MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles

DNA-length-dependent quenching of fluorescently labeled iron oxide nanoparticles with gold, graphene oxide and MoS2 nanostructures

We controlled the fluorescence emission of a fluorescently labeled iron oxide nanoparticle using three different nanomaterials with ultraefficient quenching capabilities. The control over the fluorescence emission was investigated via spacing introduced by the surface-functionalized single-stranded DNA molecules. DNA molecules were conjugated on different templates, either on the surface of the fluorescently labeled iron oxide nanoparticles or gold and nanographene oxide. The efficiency of the quenching was determined and compared with various fluorescently labeled iron oxide nanoparticle and nanoquencher combinations using DNA molecules with three different lengths. We have found that the template for DNA conjugation plays significant role on quenching the fluorescence emission of the fluorescently labeled iron oxide nanoparticles. We have observed that the size of the DNA controls the quenching efficiency when conjugated only on the fluorescently labeled iron oxide nanoparticles by setting a spacer between the surfaces and resulting change in the hydrodynamic size. The quenching efficiency with 12mer, 23mer and 36mer oligonucleotides decreased to 56%, 54% and 53% with gold nanoparticles, 58%, 38% and 32% with nanographene oxide, 46%, 38% and 35% with MoS2, respectively. On the other hand, the presence, not the size, of the DNA molecules on the other surfaces quenched the fluorescence significantly with different degrees. To understand the effect of the mobility of the DNA molecules on the nanoparticle surface, DNA molecules were attached to the surface with two different approaches. Covalently immobilized oligonucleotides decreased the quenching efficiency of nanographene oxide and gold nanoparticles to ∼22% and ∼21%, respectively, whereas noncovalently adsorbed oligonucleotides decreased it to ∼25% and ∼55%, respectively. As a result, we have found that each nanoquencher has a powerful quenching capability against a fluorescent nanoparticle, which can be tuned with surface functionalized DNA molecules.

DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles

Several properties of nanomaterials, such as morphologies (e.g., shapes and surface structures) and distance dependent properties (e.g., plasmonic and quantum confinement effects), make nanomaterials uniquely qualified as potential choices for future applications from catalysis to biomedicine. To realize the full potential of these nanomaterials, it is important to demonstrate fine control of the morphology of individual nanoparticles, as well as precise spatial control of the position, orientation, and distances between multiple nanoparticles. In addition, dynamic control of nanomaterial assembly in response to multiple stimuli, with minimal or no error, and the reversibility of the assemblies are also required. In this Account, we summarize recent progress of using DNA as a powerful programmable tool to realize the above goals. First, inspired by the discovery of genetic codes in biology, we have discovered DNA sequence combinations to control different morphologies of nanoparticles during their growth process and have shown that these effects are synergistic or competitive, depending on the sequence combination. The DNA, which guides the growth of the nanomaterial, is stable and retains its biorecognition ability. Second, by taking advantage of different reactivities of phosphorothioate and phosphodiester backbone, we have placed phosphorothioate at selective positions on different DNA nanostructures including DNA tetrahedrons. Bifunctional linkers have been used to conjugate phosphorothioate on one end and bind nanoparticles or proteins on the other end. In doing so, precise control of distances between two or more nanoparticles or proteins with nanometer resolution can be achieved. Furthermore, by developing facile methods to functionalize two hemispheres of Janus nanoparticles with two different DNA sequences regioselectively, we have demonstrated directional control of nanomaterial assembly, where DNA strands with specific hybridization serve as orthogonal linkers. Third, by using functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic control of assemblies of gold nanoparticles, quantum dots, carbon nanotubes, and iron oxide nanoparticles in response to one or more stimuli cooperatively have been achieved, resulting in colorimetric, fluorescent, electrochemical, and magnetic resonance signals for a wide range of targets, such as metal ions, small molecules, proteins, and intact cells. Fourth, by mimicking biology, we have employed DNAzymes as proofreading units to remove errors in nanoparticle assembly and further used DNAzyme cascade reactions to modify or repair DNA sequences involved in the assembly. Finally, by taking advantage of different affinities of biotin and desthiobiotin toward streptavidin, we have demonstrated reversible assembly of proteins on DNA origami.

