MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles

Enzyme-Programmed Self-Assembly of Nanoparticles

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

Dual Nanoparticle Conjugates for Highly Sensitive and Versatile Sensing Using 19 F Magnetic Resonance Imaging

Fluorine magnetic resonance imaging (19 F MRI) has emerged as an attractive alternative to conventional 1 H MRI due to enhanced specificity deriving from negligible background signal in this modality. We report a dual nanoparticle conjugate (DNC) platform as an aptamer-based sensor for use in 19 F MRI. DNC consists of core-shell nanoparticles with a liquid perfluorocarbon core and a mesoporous silica shell (19 F-MSNs), which give a robust 19 F MR signal, and superparamagnetic iron oxide nanoparticles (SPIONs) as magnetic quenchers. Due to the strong magnetic quenching effects of SPIONs, this platform is uniquely sensitive and functions with a low concentration of SPIONs (4 equivalents) relative to 19 F-MSNs. The probe functions as a "turn-on" sensor using target-induced dissociation of DNA aptamers. The thrombin binding aptamer was incorporated as a proof-of-concept (DNCThr ), and we demonstrate a significant increase in 19 F MR signal intensity when DNCThr is incubated with human α-thrombin. This proof-of-concept probe is highly versatile and can be adapted to sense ATP and kanamycin as well. Importantly, DNCThr generates a robust 19 F MRI "hot-spot" signal in response to thrombin in live mice, establishing this platform as a practical, versatile, and biologically relevant molecular imaging probe.

Manipulating Physicochemical Properties of Biosensor Platform with Polysuccinimide-Silica Nanocomposite for Enhanced Protein Detection

As point-of-care testing (POCT) is becoming the new paradigm of medical diagnostics, there is a growing need to develop reliable POCT devices that can be conveniently operated in a minimally invasive manner. However, the clinical potential of POCT diagnostics is yet to be realized, mainly due to the limited and inconsistent amount of collected samples on these devices, undermining their accuracy. This study proposes a new biosensing platform modified with a functional polysuccinimide (PSI)-silica nanoparticle (SNP) composite system that can substantially increase the protein conjugation efficiency by modulating physicochemical interaction with proteins by several hundred percent from an unmodified device. The efficacy of this PSI-SNP system is further validated by applying it on the surface of a microneedle array (MN), which has emerged as a promising POCT device capable of accessing interstitial fluid through minimal penetration of the skin. This PSI-SNP MN is demonstrated to detect a wide array of proteins with high sensitivity on par with conventional whole serum analysis, validated by in vivo animal testing, effectively displaying broad applicability in biomedical engineering.

Monitoring the Formation of Fibrin Clots as Part of the Coagulation Cascade Using Fluorescent Single-Walled Carbon Nanotubes

Blood coagulation is a critical defense mechanism against bleeding that results in the conversion of liquid blood into a solid clot through a complicated cascade, which involves multiple clotting factors. One of the final steps in the coagulation pathway is the conversion of fibrinogen to insoluble fibrin mediated by thrombin. Because coagulation disorders can be life-threatening, the development of novel methods for monitoring the coagulation cascade dynamics is of high importance. Here, we use near-infrared (NIR)-fluorescent single-walled carbon nanotubes (SWCNTs) to image and monitor fibrin clotting in real time. Following the binding of fibrinogen to a tailored SWCNT platform, thrombin transforms the fibrinogen into fibrin monomers, which start to polymerize. The SWCNTs are incorporated within the clot and can be clearly visualized in the NIR-fluorescent channel, where the signal-to-noise ratio is improved compared to bright-field imaging in the visible range. Moreover, the diffusion of individual SWCNTs within the fibrin clot gradually slows down after the addition of thrombin, manifesting a coagulation rate that depends on both fibrinogen and thrombin concentrations. Our platform can open new opportunities for coagulation disorder diagnostics and allow for real-time monitoring of the coagulation cascade with a NIR optical signal output in the biological transparency window.

