Attachment of quantum dots or fluorescent molecules to gold nanoparticles has a variety of optical labeling and sensory applications. In this study, we use both e-beam lithography and DNA origami to examine the fluorescence enhancement of fluorescent molecules and quantum dots with a systematic approach to understanding the contribution of gold nanoparticle size and interparticle spacing. The unique design of our patterns allows us to study the effects of size and spacing of the gold nanoparticles on the enhancement of fluorescence in one quick study with constant conditions – removing undesirable effects such as differences in concentration of quantum dots or other chemistry differences that plague multiple experiments. We also discuss the fluorescence and bonding of CdSe/ZnS quantum dots to both gold as well as DNA for use in self assembled DNA constructs. Specifically, bioconjugated CdSe/ZnS core/shell quantum dots were synthesized and functionalized with MPA using both traditional ligand exchange as well as newly developed in situ functionalization techniques used to increase the quantum yield of the quantum dots. We will present fluorescent images showing results of optimal size and spacing for fluorescence as well as demonstrating attachment chemistry of the quantum dots.
Biomolecules can exhibit low-lying vibrational modes in the THz region which are detectable in transmission
given a strong molecular dipole moment and optical depth, and a spectrometer of adequate sensitivity. The nucleic
acids are particularly interesting because of applications such as label-free gene assay, bio-agent detection, etc. However
for nucleic acids, sample preparation and THz coupling are of paramount importance because of the strong absorption by
liquid water and the small concentration of molecules present in physiological solutions. Concentration methods
become necessary to make the THz vibrational modes detectable, either by concentrating the nucleic-acid sample itself
in a small volume but large area, or by concentrating the THz radiation down to the volume of the sample. This paper
summarizes one type of the first method: nanofluidic channel arrays for biological nucleic acids; and two types of the
second method: (1) a circular-waveguide pinhole, and (2) a
circular-waveguide, conical-horn coupling structure, both for
DNA crystals. The first method has been demonstrated on a very short artificial nucleic acid [small-interfering (si) RNA
(17-to-25 bp)] and a much longer, biological molecule [Lambda-phage DNA (48.5 kbp)]. The second method has been
demonstrated on small (~100 micron) single crystals of DNA grown by the sitting-drop method.
Here we report efforts towards fabrication of DNA based nanosensors, where DNA molecules were immobilized on
gold-dot arrays. AFM was used as the main characterization tool. Two major challenges associated with characterizing
these nanosensors are: 1) constructing small (<10 nm high) attachment sites on a flat surface to resolve the details of the
hybridized DNA lattice and 2) fabricating attachment sites on a surface that allows the lattices to be well separated. We
have chosen silicon as the substrate since atomically flat surfaces are readily available. For the formation of the gold-dot
arrays, we combined e-beam lithography with metal deposition via an e-beam evaporation. The fabrication process was
confirmed by AFM imaging. For DNA attachment we have used DNA functionalized on one end with multi-thiolated
dendrimers, an attachment strategy developed in our lab. After exposing the surface to the DNA solution, the DNA was
found to be attached to ~5% of the gold dots. To improve the attachment technique, oxygen plasma cleaning and ethanol
treatment have been investigated. Finally, a higher yield (65% of total scanned areas) of DNA attachment to the gold
dots was achieved.
The precise placement of molecular and nanoparticle species at predetermined locations on a substrate surface remains a
current challenge. Some barriers are particularly relevant to soft matter such as biomolecules. The advent of DNA
Origami, invented by Rothemund, provides partial solutions to some challenges while raising new challenges. In this
paper, two particular levels of molecular placement will be discussed, associating large DNA based molecular
nanostructures with traditional lithographic nanostructures and the association of molecular scale species with particular
locations within large Origami structures. Typical plasmid based DNA Origami nanostructures are approximately 100
nm in diameter. This size scale closely matches that of gold nanoscale structures which are readily produced using ebeam
and other lithographic techniques. The strategy for associating large DNA based nanostructures with these
lithographic structures employs the placement of thiol terminated DNA molecules within the molecular assembly,
positioned to allow tethering of the biomolecular nanostructure to the substrate through gold-thiol bonds. Although a
number of soft chemistry mechanisms can be employed to associate DNA molecules with substrates, the use of the
origami constructs as substrates suggests that single stranded DNA provides the optimum attachment strategy. A solid
state asymmetric PCR process for ssDNA fabrication is therefore described and demonstrated. Structures generated with
the three tiered attachment strategy described here are amenable to characterization and assembly verification using
AFM and NSOM. While a complete convergence of top down and bottom up approaches cannot be claimed, it is clear
that the practice and methods of molecular lithography are rapidly advancing.
This paper reports progress in an approach to create a general purpose platform to be used in the
reproducible assembly of molecular electronic devices. We describe a method in which DNA molecules
were immobilized on patterned neutravidin surfaces. First, a silicon wafer was functionalized with (3-
aminopropyl)triethoxysilane (APTES) to produce an amine-terminated surface. The primary amine group
was then reacted with the heterobifunctional linker molecule succinimidyl-6-(biotinamido)hexanoate which
placed an active biotin group at the surface interface. These biotinylated surfaces were then patterned with
the tetrameric protein neutravidin using microcontact printing (μCP) with relief features in
polydimethylsiloxane (PDMS) stamps. The neutravidin proteins adsorb onto the surface and bind nearly
irreversibly to one or two biotin groups leaving at least two biotin binding sites on each protein available
for conjugation. Following neutravidin stamping, 1 μm long DNA molecules functionalized on one end
with biotin were attached to the patterned areas. Water contact angle (WCA) measurements were used to
characterize wettability changes of the silicon surfaces for amine and biotin functionalization. Atomic
force microscopy (AFM) was used to image the patterns of immobilized neutravidin and DNA.
The convergence of terahertz spectroscopy and single molecule experimentation offer significant promise of enhancement in sensitivity and selectivity in molecular recognition, identification and quantitation germane to military and security applications. This presentation reports the results of experiments which address fundamental barriers to the integration of large, patterned bio-compatible molecular opto-electronic systems with silicon based microelectronic systems. The central thrust of this approach is sequential epitaxy on surface bound single stranded DNA one-dimensional substrates. The challenge of producing highly structured macromolecular substrates, which are necessary in order to implement molecular nanolithography, has been addressed by combining "designer" synthetic DNA with biosynthetically derived plasmid components. By design, these one dimensional templates are composed of domains which contain sites which are recognized, and therefore addressable by either complementary DNA sequences and/or selected enzymes. Such design is necessary in order to access the nominal 2 nm linewidth potential resolution of nanolithography on these one-dimensional substrates. The recognition and binding properties of DNA ensure that the lithographic process is intrinsically self-organizing, and therefore self-aligning, a necessity for assembly processes at the requisite resolution. Another requirement of this molecular epitaxy approach is that the substrate must be immobilized. The challenge of robust surface immobilization is being addressed via the production of the equivalent of molecular tube sockets. In this application, multi-valent core-shell fluorescent quantum dots provide a mechanism to prepare surface attachment sites with a pre-determined 1:1 attachment site : substrate (DNA) molecule ratio.
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