In vitro selection of DNA aptamers for metastatic breast cancer cell recognition and tissue imaging

Cancer is a major public health issue, with metastatic cancer accounting for the overwhelming majority of cancer deaths. Early diagnosis and appropriate treatment of metastatic cancer may largely prolong the survival rate and improve the quality of life for patients. In this study, we have identified a panel of DNA aptamers specifically binding to MDA-MB-231 cells derived from metastatic site-pleural effusion, with high affinity after 15 rounds of selections using the cell-based systematic evolution of ligands by exponential enrichment (SELEX) method. The selected aptamers were subjected to flow cytometry and laser confocal fluorescence microscopy to evaluate their binding affinity and selectivity. The aptamer LXL-1 with the highest abundance in the enriched library demonstrated a low K(d) value and excellent selectivity for the recognition of the metastatic breast cancer cells. Tissue imaging results showed that truncated aptamer sequence LXL-1-A was highly specific to the corresponding tumor tissue and displayed 76% detection rate against breast cancer tissue with metastasis in regional lymph nodes. Therefore, on the basis of its excellent targeting properties and functional versatility, LXL-1-A holds great potential to be used as a molecular imaging probe for the detection of breast cancer metastasis. Our result clearly demonstrates that metastatic-cell-based SELEX can be used to generate DNA ligands specifically recognizing metastatic cancer cells, which is of great significance for metastatic cancer diagnosis and treatment.

Simple and efficient method to purify DNA-protein conjugates and its sensing applications

DNA-protein conjugates are very useful in analytical chemistry for target recognition and signal amplification. While a number of methods for conjugating DNA with proteins are known, methods for purification of DNA-protein conjugates from reaction mixture containing unreacted proteins are much less investigated. In this work, a simple and efficient approach to purify DNA-invertase conjugates from reaction mixture via a biotin displacement strategy to release desthiobiotinylated DNA-invertase conjugates from streptavidin-coated magnetic beads was developed. The conjugates purified by this approach were utilized for quantitative detection of cocaine and DNA using a personal glucose meter through structure-switching DNA aptamer sensors and competitive DNA hybridization assays, respectively. In both cases, the purified DNA-invertase conjugates showed better performance compared to the same assays using unpurified conjugates. The approach demonstrated here can be further expanded to other DNA and proteins to generate purified DNA-protein conjugates for analytical and other applications.

Current progress of aptamer-based molecular imaging

Aptamers, single-stranded oligonucleotides, are an important class of molecular targeting ligand. Since their discovery, aptamers have been rapidly translated into clinical practice. They have been approved as therapeutics and molecular diagnostics. Aptamers also possess several properties that make them uniquely suited to molecular imaging. This review aims to provide an overview of aptamers' advantages as targeting ligands and their application in molecular imaging.

Tumor-specific hyperthermia with aptamer-tagged superparamagnetic nanoparticles

Targeted therapy is a method owing to its limited side effect profile, particularly in cancer treatment. Magnetic hyperthermia, which is induced by nanoparticles (NPs) conjugated with targeting agents, can be useful in combination with chemo- or radiotherapy. In this paper, we constructed dextran-coated ferric oxide NPs conjugated with specific anti-human epidermal growth factor receptor (HER2) aptamer and used them to induce magnetic hyperthermia in cultured cells. The specificity of the tagged NPs was determined by studying their effect relative to that of non-tagged NPs against two cell lines: human adenocarcinoma SK-BR3, overexpressing the HER2 receptor; and U-87 MG, a human glioblastoma epithelial cell line, not expressing HER2. In order to confirm the interaction of the tagged NPs with the cells we used, fluorescence microscopy and fluorescence-activated cell sorting analysis were performed. All of these experiments showed that the aptamer-tagged NPs were highly specific toward the HER2-expressing cells. In addition, a ninetyfold lower dose of the tagged NPs relative to that of the non-tagged NPs was needed to achieve ~50% cell killing by hyperthermia of the SK-BR3 cell line, while for the U-87 MG cells the viability level was close to 100%. These results show that targeted NPs can be applied at substantially lower doses than non-targeted ones to achieve similar effects of hyperthermia, which should greatly limit the side effects of treatment.

Multifunctional iron oxide nanoparticles for diagnostics, therapy and macromolecule delivery

In recent years, multifunctional nanoparticles (NPs) consisting of either metal (e.g. Au), or magnetic NP (e.g. iron oxide) with other fluorescent components such as quantum dots (QDs) or organic dyes have been emerging as versatile candidate systems for cancer diagnosis, therapy, and macromolecule delivery such as micro ribonucleic acid (microRNA). This review intends to highlight the recent advances in the synthesis and application of multifunctional NPs (mainly iron oxide) in theranostics, an area used to combine therapeutics and diagnostics. The recent applications of NPs in miRNA delivery are also reviewed.

