Nano-flares for mRNA regulation and detection

Intracellular nucleic acid interactions facilitated by quantum dots: conceptualizing theranostics

The concept of theranostics arises from the unification of both diagnostic and therapeutic applications into a single package. The implementation of nanoparticles, such as semiconductor quantum dots (QDs), to achieve theranostic applications, offers great potential for development of methods that are suitable for personalized medicine. Researchers have taken advantage of the physiochemical properties of QDs to elicit novel bioconjugation techniques that enable the attachment of multifunctional moieties on the surface of QDs. In this review, the diagnostic and therapeutic applications of QDs that feature the use of nucleic acids are highlighted with a particular emphasis on the possibility of combinatorial applications. Nucleic acid research is of particular interest for gene therapy, and is relevant to the understanding of gene regulation pathways and gene expression dynamics. Recent toxicity studies featuring multifunctional QDs are also examined. Future perspectives discussing the expected development of this field conclude the article.

Multiplexed nanoflares: mRNA detection in live cells

We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are spherical nucleic acid (SNA) gold nanoparticle (Au NP) conjugates consisting of densely packed and highly oriented oligonucleotide sequences, many of which are hybridized to a reporter with a distinct fluorophore label and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra- and intracellular environments. Importantly, one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background. Compared to single-component nanoflares, these structures allow one to determine more precisely relative mRNA levels in individual cells, improving cell sorting and quantification.

Nucleic acid-gold nanoparticle conjugates as mimics of microRNA

Novel conjugates of gold nanoparticles (13±1nm) functionalized with synthetic microRNAs can enter cells without the aid of cationic co-carriers and mimic the function of endogenous microRNAs. These conjugates can regulate multiple proteins through interactions with 3′ untranslated region of the target mRNA and control cell behavior. The conjugates are a promising new tool for studying miRNA function and new candidates for miRNA replacement therapies.

DNA-polymer micelles as nanoparticles with recognition ability

The Watson-Crick binding of DNA single strands is a powerful tool for the assembly of nanostructures. Our objective is to develop polymer nanoparticles equipped with DNA strands for surface-patterning applications, taking advantage of the DNA technology, in particular, recognition and reversibility. A hybrid DNA copolymer is synthesized through the conjugation of a ssDNA (22-mer) with a poly(ethylene oxide)-poly(caprolactone) diblock copolymer (PEO-b-PCl). It is shown that, in water, the PEO-b-PCl-ssDNA(22) polymer forms micelles with a PCl hydrophobic core and a hydrophilic corona made of PEO and DNA. The micelles are thoroughly characterized using electron microscopy (TEM and cryoTEM) and small-angle neutron scattering. The binding of these DNA micelles to a surface through DNA recognition is monitored using a quartz crystal microbalance and imaged by atomic force microscopy. The micelles can be released from the surface by a competitive displacement event.

Fluorescence detection of thrombin using autocatalytic strand displacement cycle reaction and a dual-aptamer DNA sandwich assay

A sensitive and specific sandwich assay for the detection of thrombin is described. Two affiliative aptamers were used to increase the assay specificity through sandwich recognition. Recognition DNA loaded on gold nanoparticles (AuNPs) partially hybridized with the initiator DNA, which was displaced by surviving DNA. After the initiator DNA was released into the solution, one hairpin structure was opened, which in turn opened another hairpin structure. The initiator DNA was displaced and released into the solution again by another hairpin structure because of the hybridized reaction. Then the released initiator DNA initiated another autocatalytic strand displacement reaction. A sophisticated network of three such duplex formation cycles was designed to amplify the fluorescence signal. Other proteins, such as bovine serum albumin and lysozyme, did not interfere with the detection of thrombin. This approach enables rapid and specific thrombin detection with reduced costs and minimized material consumption compared with traditional assay processes. The detection limit of thrombin was as low as 4.3 × 10⁻¹³ M based on the AuNP amplification and the autocatalytic strand displacement cycle reaction. This method could be used in biological samples with excellent selectivity.

