upconversion via upconversion nanoparticles (UCNPs), although currently inefficient, serves as an energy ratchet to boost the exciton energy. Although FRET-based upconversion has been demonstrated, it suffers from low FRET efficiency and lacks the ability to modulate the FRET. We have engineered an upconversion FRET-based switch by combining lanthanide-doped UCNPs and fluorophores that demonstrates excitonic energy upconversion by nearly a factor of 2, an excited state donor to acceptor FRET efficiency of nearly 25%, and an acceptor fluorophore quantum efficiency that is close to unity. These findings offer a promising path for energy upconversion in nanophotonic applications including artificial light harvesting, excitonic circuits, photovoltaics, nanomedicine, and optoelectronics

Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn–Renger–May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm–1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices

First-Principles Studies of Substituent Effects on Squaraine Dyes

Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications

Multiscaffold DNA Origami Nanoparticle Waveguides

DNA origami templated self-assembly has shown its potential in creating rationally designed nanophotonic devices in a parallel and repeatable manner. In this investigation, we employ a multiscaffold DNA origami approach to fabricate linear waveguides of 10 nm diameter gold nanoparticles. This approach provides independent control over nanoparticle separation and spatial arrangement. The waveguides were characterized using atomic force microscopy and far-field polarization spectroscopy. This work provides a path toward large-scale plasmonic circuitry