Highly sensitive two-photon sensing of thrombin in serum using aptamers and silver nanoparticles

Thrombin plays an important role in pathological conditions. It is important, however challenging, to detect thrombin in complex biological media for clinical practice and diagnostic applications. Here we demonstrate a label-free, fast, highly sensitive and selective two-photon sensing scheme for detection of thrombin on the picomolar level. The assay is based on interactions between thrombin and a DNA aptamer, which induce aggregation of silver nanoparticles to display significantly enhanced two-photon photoluminescence. The limit of detection (LOD) of this two-photon sensing assay is as low as 3.1 pM in the buffer solution, more than 400 times lower than that of the extinction method (1.3 nM). The dynamic range of this method covers more than 4 orders of magnitude. Furthermore, this two-photon sensing assay can be applied to detection of thrombin in 100% fetal bovine serum with LOD of 1.8 nM. In addition to the unique advantages of two-photon sensing such as deep penetration and localized detection, this method could be potentially integrated with two-photon microscopy to offer additional advantages of 3D detection and mapping for potential in vivo applications.

A smart T(1)-weighted MRI contrast agent for uranyl cations based on a DNAzyme-gadolinium conjugate

Rational design of smart MRI contrast agents with high specificity for metal ions remains a challenge. Here, we report a general strategy for the design of smart MRI contrast agents for detecting metal ions based on conjugation of a DNAzyme with a gadolinium complex. The 39E DNAzyme, which has high selectivity for UO2(2+), was conjugated to Gd(III)-DOTA and streptavidin. The binding of UO2(2+) to its 39E DNAzyme resulted in the dissociation of Gd(III)-DOTA from the large streptavidin, leading to a decrease of the T1 correlation time, and a change in the MRI signal.

Recent advances and achievements in nanomaterial-based, and structure switchable aptasensing platforms for ochratoxin A detection

Aptamer-based bioreceptors that can easily adopt their surroundings have captured the attention of scientists from a wide spectrum of domains in designing highly sensitive, selective and structure switchable sensing assays. Through elaborate design and chemical functionalization, numerous aptamer-based assays have been developed that can switch their conformation upon incubation with target analyte, resulting in an enhanced output signal. To further lower the detection limits to picomolar levels, nanomaterials have attracted great interest in the design of aptamer-based sensing platforms. Associated to their unique properties, nanomaterials offer great promise for numerous aptasensing applications. This review will discuss current research activities in the aptasensing with typical example of detection of ochratoxin A (OTA). OTA, a secondary fungal metabolite, contaminates a variety of food commodities, and has several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic activities. The review will introduce advances made in the methods of integrating nanomaterials in aptasensing, and will discuss current conformational switchable design strategies in aptasensor fabrication methodologies.

Superparamagnetic iron oxide based nanoprobes for imaging and theranostics

The need to target, deliver and subsequently evaluate the efficacy of therapeutics in the treatment of a disease has provided added impetus in developing novel and highly efficient contrast agents. Superparamagnetic iron oxide nanoparticles (SPIONs) have offered tremendous potential in designing advanced magnetic resonance imaging (MRI) diagnostic agents, due to their unique physicochemical properties. There has been tremendous effort devoted in the recent past in developing synthetic methodologies through which their size, hydrodynamic radii, chemical composition and morphologies could be tailored at the nanoscale. This enables one to fine tune their magnetic behavior, and thus their MRI response. While novel synthetic strategies are being assembled for directing SPIONs to the diseased site as well as imparting them stealth and biocompatibility, it is also essential to evaluate their biological toxicological profiles. This review highlights recent advances that have been made in the synthesis of SPIONs, subsequent functionalization with desired entities, and a discussion on their use as MRI contrast agents in cardiovascular research.

Multifunctional superparamagnetic iron oxide nanoparticles: design, synthesis and biomedical photonic applications

Superparamagnetic iron oxide nanoparticles (SPIONs) have shown great promise in biomedical applications. In this review, we summarize the recent advances in the design and fabrication of core-shell and hetero-structured SPIONs and further outline some exciting developments and progresses of these multifunctional SPIONs for diagnosis, multimodality imaging, therapy, and biophotonics.

A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification

In this work, a novel signal amplification electrochemical aptasensor for the sensitive and selective detection of thrombin was successfully fabricated. The amplification method was based on the hybridization chain reaction (HCR) and a pseudobienzyme electrocatalytic system. HCR-based double-stranded DNA (dsDNA) polymers not only constructed an effective carrier for anchoring larger amounts of electron mediator methylene blue (MB) into the DNA duplexes to produce a strong differential pulse voltammetry (DPV) signal, but also resulted in the formation of hemin/G-quadruplex DNAzymes nanowires by intercalating hemin into two induced single-stranded DNA (ssDNA). With the addition of NADH into the electrolytic cell, the hemin/G-quadruplex acting as an NADH oxidase and HRP-mimicking DNAzyme for the pseudobienzyme amplifying system could in situ biocatalyze the formation of H₂O₂ with local concentrations and low transfer loss resulting in dramatic signal enhancements. The binding event can be detected by a decrease in the integrated charge of MB which electrostatically absorbed onto dsDNA polymers. In the presence of thrombin, the dsDNA polymers associated with MB and hemin/G-quadruplex structures were removed from the electrode surface, leading to a significant decrease of redox current. DPV signals of MB provided quantitative measures of the concentrations of thrombin, with a linear calibration range of 0.01-50 nM and a detection limit of 2 pM. Moreover, the resulting aptasensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay and various protein analyses.