Recent advances in engineering iron oxide nanoparticles for effective magnetic resonance imaging

Iron oxide nanoparticle (IONP) with unique magnetic property and high biocompatibility have been widely used as magnetic resonance imaging (MRI) contrast agent (CA) for long time. However, a review which comprehensively summarizes the recent development of IONP as traditional T₂ CA and its new application for different modality of MRI, such as T₁ imaging, simultaneous T₂/T₁ or MRI/other imaging modality, and as environment responsive CA is rare. This review starts with an investigation of direction on the development of high-performance MRI CA in both T₂ and T₁ modal based on quantum mechanical outer sphere and Solomon–Bloembergen–Morgan (SBM) theory. Recent rational attempts to increase the MRI contrast of IONP by adjusting the key parameters, including magnetization, size, effective radius, inhomogeneity of surrounding generated magnetic field, crystal phase, coordination number of water, electronic relaxation time, and surface modification are summarized. Besides the strategies to improve r₂ or r₁ values, strategies to increase the in vivo contrast efficiency of IONP have been reviewed from three different aspects, those are introducing second imaging modality to increase the imaging accuracy, endowing IONP with environment response capacity to elevate the signal difference between lesion and normal tissue, and optimizing the interface structure to improve the accumulation amount of IONP in lesion. This detailed review provides a deep understanding of recent researches on the development of high-performance IONP based MRI CAs. It is hoped to trigger deep thinking for design of next generation MRI CAs for early and accurate diagnosis.

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T₂ contrast capacity of iron oxide nanoparticles (IONPs) could be improved based on quantum mechanical outer sphere theory.

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IONPs could be expand to be used as effective T₁ CAs by improving q value, extending τ_s, and optimizing interface structure.

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Environment responsive MRI CAs have been developed to improve the diagnosis accuracy.

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Introducing other imaging contrast moiety into IONPs could increase the contrast efficiency.

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Optimizing in vivo behavior of IONPs have been proved to enlarge the signal difference between normal tissue and lesion.

Selection of DNA Aptamers Recognizing EpCAM-Positive Prostate Cancer by Cell-SELEX for in vitro and in vivo MR Imaging

Background

The sensitive and specific detection of pathogenic cells is important in tumor diagnosis at an early stage. Aptamers are short single-stranded oligonucleotides evolved from systematic evolution of ligands by exponential enrichment (SELEX). It has been proved that aptamers can interact with cognate target molecules with high affinity and specificity and have great potential in the development of medical imaging at molecular level.

Purpose

To select epithelial cell adhesion molecule (EpCAM) specific aptamers targeting prostate cancer and further to conjugate aptamers with GoldMag nanoparticles (a typical iron oxide core/gold shell structure) to construct magnetic molecular probes for medical imaging.

Methods

EpCAM-specific aptamers were selected by Cell-SELEX. The enrichment of specific aptamer candidates was monitored by flow cytometric analysis. Aptamers were further conjugated with GoldMag nanoparticles to construct magnetic molecular probes. The affinity and specificity of aptamer candidates and aptamer-conjugated GoldMag nanoparticles were evaluated. The MR imaging of aptamer-conjugated GoldMag nanoparticles to prostate cancer was further explored in vitro and in vivo.

Results

After 12 rounds of selection, aptamer candidates Eppc6 and Eppc14 could specifically target three types of prostate cancer cells, revealing a high affinity of Eppc6 and Eppc14. Moreover, aptamer-conjugated GoldMag nanoparticles not only exhibited good affinity to different prostate cancer cells but also produced strong T2WI signal intensity reduction distinguished from peritumoral tissue in MRI, indicating that the molecular probes possess both the affinity properties of EpCAM-specific aptamer and the superparamagnetic features of iron oxide.

Conclusion

Our study indicates that aptamer Eppc6 and Eppc14 can recognize prostate cancer cells and tissues. The aptamer-conjugated GoldMag nanoparticles constructed in the study can be used as a molecular imaging agent for detection of PCa in MRI.

Gold-Oligonucleotide Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences

Enteroviruses are ubiquitous mammalian pathogens that can produce mild to life-threatening disease. We developed a multimodal, rapid, accurate and economical point-of-care biosensor that can detect nucleic acid sequences conserved amongst 96% of all known enteroviruses. The biosensor harnesses the physicochemical properties of gold nanoparticles and oligonucleotides to provide colourimetric, spectroscopic and lateral flow-based identification of an exclusive enteroviral nucleic acid sequence (23 bases), which was identified through in silico screening. Oligonucleotides were designed to demonstrate specific complementarity towards the target enteroviral nucleic acid to produce aggregated gold–oligonucleotide nanoconstructs. The conserved target enteroviral nucleic acid sequence (≥1 × 10⁻⁷ M, ≥1.4 × 10⁻¹⁴ g/mL) initiates gold–oligonucleotide nanoconstruct disaggregation and a signal transduction mechanism, producing a colourimetric and spectroscopic blueshift (544 nm (purple) > 524 nm (red)). Furthermore, lateral-flow assays that utilise gold–oligonucleotide nanoconstructs were unaffected by contaminating human genomic DNA, demonstrated rapid detection of conserved target enteroviral nucleic acid sequence (<60 s), and could be interpreted with a bespoke software and hardware electronic interface. We anticipate that our methodology will translate in silico screening of nucleic acid databases to a tangible enteroviral desktop detector, which could be readily translated to related organisms. This will pave the way forward in the clinical evaluation of disease and complement existing strategies to overcome antimicrobial resistance.

