Milana Vasudev

Applications of colloidal quantum dots

This paper addresses a number of major trends underlying the continuing effort to realize practical optoelectronic, electronic, and information-processing devices based on ensembles of quantum dots assembled in a variety of matrix materials. The great diversity of such structures makes it possible to fabricate numerous ensemble-based devices for applications underlying photoluminescent devices, light-emitting diodes, displays, photodetectors, photovoltaic devices, and solar cells. In addition, the application of colloidal quantum dots to allied technologies such as nanobiotechnology is considered for the case of monitoring conformational changes in biomolecules using luminescent quantum dots.

Semiconductor nanostructures in biological applications

Semiconductor nanostructures in biological applications are discussed. Results are presented on the use of colloidal semiconductor quantum dots both as biological tags and as structures that interact with and influence biomolecules. Results are presented on the use of semiconducting carbon nanotubes in biological applications.

Optoelectronic Signatures of DNA-Based Hybrid Nanostructures

This paper presents a characterization of the vibrational modes of nanostructure-DNA complexes immobilized on substrates, such as silver-coated microspheres and silver nanostructure array DNA strands end terminated with titanium dioxide (TiO2) nanoparticles are used to study UV-induced cleaving of DNA molecules functionalized with indirect-bandgap semiconductors. In addition, conventional DNA-based molecular beacons were designed and applied in the detection of DNA of selected organisms. Micro-Raman (μRaman) measurements of DNA in water have proven to be a major challenge because of: 1) weak DNA signatures in solution; 2) changes in structural conformations of the DNA; and 3) environmental effects, such as temperature and pH of the solution in which DNA is suspended. We have studied optoelectronic properties of nanostructure-DNA complexes immobilized on silver nanosphere substrates as well as on Ag-coated micro- and nanostructures. In this research, self-assembled monolayers of DNA formed on these substrates were studied using μRaman techniques. These Raman spectra were used to identify prominent vibrational modes of DNA, and to characterize DNA Raman spectra for both B-DNA with a right-handed double helix, and Z-DNA with a left-handed double helix (S. C. Ha, K. Lowenhaupt, A. Rich, Y. Kim, and K. Kim, “Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases,” Nature, Vol. 437, pp. 1183-1186, 2005). These Raman-based studies of the conformational states of DNA employ pH-changing trivalent salts, methylation of cytosine bases, and alternating GC bases. Moreover, DNA strands terminated with titanium dioxide (TiO2) nanoparticles were observed to undergo cleaving upon UV illumination.

Raman and Surface-Enhanced Raman Scattering (SERS) Studies of the Thrombin-Binding Aptamer

Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

Optoelectronic Signatures of Biomolecules Including Hybrid Nanostructure-DNA Ensembles

Biological macromolecules such as DNA, proteins, and polysaccharides often display unique absorptive signatures in the THz region, useful in their identification and imaging through Raman and Fourier transform transmission spectroscopy. The optoelectronic properties of nanostructure-DNA complexes immobilized on transparent, semi-rigid substrates such as polymethyl methacrylate (PMMA) have been studied. By chemically modifying the PMMA substrates with amine terminal groups and using suitable linking agents, amine terminated DNA can be localized on these substrates. THz Fourier transform transmission spectroscopy was used to detect low-frequency vibrational modes (10-25 cm-1) within single- and double-stranded DNA molecules immobilized on PMMA attached to TiO2 nanoparticles. Additionally, DNA strands end terminated with TiO2 nanoparticles are used in this study to cleave the DNA at guanine (G) rich sites due to trapping of photo-induced charge carriers from the TiO2 at these sites. Theoretical modeling of charge transport through DNA via polaron transport is discussed in detail. By examining the vibrational modes of DNA, as well as the transport of charge in DNA this study underlies potential applications involving DNA micro-arrays, DNA-based sensors, and DNA-based THz devices.

Colloidal quantum dots as optoelectronic elements

Novel optoelectronic systems based on ensembles of semiconductor nanocrystals are addressed in this paper. Colloidal semiconductor quantum dots and related quantum-wire structures have been characterized optically; these optical measurements include those made on self-assembled monolayers of DNA molecules terminated on one end with a common substrate and on the other end with TiO2 quantum dots. The electronic properties of these structures are modeled and compared with experiment. The characterization and application of ensembles of colloidal quantum dots with molecular interconnects are considered. The chemically-directed assembly of ensembles of colloidal quantum dots with biomolecular interconnects is demonstrated with quantum dot densities in excess of 10 cm. A number of novel photodetectors have been designed based on the combined use of double-barrier quantum-well injectors, colloidal quantum dots, and conductive polymers. Optoelectronic devices including photodetectors and solar cells based on threedimensional ensembles of quantum dots are considered along with underlying phenomena such as miniband formation and the robustness of minibands to displacements of quantum dots in the ensemble.

Integrated Nanostructure–Semiconductor Molecular Complexes as Tools for THz Spectral Studies of DNA

The study of the THz spectral properties of DNA is facilitated by the use of integrated nanostructure-biomolecule structures since they provide: 1) a means of monitoring correlations in DNA THz spectra with molecular conformation; 2) a means of identifying specific DNA molecules in samples being characterized via THz signatures; and 3) a means of single-molecule detection. Specifically, molecular beacons, based on single strands of DNA, are used as hybridization probes that can potentially detect single nucleotide polymorphisms. This technique combines the use of semiconductor quantum dots (QDs) that fluoresce and the gold nanoparticles as a quencher moiety. This QD-oligonucleotide complex can recognize and pair with its complementary DNA strand. This high affinity of DNA oligonucleotides for its complementary strand has been used to form a simple semiconductor probe for ultra sensitive DNA detection. MicroRaman (¿Raman) signatures of DNA self-assembled on a variety of substrates will be discussed in terms of the THz spectra of DNA. This study will highlight the fabrication of the substrates, AFM and Raman analyses of these DNA-functionalized substrates and the use of these substrates to understand THz spectra of DNA under a variety of conditions, as well as the photoluminescence spectra of the DNA-nanoparticle complexes to study the molecular conformation changes and study of single polynucleotide polymorphism.