Aptamer-conjugated magnetic nanoparticles enable efficient targeted detection of integrin αvβ3 via magnetic resonance imaging

An understanding of neovascularization and/or angiogenesis in cancer is acutely required for effective cancer therapy due to concerns about tumor growth and metastasis. In particular, integrin αvβ3 is closely associated with cell migration and invasion during angiogenesis. Hence, we developed aptamer(αvβ3)-conjugated magnetic nanoparticles (Apt(αvβ3)-MNPs) to enable precise detection of integrin-expressing cancer cells using magnetic resonance imaging. Apt(αvβ3)-MNPs exhibited not only cytocompatibility, but also an efficient targeting ability with high magnetic sensitivity through in vitro/in vivo studies. The results of this study demonstrate that Apt(αvβ3)-MNPs have the potential to be used for accurate tumor diagnosis and therapy.

Aptamer-modified nanoparticles as biosensors

Aptamers are short oligonucleotides that are capable of selectively binding to their corresponding target. Therefore, they can be thought of as a nucleic acid-based alternative to antibodies and can substitute for their amino acid-based counterparts in analytical applications, including as receptors in biosensors. Here they offer several advantages because their nucleic acid nature and their binding via an induced fit mechanism enable novel sensing strategies. In this article, the utilization of aptamers as novel bio-receptors in combination with nanoparticles as transducer elements is reviewed. In addition to these analytical applications, the medical relevance of aptamer-modified nanoparticles is described.

A dual-amplification aptasensor for highly sensitive detection of thrombin based on the functionalized graphene-Pd nanoparticles composites and the hemin/G-quadruplex

In this work, an advanced sandwich-type electrochemical aptasensor for thrombin was proposed by integrating hemin/G-quadruplex with functionalized graphene-Pd nanoparticles composites (PdNPs-RGs). The hemin/G-quadruplex formed by intercalating hemin into thrombin binding aptamer (TBA), firstly acted as a NADH oxidase, assisting the oxidation of NADH to NAD(+) accompanying with the generation of H(2)O(2) in the presence of dissolved O(2). Subsequently, the hemin/G-quadruplex acted as HRP-mimicking DNAzyme that rapidly bioelectrocatalyze the reduction of the produced H(2)O(2). At the same time, the Pd nanoparticles supported on p-iodoaniline functionalized graphene were also adopted to catalyze the reduction of H(2)O(2). Thus, with the dual catalysis, a dramatically amplified electrochemical signal could be obtained. Besides, the avidin-biotin system for binding aptamer sequences on electrodes not only improved the sensitivity of thrombin analysis but also obtained an acceptable repeatability of the aptasensor. With several factors mentioned above, a wide linear ranged from 0.1 pM to 50 nM was acquired with a relatively low detection limit of 0.03 pM (defined as S/N=3). These excellent performances provided our approach a promising way for ultrasensitive assay in electrochemical aptasensors.

Target binding improves relaxivity in aptamer-gadolinium conjugates

MRI contrast agents (CA) have been heavily used over the past several decades to enhance the diagnostic value of the obtained images. From a design perspective, two avenues to improve the efficacy of contrast agents are readily evident: optimization of magnetic properties of the CA, and optimization of the pharmacokinetics and distribution of the CA in the patient. Contrast agents consisting of DNA aptamer-gadolinium(III) conjugates provide a single system in which these factors can be addressed simultaneously. In this proof-of-concept study, the 15mer thrombin aptamer was conjugated to diethylenetriaminepentaacetic (DTPA) dianhydride to form a monoamide derivative of the linear open-chain chelate present in the commonly used contrast agent Magnevist(®). The stability of the conjugated DNA aptamer-DTPA-Gd(III) chelate in a transmetallation study using Zn(II) was found to be similar to that reported for DTPA-Gd(III). Relaxivity enhancements of 35 ± 4 and 20 ± 1 % were observed in the presence of thrombin compared to a control protein at fields of 9.4 and 1.5 T, respectively. The inclusion of spacers between the aptamer and the DTPA to eliminate possible steric effects was also investigated but not found to improve the relaxation enhancement achieved in comparison to the unaltered aptamer conjugate.