Exploring the Unique Contrast Properties of Aptamer-Gadolinium Conjugates in Magnetic Resonance Imaging for Targeted Imaging of Thrombi

Objective: An important clinical question in the determination of the extent of thrombosis-related vascular conditions is the identification of blood clot location. Fibrin is a major molecular constituent of blood clots and can, therefore, be utilized in molecular imaging. In this proof-of-concept study, we sought to prepare a fibrin-targeting magnetic resonance imaging contrast agent, using a Gd(III)-loaded fibrinogen aptamer (FA) chelate conjugate (Gd(III)-NOTA-FA) (NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid), to endow the ability to specifically accumulate at the location of blood clots, thereby enhancing contrast capabilities. Methods: The binding affinity of FA for fibrin was confirmed by fluorescence microscopy and microscale thermophoresis. The preparation and effective loading of the chelate-aptamer conjugates were confirmed by mass spectrometry and a xylenol orange colorimetric test. Longitudinal and transverse relaxivities and the effects of target binding were assessed using T1- and T2-map sequences at 7 T. T1- and T2-weighted images were acquired after blood clots were treated with Gd(III)-NOTA-FA. Collagen was used as the protein control, while an unrelated aptamer sequence, FB139, was used as the aptamer control. Results: FA demonstrated a high affinity and selectivity toward the polymeric protein, with a K_d of 16.6 nM, confirming an avidity over fibrinogen. The longitudinal (r1) and transverse (r2) relaxivities of Gd(III)-NOTA-FA demonstrated that conjugation to the long aptamer strand shortened T1 relaxation times and increased T2 relaxation times (3.04 and 38.7 mM^-1 s^-1, respectively). These effects were amplified by binding to the fibrin target (1.73 and 46.5 mM^-1 s^-1, respectively). In vitro studies with thrombin-polymerized human blood (clots) in whole blood showed an unexpected enhancement of signal intensity (hyperintense) produced exclusively at the location of the clot during the T2-weighted scan, while the presence of fibrinogen within a whole blood pool resulted in T1 signal intensity enhancement throughout the pool. This is advantageous, as simply reversing the type of a scan from a typical T1-weighted to a T2-weighted would allow to selectively highlight the location of blood clots. Conclusions: Gd(III)-NOTA-FA can be used for molecular imaging of thrombi, through fibrin-targeted delivery of contrast to the location of blood clots in T2-weighted scans.

Stimulus-Responsive Nanoparticle Magnetic Resonance Imaging Contrast Agents: Design Considerations and Applications

Magnetic resonance imaging (MRI) has been widely used for disease diagnosis because it can noninvasively obtain anatomical details of various diseases through accurate contrast between soft tissues. Over one-third of MRI examinations are performed with the assistance of contrast agents. Traditional contrast agents typically display an unchanging signal, thus exhibiting relatively low sensitivity and poor specificity. Currently, advances in stimulus-responsive contrast agents which can alter the relaxation signal in response to a specific change in their surrounding environment provide new opportunities to overcome such limitation. The signal changes based on stimulus also reflects the physiological and pathological conditions of the site of interests. In this review, how to design stimulus-responsive nanoparticle MRI contrast agents from the perspective of theory and surface design is comprehensively discussed. Key structural features including size, clusters, shell features, and surface properties are used for tuning the T₁ and T₂ relaxation properties. The reversible or non-reversible signal changes highlight the contrast agents have undergone structural changes based on certain stimulus, as an indication for disease diagnosis or therapeutic efficacy.

Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition

Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.