Theranostics: combining imaging and therapy

Employing theranostic nanoparticles, which combine both therapeutic and diagnostic capabilities in one dose, has promise to propel the biomedical field toward personalized medicine. This review presents an overview of different theranostic strategies developed for the diagnosis and treatment of disease, with an emphasis on cancer. Herein, therapeutic strategies such as nucleic acid delivery, chemotherapy, hyperthermia (photothermal ablation), photodynamic, and radiation therapy are combined with one or more imaging functionalities for both in vitro and in vivo studies. Different imaging probes, such as MRI contrast agents (T(1) and T(2) agents), fluorescent markers (organic dyes and inorganic quantum dots), and nuclear imaging agents (PET/SPECT agents), can be decorated onto therapeutic agents or therapeutic delivery vehicles in order to facilitate their imaging and, in so doing, gain information about the trafficking pathway, kinetics of delivery, and therapeutic efficacy; several such strategies are outlined. The creative approaches being developed for these classes of therapies and imaging modalities are discussed, and the recent developments in this field along with examples of technologies that hold promise for the future of cancer medicine are highlighted.

Quantitative detection of adenosine in urine using silver enhancement of aptamer-gold nanoparticle aggregation and progressive dilution

We implement the progressive dilution strategy to bring assays based on gold nanoparticles to a quantitative level. This is demonstrated by the detection of adenosine in urine by combining progressive dilution with the silver enhancement of aptamer-gold nanoparticle aggregation, giving good accuracy, high selectivity, and an unlimited dynamic range above LOD.

Gold nanoparticle-based simple colorimetric and ultrasensitive dynamic light scattering assay for the selective detection of Pb(II) from paints, plastics, and water samples

Pb (II) is a common water pollutant with high toxicity. According to the CDC, about 310,000 U.S. children of ages 1-5 have high levels of lead in their blood that it is due to the exposure to lead from plastic toys and other products. As a result, the development of ultrasensitive assays for the real-time detection of Pb(II) from plastic toys and paints is very important for water controlling, clinical toxicology and industrial processes. Driven by the need to detect trace amounts of Pb(II) from water samples, we report a label-free, highly selective and ultra sensitive glutathione modified gold nanoparticle based dynamic light scattering (DLS) probe for Pb(II) recognition in 100 ppt level from aqueous solution with excellent discrimination against other heavy metals. The sensitivity of our assay to detect Pb(II) level in water is almost 2 orders of magnitude higher than the EPA standard limit. We have also demonstrated that our DLS assay is capable of measuring the amount of Pb(II) in paint, plastic toys, and water from MS river. A possible mechanism and operating principles of our DLS assay have been discussed. Ultimately, this nanotechnology driven assay could have enormous potential applications in rapid, on-site monitoring of Pb(II) from day-to-day sample.

Selective enhancement of nucleases by polyvalent DNA-functionalized gold nanoparticles

We demonstrate that polyvalent DNA-functionalized gold nanoparticles (DNA-Au NPs) selectively enhance ribonuclease H (RNase H) activity while inhibiting most biologically relevant nucleases. This combination of properties is particularly interesting in the context of gene regulation, since high RNase H activity results in rapid mRNA degradation and general nuclease inhibition results in high biological stability. We have investigated the mechanism of selective RNase H activation and found that the high DNA density of DNA-Au NPs is responsible for this unusual behavior. This work adds to our understanding of polyvalent DNA-Au NPs as gene regulation agents and suggests a new model for selectively controlling protein-nanoparticle interactions.

Quantum dot-antisense oligonucleotide conjugates for multifunctional gene transfection, mRNA regulation, and tracking of biological processes

It was demonstrated that oligonucleotides, independent of their base sequence and length, could effectively induce the cellular uptake of mercapto acid-capped CdTe QDs after the oligonucleotides were covalently attached on the surface of the QDs. Following these experimental observations, a conjugate composed of covalently linked anti-survivin antisense oligonucleotides (ASON) and CdTe QDs was designed and synthesized. Then, the survivin mRNA down-regulation and the apoptosis of HeLa cells induced by ASON were studied. Systematic experimental results revealed that CdTe-ASON could effectively induce the apoptosis of HeLa cells, while CdTe QDs offered the possibility to visualize the specific intracellular localization of the CdTe-ASON probes strongly associated with their biological functions.