Bioengineered probes for molecular magnetic resonance imaging in the nervous system

The development of molecular imaging probes has changed the nature of neurobiological research. Some of the most notable successes have involved the use of biological engineering techniques for the creation of fluorescent protein derivatives for optical imaging, but recent work has also led to a number of bioengineered probes for magnetic resonance imaging (MRI), the preeminent technique for noninvasive investigation of brain structure and function. Molecular MRI agents are beginning to be applied for experiments in the nervous system, where they have the potential to bridge from molecular to systems or organismic levels of analysis. Compared with canonical synthetic small molecule agents, biomolecular or semibiosynthetic MRI contrast agents offer special advantages due to their amenability to molecular engineering approaches, their properties in some cases as catalysts, and their specificity in targeting and ligand binding. Here, we discuss an expanding list of instances where biological engineering techniques have aided in the design of MRI contrast agents and reporter systems, examining both advantages and limitations of these types of probes for studies in the central nervous system.

Polyvalent nucleic acid aptamers and modulation of their activity: a focus on the thrombin binding aptamer

Nucleic acid-based aptamers can be selected from combinatorial libraries of synthetic oligonucleotides to bind, with affinity and specificity similar to antibodies, a wide range of biomedically relevant targets. Compared to protein therapeutics, aptamers exhibit significant advantages in terms of size, non-immunogenicity and wide synthetic accessibility. Various chemical modifications have been introduced in the natural oligonucleotide backbone of aptamers in order to increase their half-life, as well as their pharmacological properties. Very effective alternative approaches, devised in order to improve both the aptamer activity and stability, were based on the design of polyvalent aptamers, able to establish multivalent interactions with the target: thus, multiple copies of an aptamer can be assembled on the same molecular- or nanomaterial-based scaffold. In the present review, the thrombin binding aptamers (TBAs) are analyzed as a model system to study multiple-aptamer constructs aimed at improving their anticoagulation activity in terms of binding to the target and stability to enzymatic degradation. Indeed - even if the large number of chemically modified TBAs investigated in the last 20 years has led to encouraging results - a significant progress has been obtained only recently with bivalent or engineered dendritic TBA aptamers, or assemblies of TBAs on nanoparticles and DNA nanostructures. Furthermore, the modulation of the aptamers activity by means of tailored drug-active reversal agents, especially in the field of anticoagulant aptamers, as well as the reversibility of the TBA activity through the use of antidotes, such as porphyrins, complementary oligonucleotides or of external stimuli, are discussed.

Label-free, nucleotide-mediated dispersion of magnetic nanoparticles for "non-sandwich type" MRI-based quantification of enzyme

In the present work, we demonstrate that nucleotide can adsorb efficiently on the surface of carboxylic acid-functionalized nanoparticles and stabilize the particles against aggregation. In the present study we take magnetic nanoparticles (MNPs), manganese oxide nanoparticles (MnO), and upconversion nanophosphors (UCNPs) as models. The result shows that not only MNPs, but also other kinds of nanoparticles that have similar surface properties can be dispersed and stabilized by nucleotides. Interestingly, adenosine bearing different numbers of phosphate groups has distinct stabilizing effect. On the basis of this observation, we developed a magnetic relaxation-based enzyme assay for quantitative analysis of alkaline phosphatase. A detection limit of 0.002 U/μL for calf intestine alkaline phosphatase (CIAP) could be obtained, which is lower than the gold nanoparticle-based colorimetric method. In contrast to the conventional magnetic relaxation switches (MRSw), this assay was achieved without covalent modification and separation steps, sandwich type binding was not required as well, which would potentially expand the application of magnetic relaxation-based analysis.

A responsive particulate MRI contrast agent for copper(I): a cautionary tale

A responsive MION-based MRI contrast agent for the detection of copper(I) is presented. Induced agglomeration of azide and acetylene-functionalized magnetite nanoparticles via Cu(I)-catalysed Huisgen cycloaddition leads to significant decrease in longitudinal relaxivity due to the slow exchange of water molecules trapped within the cluster with bulk solvent. Agglomeration leads to an initial two-fold increase followed by a sharp and almost complete loss in transverse relaxivity for clusters larger than 200 nm in size. The decrease in r(2) for clusters reaching the static dephasing regime has two significant implications for particulate responsive MRI contrast agents. First, the maximum increase in r(2) is barely two-fold, second, since r(2) does not increase continuously with increasing cluster size, the r(1)/r(2) ratio cannot be used to determine the concentration of an analyte ratiometrically.

Pattern recognition of cancer cells using aptamer-conjugated magnetic nanoparticles

Biocompatible magnetic nanosensors based on reversible self-assembly of dispersed magnetic nanoparticles into stable nanoassemblies have been used as effective magnetic relaxation switches (MRSw) for the detection of molecular interactions. We report, for the first time, the design of MRSw based on aptamer-conjugated magnetic nanoparticles (ACMNPs). The ACMNPs capitalize on the ability of aptamers to specifically bind target cancer cells, as well as the large surface area of MNPs to accommodate multiple aptamer binding events. The ACMNPs can detect as few as 10 cancer cells in 250 μL of sample. The ACMNPs' specificity and sensitivity are also demonstrated by detection in cell mixtures and complex biological media, including fetal bovine serum, human plasma, and whole blood. Furthermore, by using an array of ACMNPs, various cell types can be differentiated through pattern recognition, thus creating a cellular molecular profile that will allow clinicians to accurately identify cancer cells at the molecular and single-cell level.

