Dual-Specific Interaction to Detect DNA on Gold Nanoparticles (original) (raw)
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Fluorescence Near Gold Nanoparticles for DNA Sensing
Analytical Chemistry, 2011
We investigated fluorescence quenching and enhancement near gold nanoparticles (GNP) of various sizes using fluorescently labeled hairpin DNA probes of different lengths. A closed hairpin caused intimate contact between the fluorophore and the gold, resulting in an efficient energy transfer (quenching). Upon hybridization with complementary DNA, the DNA probes were stretched yielding a strong increase in fluorescence signal. By carefully quantifying the amount of bound fluorescent probes and the GNP concentrations, we were able to determine the quenching and enhancement efficiencies. We also studied the size and distance dependence theoretically, using both FDTD simulations and the Gersten-Nitzan model and obtained a good agreement between experiments and theory. On the basis of experimental and theoretical studies, we report over 96.8% quenching efficiency for all particle sizes tested and a maximal signal increase of 1.23 after DNA hybridization. The described results also demonstrate the potential of gold nanoparticles for label free DNA sensing.
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
Gold nanoparticles as novel label for DNA diagnostics
Expert Review of Molecular Diagnostics, 2002
The growing interest in DNA diagnostics, especially in combination with the need for highly-paralleled and miniaturized hybridization assays, is today addressed by fluorescence DNA chips. Fluorescence detection is approved and highly developed, however, it has also problematic aspects, e.g., the low stability of the dyes, the influence of the physicochemical environment onto the signal intensity and the expensive set-up for detection. A novel detection scheme based on metal nanoparticles was proposed to overcome these problems and is discussed in this review.
Colorimetric detection of single- and double-stranded DNA on gold nanoparticles
In this work we report the use of gold nanoparticles (AuNPs) for optical detection of single and double-stranded DNA. The linkage of DNA sequences to gold nanoparticles was demonstrated by the modification of spectral position and intensity of plasmon resonance band and the chemical stabilization that DNA confers to gold particles against a standard aggregation test.
Intercalating Gold Nanoparticles as Universal Labels for DNA Detection
Small, 2007
There is an increasing demand for simple, sensitive, and low-cost methods for the specific detection of nucleic acids because of their importance in the molecular diagnosis of disease, food testing, forensic science, and environmental testing .[1] Although a variety of alternative detection tech-A C H T U N G T R E N N U N G niques are being explored, the vast majority of tests are still based on fluorescent oligonucleotide probes. [2, 3] Purchasing these probes from commercial sources is expensive and time consuming, and each individually labeled probe may be up to tenfold more expensive than the unlabeled equivalent. They also require expensive imaging equipment for detection and are prone to signal loss due to photobleaching. Some of these drawbacks can be avoided by using gold nanoparticles (GNPs) instead of fluorescent dyes. [4-6] The extinction coefficients of these particles are about 10 5 times greater than fluorescein [6] and therefore low concentrations can be seen with the unaided eye. This property has been exploited in rapid immunoassay devices for many years [7] and, more recently, similar devices have been used to detect nucleic acids. Lee and co-workers hybridized polymerase chain-reaction (PCR) products to bioA C H T U N G T R E N N U N G tinylated detector probes and mixed them with GNPs conjugated to antibiotin. [8] They then immersed a rapid test device into the mixture and identified up to three PCR amplicons in the same sample by virtue of the color developed by bound GNPs. Although devices such as this allow nucleic acids to be identified by untrained users without additional equipment, they are unnecessarily complicated and expensive because they are based on antibodies and haptens. Ioannou and co-workers [9] eliminated the requirement for antibodies by conjugating thiolated oligonucleotides directly to the GNPs by the method first reported by Mirkin et al., [10] and then used the conjugates to detect PCR products in a rapid test device. Unfortunately thiolated oligonucleotides are also expensive and the Mirkin conjugation method requires an excess of them to be mixed with the GNPs. Thiolated oligonucleo-A C H T U N G T R E N N U N G tides conjugated to GNPs have also been used to detect multiple target sequences hybridized to microarrays, [11-13] but each target requires GNPs conjugated to a different oligonucleotide sequence and therefore the expense is even greater. The expense