Tailoring DNA structure to increase target hybridization kinetics on surfaces

We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.

Cellular response of polyvalent oligonucleotide-gold nanoparticle conjugates

Nanoparticles are finding utility in myriad biotechnological applications, including gene regulation, intracellular imaging, and medical diagnostics. Thus, evaluating the biocompatibility of these nanomaterials is imperative. Here we use genome-wide expression profiling to study the biological response of HeLa cells to gold nanoparticles functionalized with nucleic acids. Our study finds that the biological response to gold nanoparticles stabilized by weakly bound surface ligands is significant (cells recognize and react to the presence of the particles), yet when these same nanoparticles are stably functionalized with covalently attached nucleic acids, the cell shows no measurable response. This finding is important for researchers studying and using nanomaterials in biological settings, as it demonstrates how slight changes in surface chemistry and particle stability can lead to significant differences in cellular responses.

The in vivo performance of plasmonic nanobubbles as cell theranostic agents in zebrafish hosting prostate cancer xenografts

Cell theranostics is a new approach that unites diagnosis, therapy and confirmation (guidance) of the results of therapy in one single process at cell level, thus principally improving both the rapidity and precision of treatment. The ideal theranostic agent will support all three of the above functions in vivo with cellular resolution, allowing individual assessment of disease state and the elimination of diseased cells while leaving healthy cells intact. We have developed and evaluated plasmonic nanobubbles (PNBs) as an in vivo tunable theranostic cellular agent in zebrafish hosting prostate cancer xenografts. PNBs were selectively generated around gold nanoparticles in cancer cells in the zebrafish with short single laser pulses. By varying the energy of the laser pulse, we dynamically tuned the PNB size in a theranostic sequence of two PNBs: an initial small PNB detected a cancer cell through optical scattering, followed by a second bigger PNB, which mechanically ablated this cell without damage to surrounding tissue, while its optical scattering confirmed the destruction of the cell. Thus PNBs supported the diagnosis and guided ablation of individual human cancer cells in a living organism without damage to the host.

The Polyvalent Gold Nanoparticle Conjugate-Materials Synthesis, Biodiagnostics, and Intracellular Gene Regulation

Advances in nanoscale directed assembly strategies have enabled researchers to analogize atomic assembly via chemical reactions and nanoparticle assembly, creating a new nanoscale "periodic table." We are just beginning to realize the nanoparticle equivalents of molecules and extended materials and are currently developing the ground rules for creating programmable nanometer-scale coordination environments. The ability to create a diverse set of nanoscale architectures from one class of nanoparticle building blocks would allow for the synthesis of designer materials, wherein the physical properties of a material could be predicted and controlled a priori. Our group has taken the first steps toward this goal and developed a means of creating tailorable assembly environments using DNA-nanoparticle conjugates. These nanobioconjugates combine the discrete plasmon resonances of gold nanoparticles with the synthetically controllable and highly selective recognition properties of DNA. Herein, we elucidate the beneficial properties of these materials in diagnostic, therapeutic, and detection capabilities and project their potential use as nanoscale assembly agents to realize complex three-dimensional nanostructures.

Using DNA to Link Gold Nanoparticles, Polymers and Molecules: a Theoretical Perspective

This Perspective describes theoretical studies aimed at understanding the structural and thermal properties of materials in which DNA is used to link gold nanoparticles, or polymers or organic molecules. Particularly in the case of gold nanoparticles, the materials derived from this structural motif have proven to be important for biological sensing and other applications, however additional applications may arise as a result of recent advances in the preparation of crystalline materials based on DNA-linked particles. From a theory perspective these are challenging materials to describe due to the large number of atoms, and the polyelectrolyte character of DNA, however there has been important progress recently using all-atom and coarse-grained molecular dynamics, and with analytical theory. Among topics that we discuss are the structure and density of DNA when attached to gold particles, and the size and melting properties of DNA-linked nanoparticles in different environments.

