Packed DNA Denatures on Gold Nanoparticles (original) (raw)
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Controlling the Adsorption and Reactivity of DNA on Gold
Langmuir, 2003
Toward the construction of double stranded DNA-based biosensors, packing of thiolated double-stranded DNA adsorbed on gold nanoparticles was observed to induce DNA denaturation. The denaturation was investigated as a function of DNA density, nanoparticle surface area, and DNA length. Direct correlation was found between DNA surface coverage and the denaturation. Denaturation occurred only at high densities of adsorbed DNA and was dependent on DNA length and therefore stability, providing guidelines for controlled adsorption of dsDNA on GNPs. Our results invoke a model in which the formation of a thiol-gold bond competes with the free energy associated with the denaturation of two DNA strands. Denaturation vacates space for additional molecules to bind through a thiol-gold bond.
Thiol-Specific and Nonspecific Interactions between DNA and Gold Nanoparticles
Langmuir, 2006
The contribution of nonspecific interactions to the overall interactions of thiol-ssDNA and dsDNA macromolecules with gold nanoparticles was investigated. A systematic investigation utilizing dynamic light scattering and cryogenic transmission electron microscopy has been performed to directly measure and visualize the changes in particle size and appearance during functionalization of gold nanoparticles with thiol-ssDNA and nonthiolated dsDNA. The results show that both thiol-ssDNA and dsDNA do stabilize gold nanoparticle dispersions, but possible nonspecific interactions between the hydrophobic DNA bases and the gold surface promote interparticle interactions and cause aggregation within rather a short period of time. We also discuss the adsorption mechanisms of dsDNA and thiol-ssDNA to gold particles. LA0530438 . Relaxation time distributions at θ ) 70°for gold nanoparticles dispersed in water, phosphate buffer (10 mM pH 7 and 0.3 M NaCl), and 1:1 volume mixtures of dsDNA or thiol-ssDNA in buffer and gold NP in water.
Langmuir, 2011
Gold nanoparticles functionalized with thiol-modified DNA have been widely used in making various nanostructures, colorimetric biosensors, and drug delivery vehicles. Over the past 15 years, significant progress has been made to improve the stability of such functionalized nanoparticles. The stability of the gold-thiol bond in this system, however, has not been studied in a systematic manner. Most information on the gold-thiol bond was obtained from the study of self-assembled monolayers (SAMs). In this study, we employed two fluorophore-labeled and thiol-modified DNAs. The long-term stability of the thiol-gold bond as a function of time, salt, temperature, pH, and organic solvent has been studied. We found that the bond spontaneously dissociated under all tested conditions. The dissociation was favored at high salt, high pH, high temperature and little DNA degradation was observed in our system. Most organic solvents showed a moderate protection effect on the gold-thiol bond. The stability of the gold-thiol bond in the DNA system was also compared with that in SAMs. While there are many similarities, we also observed opposite trends for the salt and ethanol effect. This study suggests that the purified DNA-functionalized gold nanoparticles should be freshly prepared and used in a day or two. Long term storage should be carried out at relatively low temperature in low salt and slight acidic buffers.
Polarity control for nonthiolated DNA adsorption onto gold nanoparticles
Gold nanoparticles (AuNPs) functionalized with thiolated DNA have enabled many studies in nanoscience. The strong thiol/gold affinity and the nanoscale curvature of AuNPs allow the attached DNA to adapt an upright conformation favorable for hybridization. Recently, it has been shown that nonthiolated DNA can also be attached via DNA base adsorption. Without a thiol label, both ends of the DNA and even internal bases could be adsorbed, decreasing the specificity of subsequent molecular recognition reactions. In this work, we employed a modular sequence design approach to systematically study the effect of DNA sequence on adsorption polarity. A block of poly adenine (poly-A) could be used to achieve a high density of DNA attachment. When the poly-A block length is short (e.g., below 5−7), the loading was independent of the block length, and the conjugate cannot hybridize to its cDNA effectively, suggesting a random attachment controlled by adsorption kinetics. Increasing the block length leads to reduced capacity but improved hybridization, suggesting that more DNA with the desired conformation was adsorbed due to the thermodynamic effects of poly-A binding. The design can be further improved by including capping sequences rich in T or G. Finally, a more general double-stranded DNA approach was described to be suitable for DNA that cannot satisfy the above-mentioned design requirements.
Dual-Specific Interaction to Detect DNA on Gold Nanoparticles
Sensors, 2013
An approach to selectively and efficiently detect single strand DNA is developed by using streptavidin coated gold nanoparticles (StAuNPs) as efficient quenchers. The central concept for the successful detection is the combination the of streptavidin-biotin interaction with specific probe-target DNA hybridization. Biotin labeled probe DNAs act as "bridges" to bring Cy5 labeled targets to the particle surface and the fluorophore dye can be rapidly and efficiently quenched by StAuPNs. By measuring the changes of photoluminescence intensity of Cy5, an efficient, selective, and reversed detection of DNA hybridization is realized. The methodology may pave a new way for simple and rapid detections of biomolecules.