of thiolated oligonucleotides and multiple probes can be avoided by replacing them with universal labels that distinguish double-stranded hybridization products from single-stranded capture probes. The first report of a universal GNP label for DNA was by Li and Rothberg, who performed homogenous assays for DNA with citrate-stabilized GNPs. [14] This approach is based on the superior affinity of citrate-stabilized GNPs for singlestranded DNA, which, unlike double-stranded DNA, prevents salt-induced flocculation. More recently, Golovlev and co-workers have used positively A C H T U N G T R E N N U N G charged GNPs to distinguish between single-and double-stranded DNA. [15] In this approach the particles have a higher affinity for doublestranded DNA and therefore they can be used to identify hybridization products in microarray analysis. While these
Nanotechnology, 2007
We report a gold-nanoparticle-based miniaturized, inexpensive and battery-operated ultra-sensitive fluorescence resonance energy transfer (FRET) probe for screening biological agents DNA at the femtomolar level. We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized organic dyes and gold nanoparticles as nanoprobes. In the presence of various target sequences, detection of sequence-specific DNA is possible via an independent hybridization process. As proof of concept, multiplexed detection of two target sequences, (1) oligonucleotide sequence associated with the anthrax lethal factor and (2) sequence related to positions 1027-1057 of the E. coli 23S rDNA, have been demonstrated with high sensitivity and specificity. The quenching efficiency as a function of distance is investigated. The mechanism of distant dependence fluorescence quenching has been discussed.
DNA functionalized gold nanoparticles for bioanalysis
Analytical Methods, 2009
Gold nanoparticles (Au NPs) have become one of the most interesting sensing materials because of their unique size-and shape-dependent optical properties, high extinction coefficients, and superquenching capability. Au NPs that are bioconjugated with DNA (DNA-Au NPs) have been demonstrated for selective and sensitive detection of analytes such as mercury(II) ions, platelet-derived growth factor (PDGF), and adenosine triphosphate (ATP). This review focuses on approaches using DNA-Au NPs for colorimetric, fluorescent, and scattering detection of biopolymers and small solutes. We highlight the important roles that the size and concentration of Au NPs, the length and sequence of DNA, the nature of the capping agents, and the ionic strength and pH of solution play in determining the specificity and sensitivity of the nanosensors for the analytes. The advantages and disadvantages of different detection methods for sensing of interesting analytes using DNA-Au NPs will be discussed. has worked on the preparation and applications of functional nanomaterials for highly selective and sensitive detection of heavy metal ions, proteins, and DNA. He obtained his PhD degree from the
Electrochemical Sensing of DNA Using Gold Nanoparticles
Electroanalysis, 2007
The electrochemical properties of gold nanoparticles (AuNPs) have led to their widespread use as DNA labels. This fact has improved the design strategies for the electrochemical detection of DNA through hybridization event monitoring. The reported DNA hybridization detection modes are based on either AuNP detection after dissolving or the direct detection of the AuNP/DNA conjugates anchored onto the genosensor surface. Various enhancement strategies have been reported so as to improve the detection limit. Most are based on catalytic deposition of silver onto AuNP. Other strategies based on the use of AuNPs as carrier/amplifier of other labels will be also revised. The developed techniques are characterized by sensitivities and specificities that enable further applications of the developed DNA sensors in several fields.
Nucleic acid detection strategy using gold nanoprobe of two diverse origin
IET Nanobiotechnology, 2019
In recent years, nanoparticles especially with gold and silver nanoparticles based point of care diagnostic methods is being developed for the lethal diseases like dengue. This study focused to work on the dengue virus detection in a simplest method using gold nanoparticles probe (AuNPs) with thiol tagged single strand DNA (ss-DNA). A sensitive, fluorescence-based detection strategy was designed to examine and quantified the hybridisation process and also elucidated the behaviour of AuNPs before and after interaction of biomolecule. The detection process was focused on aggregation of gold nanoprobe in the presence of complementary strand (target region). Hence the percentage of aggregation was measured and as a result, the limit of detection was found to be 10 −6 dilutions. Current detection method was highly sensitive, easy to perform and the reaction timing is rapid between 5 and 10 min, and it can be observed through naked eye.