Accumulation of magnetic iron oxide nanoparticles coated with variably sized polyethylene glycol in murine tumors

Iron oxide nanoparticles have found widespread applications in different areas including cell separation, drug delivery and as contrast agents. Due to water insolubility and stability issues, nanoparticles utilized for biological applications require coatings such as the commonly employed polyethylene glycol (PEG). Despite its frequent use, the influence of PEG coatings on the physicochemical and biological properties of iron nanoparticles has hitherto not been studied in detail. To address this, we studied the effect of 333-20,000 Da PEG coatings that resulted in larger hydrodynamic size, lower surface charge, longer circulation half-life, and lower uptake in macrophage cells when the particles were coated with high molecular weight (M(w)) PEG molecules. By use of magnetic resonance imaging, we show coating-dependent in vivo uptake in murine tumors with an optimal coating M(w) of 10,000 Da.

Label-free catalytic and molecular beacon containing an abasic site for sensitive fluorescent detection of small inorganic and organic molecules

In this work, two methods with complementary features, catalytic and molecular beacon (CAMB) and label-free fluorescent sensors using an abasic site, have been combined into new label-free CAMB sensors that possess advantages of each method. The label-free method using a dSpacer-containing molecular beacon makes CAMB more cost-effective and less interfering with the catalytic activity, while CAMB allows the label-free method to use true catalytic turnovers for signal amplifications, resulting in a new label-free CAMB sensor for Pb(2+) ion, with a detection limit of 3.8 nM while maintaining the same selectivity. Furthermore, by using CAMB to overcome the label-free method's limitation of requiring excess enzyme strands, a new label-free CAMB sensor using aptazyme is also designed to detect adenosine down to 1.4 μM, with excellent selectivity over other nucleosides.

Nucleic acid aptamers: clinical applications and promising new horizons

Aptamers are a special class of nucleic acid molecules that are beginning to be investigated for clinical use. These small RNA/DNA molecules can form secondary and tertiary structures capable of specifically binding proteins or other cellular targets; they are essentially a chemical equivalent of antibodies. Aptamers have the advantage of being highly specific, relatively small in size, and non-immunogenic. Since the discovery of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like cancer, HIV, and macular degeneration. In the last two decades, many aptamers have been clinically developed as inhibitors for targets such as vascular endothelial growth factor (VEGF) and thrombin. The first aptamer based therapeutic was FDA approved in 2004 for the treatment of age-related macular degeneration and several other aptamers are currently being evaluated in clinical trials. With advances in targeted-therapy, imaging, and nanotechnology, aptamers are readily considered as potential targeting ligands because of their chemical synthesis and ease of modification for conjugation. Preclinical studies using aptamer-siRNA chimeras and aptamer targeted nanoparticle therapeutics have been very successful in mouse models of cancer and HIV. In summary aptamers are in several stages of development, from pre-clinical studies to clinical trials and even as FDA approved therapeutics. In this review, we will discuss the current state of aptamers in clinical trials as well as some promising aptamers in pre-clinical development.

Molecular imaging with nucleic acid aptamers

With many desirable properties such as ease of synthesis, small size, lack of immunogenicity, and versatile chemistry, aptamers represent a class of targeting ligands that possess tremendous potential in molecular imaging applications. Non-invasive imaging of various disease markers with aptamer-based probes has many potential clinical applications such as lesion detection, patient stratification, treatment monitoring, etc. In this review, we will summarize the current status of molecular imaging with aptamer-based probes. First, fluorescence imaging will be described which include both direct targeting and activatable probes. Next, we discuss molecular magnetic resonance imaging and targeted ultrasound investigations using aptamer-based agents. Radionuclide-based imaging techniques (single-photon emission computed tomography and positron emission tomography) will be summarized as well. In addition, aptamers have also been labeled with various tags for computed tomography, surface plasmon resonance, dark-field light scattering microscopy, transmission electron microscopy, and surface-enhanced Raman spectroscopy imaging. Among all molecular imaging modalities, no single modality is perfect and sufficient to obtain all the necessary information for a particular question. Thus, a multimodality probe has also been constructed for concurrent fluorescence, gamma camera, and magnetic resonance imaging in vivo. Although the future of aptamer-based molecular imaging is becoming increasingly bright and many proof-of-principle studies have already been reported, much future effort needs to be directed towards the development of clinically translatable aptamer-based imaging agents which will eventually benefit patients.

