Detection of non-cross-linking interaction between DNA-modified gold nanoparticles and a DNA-modified flat gold surface using surface plasmon resonance imaging on a microchip

Biomarker Analysis on a Power-free Microfluidic Chip Driven by Degassed Poly(dimethylsiloxane)

Point-of-care testing (POCT) of biomarkers, such as proteins and nucleic acids, is a hot topic in modern medical engineering toward the early diagnosis of various diseases including cancer. Although microfluidic chips show great promise as a new platform for POCT, external pumps and valves for driving those chips have hindered the realization of POCT on the chips. To eliminate the need for pumps and valves, a power-free microfluidic pumping method utilizing degassed poly(dimethylsiloxane) (PDMS) was invented in 2004. In this article, the working principle of the degas-driven power-free microfluidic chip is first described, and then applications of those chips to biomarker analysis are reviewed. The biomarker analysis on the chip was typically achieved with a small sample volume of ∼1 μL and a short analysis time of ∼20 min. For protein analysis, the sandwich immunoassay format was adopted. The limit of detection (LOD) was improved by three orders of magnitude by using laminar flow-assisted dendritic amplification (LFDA), which was a newly devised amplification method specialized for microfluidic chips. For analysis of nucleic acids such as DNA and microRNA, the sandwich hybridization format was adopted, and the LFDA was also effective to reduce the LOD. With the LFDA, typical LOD values for proteins and nucleic acids were both around 1 pM.

Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair

We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.

DNA dangling-end-induced colloidal stabilization of gold nanoparticles for colorimetric single-nucleotide polymorphism genotyping

A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.

Early lung cancer diagnosis by biosensors

Lung cancer causes an extreme threat to human health, and the mortality rate due to lung cancer has not decreased during the last decade. Prognosis or early diagnosis could help reduce the mortality rate. If microRNA and tumor-associated antigens (TAAs), as well as the corresponding autoantibodies, can be detected prior to clinical diagnosis, such high sensitivity of biosensors makes the early diagnosis and prognosis of cancer realizable. This review provides an overview of tumor-associated biomarker identifying methods and the biosensor technology available today. Laboratorial researches utilizing biosensors for early lung cancer diagnosis will be highlighted.

Surface plasmon resonance imaging for nucleic acid detection

Surface plasmon resonance imaging (SPRI) is a powerful tool for simple, fast and cheap nucleic acid detection. Great efforts have been made during the last decade with the aim of developing even more sensitive and specific SPRI-based methods to be used for the direct detection of DNA and RNA. Here, after a description of the fundamentals of SPRI, the state of the art of recent platform and assay developments is presented, with special attention given to advances in SPRI signal enhancement procedures.

Structural characterization of nanoparticles from thermoresponsive poly(N-isopropylacrylamide)-DNA conjugate

Poly(N-isopropylacrylamide) (PNIPAAm) grafted with single-stranded (ss) DNA conjugate (PNIPAAm-g-DNA) self-assembles above its lower critical solution temperature to form colloidal particles. When the ssDNA within the particle hybridizes with its complementary DNA, the particles aggregate above a certain threshold of salt concentration with drastically increased turbidity in solution. Detailed structural information of the particle was obtained mainly by small-angle X-ray scattering. The influence of copolymer composition on the morphology of particle and non-crosslinking aggregation was examined. The particle consists of hydrophobic PNIPAAm core surrounded by hydrophilic DNA strands. The increase in DNA fraction brought about a significant decrease in core size, whereas the shell thickness little changed and corresponded to the length of DNA. A structural model with a sticky potential was applied to the analysis of particle aggregate. This analysis provided that the particles aggregate while the coronal layers interpenetrate each other. The interaction between the particles was quantified in terms of the sticky potential and showed a trend to be influenced by the particle size rather than the graft density of DNA strands on the particle.

Systematic characterization of degas-driven flow for poly(dimethylsiloxane) microfluidic devices

Degas-driven flow is a novel phenomenon used to propel fluids in poly(dimethylsiloxane) (PDMS)-based microfluidic devices without requiring any external power. This method takes advantage of the inherently high porosity and air solubility of PDMS by removing air molecules from the bulk PDMS before initiating the flow. The dynamics of degas-driven flow are dependent on the channel and device geometries and are highly sensitive to temporal parameters. These dependencies have not been fully characterized, hindering broad use of degas-driven flow as a microfluidic pumping mechanism. Here, we characterize, for the first time, the effect of various parameters on the dynamics of degas-driven flow, including channel geometry, PDMS thickness, PDMS exposure area, vacuum degassing time, and idle time at atmospheric pressure before loading. We investigate the effect of these parameters on flow velocity as well as channel fill time for the degas-driven flow process. Using our devices, we achieved reproducible flow with a standard deviation of less than 8% for flow velocity, as well as maximum flow rates of up to 3 nL∕s and mean flow rates of approximately 1-1.5 nL∕s. Parameters such as channel surface area and PDMS chip exposure area were found to have negligible impact on degas-driven flow dynamics, whereas channel cross-sectional area, degas time, PDMS thickness, and idle time were found to have a larger impact. In addition, we develop a physical model that can predict mean flow velocities within 6% of experimental values and can be used as a tool for future design of PDMS-based microfluidic devices that utilize degas-driven flow.

Influence of the number of nanoparticles on the enhancement properties of surface-enhanced Raman scattering active area: sensitivity versus repeatability

In the present work, the combination of chemical immobilization with electron beam lithography enables the production of sensitive and reproducible SERS-active areas composed of stochastic arrangements of gold nanoparticles. The number of nanoparticles was varied from 2 to 500. Thereby a systematic analysis of these SERS-active areas allows us to study SERS efficiency as a function of the number of nanoparticles. We found that the experimental parameters are critical, in particular the size of the SERS-active area must be comparable to the effective area of excitation to obtained reproducible SERS measurements. The sensitivity has also been studied by deducing the number of NPs that generate the enhancement. With this approach we demonstrates that the maximum enhancement, the best sensitivity, is obtained with the smallest number of nanoparticles that is resonant at a given excitation wavelength.

Rapid naked-eye detection of mercury ions based on non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles

Colorimetric detection of mercury ions (Hg(2+)) with the naked eye was accomplished within 1 min by a combination of non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles and complex formation of thymine-Hg(2+)-thymine.

Self-aggregation of oligonucleotide-functionalized gold nanoparticles and its applications for highly sensitive detection of DNA

A new self-aggregation phenomenon of single strand DNA-modified gold nanoparticles has been demonstrated and applied to highly sensitive DNA detection.