Langmuir, 2012
The last 16 years have witnessed the landmark development of polyvalent thiolated DNA-functionalized gold nanoparticles (AuNP's) possessing striking properties within the emerging field of nanobiotechnology. Many novel properties of this hybrid nanomaterial are attributed to the dense DNA shell. However, the question of whether nonthiolated polyvalent DNA−AuNP could be fabricated with a high DNA density and properties similar to those of its thiolated counterpart has not been explored in detail. Herein, we report that by simply tuning the pH of the DNA−AuNP mixture an ultrahigh capacity of nonthiolated DNA can be conjugated to AuNP's in a few minutes, resulting in polyvalent DNA−AuNP conjugates with cooperative melting behavior, a typical property of polyvalent thiolated DNA-functionalized AuNP's. With this method, large AuNP's (e.g., 50 nm) can be functionalized to achieve the colorimetric detection of sub-nanometer DNA. Furthermore, this fast, stable DNA loading was employed to separate AuNP's of different sizes. We propose that a large fraction of the attached DNAs are adsorbed via one or a few terminal bases to afford the high loading capacity and the ability to hybridize with the complementary DNA. This discovery not only offers a time-and cost-effective way to functionalize AuNP's with a high density of nonthiolated DNA but also provides new insights into the fundamental understanding of how DNA strands with different sequences interact with AuNP's.
Electroanalysis, 2010
This paper presents a way of modification of crystalline gold surface with a high quality layer of gold nanoparticles (Au NPs) via self-assembled dithiol. The application of additional Au NPs monolayer prepared at various temperatures was tested with three types of biosensors previously described in the literature. The examined DNA biosensors differed by the detection method and the way of the immobilization of DNA probe at the modified gold electrode surface. For the immobilization of DNA probe in the sensing layer either the formation of SAM or the affinity binding (biotin -sterptavidin) or covalent attachment were used. The necessary condition of successful preparation of a perfect such monolayer is the preparation temperature of 4 8C. The preparation of Au NPs layers at higher than 4 8C temperatures leads to poor repeatability and unsatisfactory precision of the measurements. The application of the perfect Au monolayer lowers the detection limit (circa by 10 to 100 times) for all tested DNA biosensors.
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 2018
Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orien...
2007
The first section of this thesis focuses on applications of DNA-modified gold nanoparticles (AuNPs) while the second part addresses the fundamental properties that arise from conjugating DNA to inorganic AuNPs. Two types of applications are discussed. The first application utilizes the colorimetric properties of AuNPs to screen duplex and triplex DNA binding molecules. Small molecules that bind to double and triple helix DNA often stabilize the DNA helix and increase the denaturation temperature. These molecules are of interest for their properties as anti-cancer drugs and gene regulation agents. When these molecules are combined with AuNP assemblies linked with DNA, the small molecules bind to the DNA interconnects and stabilize the assembly. The increased stability of the assembly can be monitored as a function of temperature and the relative binding strength of the DNA binders can be assessed. These assays have been further developed for processing in a chip based format. DNA-modified AuNPs also have been used to build complex higher order architectures. These materials can be programmed to assemble based upon the DNA recognition properties, however, control over the architectural parameters of these structures have been limited. In this thesis, we demonstrate the ability to utilize the synthetic programmability of DNA to direct the organization of AuNPs into different crystalline structures, depending upon the choice of DNA linkers and environmental conditions. FCC and BCC structures are investigated in detail by synchrotron small angle X-ray scattering experiments. The fundamental properties of these materials, specifically the enhanced binding properties and the sharp melting transitions, are investigated. Concentration dependent melting LIST OF SCHEMES CHAPTER ONE Scheme 1.1. DNA-modified AuNPs and free oligonucleotides as anti-sense agents for gene silencing……………………………………………………………………………………….....24 CHAPTER TWO Scheme 2.1. Schematic representation of structure and color change of nanoparticle/DNA binding molecule assemblies at a specific temperature………………………………………….36 CHAPTER THREE Scheme 3.1. Representation of structure and color change of nanoassembly in the presence of triplex binder at room temperature………………………………………………………………46 CHAPTER FOUR Scheme 4.1. Scanometric detection of duplex DNA binders on a microarray…………………..60 Scheme 4.2. Scanometric detection of triplex DNA binders on a microarray…………………61 CHAPTER FIVE Scheme 5.1. a, AuNP-DNA conjugates can be programmed to assemble into different crystallographic arrangements by changing the sequence of the DNA linkers. b, Single component assembly system where AuNPs are assembled using one DNA sequence, linker-A. c, Binary component assembly system where AuNPs are assembled using two different DNA linkers-X and-Y……………………………………..…………………………………………..76