Magnetic nanocarriers of doxorubicin coated with poly(ethylene glycol) and folic acid: relation between coating structure, surface properties, colloidal stability, and cancer cell targeting

We report the efficient one-step synthesis and detailed physicochemical evaluation of novel biocompatible nanosystems useful for cancer therapeutics and diagnostics (theranostics). These systems are the superparamagnetic iron oxide nanoparticles (SPIONs) carrying the anticancer drug doxorubicin and coated with the covalently bonded biocompatible polymer poly(ethylene glycol) (PEG), native and modified with the biological cancer targeting ligand folic acid (PEG-FA). These multifunctional nanoparticles (SPION-DOX-PEG-FA) are designed to rationally combine multilevel mechanisms of cancer cell targeting (magnetic and biological), bimodal cancer cell imaging (by means of MRI and fluorescence), and bimodal cancer treatment (by targeted drug delivery and by hyperthermia effect). Nevertheless, for these concepts to work together, the choice of ingredients and particle structure are critically important. Therefore, in the present work, a detailed physicochemical characterization of the organic coating of the hybrid nanoparticles is performed by several surface-specific instrumental methods, including surface-enhanced Raman scattering (SERS) spectroscopy, X-ray photoelectron spectrometry (XPS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS). We demonstrate that the anticancer drug doxorubicin is attached to the iron oxide surface and buried under the polymer layers, while folic acid is located on the extreme surface of the organic coating. Interestingly, the moderate presence of folic acid on the particle surface does not increase the particle surface potential, while it is sufficient to increase the particle uptake by MCF-7 cancer cells. All of these original results contribute to the better understanding of the structure-activity relationship for hybrid biocompatible nanosystems and are encouraging for the applications in cancer theranostics.

Hybrid magnetic nanostructures (MNS) for magnetic resonance imaging applications

The development of MRI contrast agents has experienced its version of the gilded age over the past decade, thanks largely to the rapid advances in nanotechnology. In addition to progress in single mode contrast agents, which ushered in unprecedented R(1) or R(2) sensitivities, there has also been a boon in the development of agents covering more than one mode of detection. These include T(1)-PET, T(2)-PET T(1)-optical, T(2)-optical, T(1)-T(2) agents and many others. In this review, we describe four areas which we feel have experienced particular growth due to nanotechnology, specifically T(2) magnetic nanostructure development, T(1)/T(2)-optical dual mode agents, and most recently the T(1)-T(2) hybrid imaging systems. In each of these systems, we describe applications including in vitro, in vivo usage and assay development. In all, while the benefits and drawbacks of most MRI contrast agents depend on the application at hand, the recent development in multimodal nanohybrids may curtail the shortcomings of single mode agents in diagnostic and clinical settings by synergistically incorporating functionality. It is hoped that as nanotechnology advances over the next decade, it will produce agents with increased diagnostics and assay relevant capabilities in streamlined packages that can meaningfully improve patient care and prognostics. In this review article, we focus on T(2) materials, its surface functionalization and coupling with optical and/or T(1) agents.

Optimization of the structure-switching aptamer-based fluorescence polarization assay for the sensitive tyrosinamide sensing

In this paper, a structure-switching aptamer assay based on a fluorescence polarization (FP) signal transduction approach and dedicated to the L-tyrosinamide sensing was described and optimized. A fluorescently labelled complementary strand (CS) of the aptamer central region was used as a probe. The effects of critical parameters such as buffer composition and pH, temperature, aptamer:CS stoichiometry, nature of the dye (Fluorescein (F) or Texas Red (TR)) and length of the CS (15-, 12-, 9- and 6-mer) on the assay analytical performances were evaluated. Under optimized experimental conditions (10 mM Tris-HCl, 5 mM MgCl(2) and 25 mM NaCl, pH 7.5 temperature of 22°C and stoichiometry 1:1), the results showed that, for a 12-mer CS, the F dye moderately increased the method sensitivity in comparison to the TR label. The F labelled 9-mer CS, however, did not allow the hybrid formation with the functional nucleic acid, thus emphasizing the importance of the nature of the fluorophore. In contrast, the same 9-mer CS labelled with the TR dye was able to effectively associate with the aptamer and was easily displaced upon target binding as demonstrated by a significant improvement of the sensitivity and a detection limit of 250 nM, comparable to those reported with direct aptasensing methods. The present study demonstrates that not only the CS length but also the nature of the dye played a preponderant role in the performance of the structure-switching aptamer assay, highlighting the importance of interdependently controlling these two factors for an optimal FP-based sensing platform.