Gold nanoparticles for biology and medicine

Gold colloids have fascinated scientists for over a century and are now heavily utilized in chemistry, biology, engineering, and medicine. Today these materials can be synthesized reproducibly, modified with seemingly limitless chemical functional groups, and, in certain cases, characterized with atomic-level precision. This Review highlights recent advances in the synthesis, bioconjugation, and cellular uses of gold nanoconjugates. There are now many examples of highly sensitive and selective assays based upon gold nanoconjugates. In recent years, focus has turned to therapeutic possibilities for such materials. Structures which behave as gene-regulating agents, drug carriers, imaging agents, and photoresponsive therapeutics have been developed and studied in the context of cells and many debilitating diseases. These structures are not simply chosen as alternatives to molecule-based systems, but rather for their new physical and chemical properties, which confer substantive advantages in cellular and medical applications.

Self-assembled gold nanoparticle molecular probes for detecting proteolytic activity in vivo

Target-activatable fluorogenic probes based on gold nanoparticles (AuNPs) functionalized with self-assembled heterogeneous monolayers of dye-labeled peptides and poly(ethylene glycol) have been developed to visualize proteolytic activity in vivo. A one-step synthesis strategy that allows simple generation of surface-defined AuNP probe libraries is presented as a means of tailoring and evaluating probe characteristics for maximal fluorescence enhancement after protease activation. Optimal AuNP probes targeted to trypsin and urokinase-type plasminogen activator required the incorporation of a dark quencher to achieve 5- to 8-fold signal amplification. These probes exhibited extended circulation time in vivo and high image contrast in a mouse tumor model.

Multifunctional oval-shaped gold-nanoparticle-based selective detection of breast cancer cells using simple colorimetric and highly sensitive two-photon scattering assay

Breast cancer is the most common cancer among women, and it is the second leading cause of cancer deaths in women today. The key to the effective and ultimately successful treatment of diseases such as cancer is early and accurate diagnosis. Driven by the need, in this article, we report for the first time a simple colorimetric and highly sensitive two-photon scattering assay for highly selective and sensitive detection of breast cancer SK-BR-3 cell lines at a 100 cells/mL level using a multifunctional (monoclonal anti-HER2/c-erb-2 antibody and S6 RNA aptamer-conjugated) oval-shaped gold-nanoparticle-based nanoconjugate. When multifunctional oval-shaped gold nanoparticles are mixed with the breast cancer SK-BR-3 cell line, a distinct color change occurs and two-photon scattering intensity increases by about 13 times. Experimental data with the HaCaT noncancerous cell line, as well as with MDA-MB-231 breast cancer cell line, clearly demonstrated that our assay was highly sensitive to SK-BR-3 and it was able to distinguish from other breast cancer cell lines that express low levels of HER2. The mechanism of selectivity and the assay's response change have been discussed. Our experimental results reported here open up a new possibility of rapid, easy, and reliable diagnosis of cancer cell lines by monitoring the colorimetric change and measuring TPS intensity from multifunctional gold nanosystems.

Tunable plasmonic nanobubbles for cell theranostics

Combining diagnostic and therapeutic processes into one (theranostics) and improving their selectivity to the cellular level may offer significant benefits in various research and disease systems and currently is not supported with efficient methods and agents. We have developed a novel method based on the gold nanoparticle-generated transient photothermal vapor nanobubbles, that we refer to as plasmonic nanobubbles (PNB). After delivery and clusterization of the gold nanoparticles (NP) to the target cells the intracellular PNBs were optically generated and controlled through the laser fluence. The PNB action was tuned in individual living cells from non-invasive high-sensitive imaging at lower fluence to disruption of the cellular membrane at higher fluence. We have achieved non-invasive 50-fold amplification of the optical scattering amplitude with the PNBs (relative to that of NPs), selective mechanical and fast damage to specific cells with bigger PNBs, and optical guidance of the damage through the damage-specific signals of the bubbles. Thus the PNBs acted as tunable theranostic agents at the cellular level and in one process that have supported diagnosis, therapy and guidance of the therapy.