Mega-Nano Detection of Foodborne Pathogens and Transgenes Using Molecular Beacon and Semiconductor Quantum Dot Technologies

Signature molecules derived from Listeria monocytogenes, Bacillus thuringiensis, and Salmonella Typhimurium were detected directly on food substrates (mega) by coupling molecular beacon technology utilizing fluorescent resonance energy transfer (FRET), luminescent nanoscale semiconductor quantum dots, and nanoscale quenchers. We designed target DNA sequences for detecting hlyA, Bt cry1Ac, and invA genes from L. monocytogenes, B. thuringiensis and Salmonella Typhimurium, respectively, and prepared molecular beacons for specific targets for use in real-time monitoring. We successfully detected increased fluorescence in the presence of signature molecules at molecular beacon (MB) concentrations from 1.17 nM to 40 nM, depending upon system tested in (water, milk or plant leaves), respective target (hlyA, Bt cry1Ac, or invA) and genomic DNA target concentration (50-800 ng). We were able to detect bacterial genomic DNA derived from L. monocytogenes and Salmonella sp. in a food system, 2% milk (> 20% of total volume). Furthermore, we infiltrated the Bt cry1Ac beacon in the presence of genomic DNA extracted from B. thuringiensis into Arabidopsis thaliana leaves and observed increased fluorescence in the presence of the target, indicating the ability to use these beacons in a plant system.

ENVIRONMENTAL EFFECTS INFLUENCING THE VIBRATIONAL MODES OF DNA: NANOSTRUCTURES COUPLED TO BIOMOLECULES

The interactions of charges in DNA with the vibrational modes in DNA depend on the spectra of these vibrational modes. Using (a) the Su-Schrieffer-Heeger (SSH) Hamiltonian approach, (b) integrated structures of DNA and manmade nanostructures, and (c) gel electrophoresis techniques,1 the interaction between charges in DNA and the vibrational modes of DNA are investigated. As is well-known, DNA has a rich spectrum of modes in the THz spectral regime. The use of manmade nanostructures integrated with DNA facilitates the engineering of nanoscale systems useful in studying the role of environmental effects on the vibrational modes of DNA as well as the interaction of these modes with charge carriers in DNA. Among the DNA-based structures considered in this account are: B-DNA and Z-DNA strands related by a conformational change; and DNA molecules bound on one terminal to indirect bandgap semiconductor quantum dots. Gel electrophoresis is used as a tool for the analysis of carrier interactions in novel integrated DNA-manmade-nanostructure complexes, and models based on the SSH Hamiltonian2 are employed as a means of analyzing the interactions between the vibrational modes of DNA and charge carriers in DNA.3-4

INTERACTIONS OF THz VIBRATIONAL MODES WITH CHARGE CARRIERS IN DNA: POLARON-PHONON INTERACTIONS

This paper presents models and experimental measurements that shed light on THz-phonon mediated transport of polarons in biomolecules. Polaron transport in DNA has been considered recently in view of the expected derealization of charge carriers on a one-dimensional wire as well as the highly charged nature of DNA.1,2 An understanding of the electrical transport properties and THz-phonon interactions of biomolecules is important in view of DNAs potential applications both as electrically conductive wires and as structures that facilitate the chemically-directed assembly of massively integrated ensembles of nanoscale semiconducting elements into terascale integrated networks. Moreover, understanding these interactions provides information of the THz spectrum of vibrational modes in DNA. A primary focus of this paper is on charge transport in biomolecules using indirect-bandgap colloidal nanocrystals linked with biomolecules.3 Through a combination of theoretical and experimental approaches,4-7 this paper focuses on understanding the electrical properties and THz-frequency interactions of DNA. Moreover, this paper presents observed charge transport phenomena in DNA and discusses how these measurements are related to carrier scattering from the THz vibrational modes in DNA. Indeed, carrier transport in DNA is analyzed in light of theoretical calculations of the effects of THz-frequency phonon emission by propagating carriers, THz-frequency phonon absorption by propagating and trapped carriers, and effective mass calculations for specific sequences of the DNA bases.1-7 These studies focus on THz-phonon-mediated processes since an extra carrier on a one-dimensional chain minimizes its energy by forming an extended polaron, and since many biomolecules, including DNA, exhibit THz vibrational spectra.8 Accordingly, these calculations focus on THz-phonon-mediated processes. These results are discussed in terms of the role of THz-phonon-mediated charge trapping and detrapping effects near guanine-rich regions of the DNA as well as on the understanding and identification of DNA with specific base sequences that promote charge transport. As in previous studies, optical excitation is used to inject carriers into DNA wires. Moreover, this paper reports on the use of gel electrophoresis to study charge-induced cleavage of DNA and the related transport of charge in DNA. Phonon absorption and emission from polarons in DNA,9 is analyzed using parameters from the well-known Su-Schrieffer-Heeger Hamiltonian.