Aptamer-assembled nanomaterials for biosensing and biomedical applications

Aptamers represent a class of single-stranded DNA or RNA oligonucleotides that play important roles in biosensing and biomedical applications. However, aptamers can gain more flexibility as molecular recognition tools by taking advantage of the unique chemical and physical properties provided by nanomaterials. Such aptamer-nanomaterial conjugates are having an increasing impact in the fields of biosensing, bioimaging, and therapy. The recent advances and limitations of aptamer-assembled nanomaterials in biosensing and biomedical applications are briefly introduced and discussed.

Quantifying the nanomachinery of the nanoparticle-biomolecule interface

A study is presented of the nanomechanical phenomena experienced by nanoparticle-conjugated biomolecules. A thermodynamic framework is developed to describe the binding of thrombin-binding aptamer (TBA) to thrombin when the TBA is conjugated to nanorods. Binding results in nanorod aggregation (viz. directed self-assembly), which is detectable by absorption spectroscopy. The analysis introduces the energy of aggregation, separating it into TBA-thrombin recognition and surface-work contributions. Consequently, it is demonstrated that self-assembly is driven by the interplay of surface work and thrombin-TBA recognition. It is shown that the work at the surface is about -10 kJ mol(-1) and results from the accumulation of in-plane molecular forces of pN magnitude and with a lifetime of <1 s, which arises from TBA nanoscale rearrangements fuelled by thrombin-directed nanorod aggregation. The obtained surface work can map aggregation regimes as a function of different nanoparticle surface conditions. Also, the thermodynamic treatment can be used to obtain quantitative information on surface effects impacting biomolecules on nanoparticle surfaces.

Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets

Portable, low-cost and quantitative detection of a broad range of targets at home and in the field has the potential to revolutionize medical diagnostics and environmental monitoring. Despite many years of research, very few such devices are commercially available. Taking advantage of the wide availability and low cost of the pocket-sized personal glucose meter-used worldwide by diabetes sufferers-we demonstrate a method to use such meters to quantify non-glucose targets, ranging from a recreational drug (cocaine, 3.4 µM detection limit) to an important biological cofactor (adenosine, 18 µM detection limit), to a disease marker (interferon-gamma of tuberculosis, 2.6 nM detection limit) and a toxic metal ion (uranium, 9.1 nM detection limit). The method is based on the target-induced release of invertase from a functional-DNA-invertase conjugate. The released invertase converts sucrose into glucose, which is detectable using the meter. The approach should be easily applicable to the detection of many other targets through the use of suitable functional-DNA partners (aptamers, DNAzymes or aptazymes).

Cancer cell invasion: treatment and monitoring opportunities in nanomedicine

Cell invasion is an intrinsic cellular pathway whereby cells respond to extracellular stimuli to migrate through and modulate the structure of their extracellular matrix (ECM) in order to develop, repair, and protect the body's tissues. In cancer cells this process can become aberrantly regulated and lead to cancer metastasis. This cellular pathway contributes to the vast majority of cancer related fatalities, and therefore has been identified as a critical therapeutic target. Researchers have identified numerous potential molecular therapeutic targets of cancer cell invasion, yet delivery of therapies remains a major hurdle. Nanomedicine is a rapidly emerging technology which may offer a potential solution for tackling cancer metastasis by improving the specificity and potency of therapeutics delivered to invasive cancer cells. In this review we examine the biology of cancer cell invasion, its role in cancer progression and metastasis, molecular targets of cell invasion, and therapeutic inhibitors of cell invasion. We then discuss how the field of nanomedicine can be applied to monitor and treat cancer cell invasion. We aim to provide a perspective on how the advances in cancer biology and the field of nanomedicine can be combined to offer new solutions for treating cancer metastasis.

Targeted magnetic hyperthermia

Many nanotechnologies, which enable unique approaches to treat cancer, have been developed based upon non-toxic organic and inorganic materials to improve current cancer treatments. The use of inorganic materials to form magnetic nanoparticles for hyperthermia therapy is of great interest for localized treatment of cancers without effecting adjacent healthy tissue. Extensive clinical trials have begun using magnetic hyperthermia in animal models. The purpose of this article is to address different factors that affect targeting, heating and biodistribution to safely control the therapeutic efficacy of targeted magnetic hyperthermia. This method involves accumulation of magnetic nanoparticles at a tumor site and then manipulating the magnetic properties of the nanoparticles to heat the targeted tissues.

A smart magnetic resonance imaging contrast agent responsive to adenosine based on a DNA aptamer-conjugated gadolinium complex

We report a general strategy for developing a smart MRI contrast agent for the sensing of small molecules such as adenosine based on a DNA aptamer that is conjugated to a Gd compound and a protein streptavidin. The binding of adenosine to its aptamer results in the dissociation of the Gd compound from the large protein, leading to decreases in the rotational correlation time and thus change of MRI contrast.