Aptamers in Drug Design: An Emerging Weapon to Fight a Losing Battle

Implementation of novel and biocompatible polymers in drug design is an emerging and rapidly growing area of research. Even though we have a large number of polymer materials for various applications, the biocompatibility of these materials remains as a herculean task for researchers. Aptamers provide a vital and efficient solution to this problem. They are usually small (ranging from 20 to 60 nucleotides, single-stranded DNA or RNA oligonucleotides which are capable of binding to molecules possessing high affinity and other properties like specificity. This review focuses on different aspects of Aptamers in drug discovery, starting from its preparation methods and covering the recent scenario reported in the literature regarding their use in drug discovery. We address the limitations of Aptamers and provide valuable insights into their future potential in the areas regarding drug discovery research. Finally, we explained the major role of Aptamers like medical imaging techniques, application as synthetic antibodies, and the most recent application, which is in combination with nanomedicines.

Aptamers in Diagnostic and Molecular Imaging Applications

The origin of the term diagnostic comes from the Greek word gnosis, meaning "to know." In medicine, a diagnostic can predict the pathology risk, disease status, treatment, and prognosis, even following therapy. An early and correct diagnosis is necessary for an efficient treatment. Moreover, it is possible to predict if and why a therapy will be successful or fail, enabling the timely application of alternative therapeutic strategies. Available diagnostics are due to the advances in biotechnology; however, more sensitive, low-cost, and noninvasive methodologies are still a challenge. Knowledge about molecular characteristics provide personalized information, which is the goal of future medicine. Today, multiple diagnostic techniques have emerged, with which it is possible to distinguish molecular patterns.In this way, aptamers are the perfect tools to recognize molecular targets and can be easily modified to confer additional functions. Their versatile characteristics and low cost make aptamers ideal for diagnostic applications.This chapter is a review of aptamer-based diagnostics in biomedicine, with a special focus on probe design and molecular imaging. Graphical Abstract.

The Intrinsic Biological Identities of Iron Oxide Nanoparticles and Their Coatings: Unexplored Territory for Combinatorial Therapies

Over the last 20 years, iron oxide nanoparticles (IONPs) have been the subject of increasing investigation due to their potential use as theranostic agents. Their unique physical properties (physical identity), ample possibilities for surface modifications (synthetic identity), and the complex dynamics of their interaction with biological systems (biological identity) make IONPs a unique and fruitful resource for developing magnetic field-based therapeutic and diagnostic approaches to the treatment of diseases such as cancer. Like all nanomaterials, IONPs also interact with different cell types in vivo, a characteristic that ultimately determines their activity over the short and long term. Cells of the mononuclear phagocytic system (macrophages), dendritic cells (DCs), and endothelial cells (ECs) are engaged in the bulk of IONP encounters in the organism, and also determine IONP biodistribution. Therefore, the biological effects that IONPs trigger in these cells (biological identity) are of utmost importance to better understand and refine the efficacy of IONP-based theranostics. In the present review, which is focused on anti-cancer therapy, we discuss recent findings on the biological identities of IONPs, particularly as concerns their interactions with myeloid, endothelial, and tumor cells. Furthermore, we thoroughly discuss current understandings of the basic molecular mechanisms and complex interactions that govern IONP biological identity, and how these traits could be used as a stepping stone for future research.

Targeting strategies for superparamagnetic iron oxide nanoparticles in cancer therapy

Among various nanoparticles, superparamagnetic iron oxide nanoparticles (SPIONs) have been increasingly studied for their excellent superparamagnetism, magnetic heating properties, and enhanced magnetic resonance imaging (MRI). The conjugation of SPIONs with drugs to obtain delivery nanosystems has several advantages including magnetic targeted functionalization, in vivo imaging, magnetic thermotherapy, and combined delivery of anticancer agents. To further increase the targeting efficiency of drugs through a delivery nanosystem based on SPIONs, additional targeting moieties including transferrin, antibodies, aptamers, hyaluronic acid, folate, and targeting peptides are coated onto the surface of SPIONs. Therefore, this review summarizes the latest progresses in the conjugation of targeting molecules and drug delivery nanosystems based on SPIONs, especially focusing on their performances to develop efficient targeted drug delivery systems for tumor therapy. STATEMENT OF SIGNIFICANCE: Some magnetic nanoparticle-based nanocarriers loaded with drugs were evaluated in patients and did not produce convincing results, leading to termination of clinical development in phase II/III. An alternative strategy for drug delivery systems based on SPIONs is the conjugation of these systems with targeting segments such as transferrin, antibodies, aptamers, hyaluronic acid, folate, and targeting peptides. These targeting moieties can be recognized by specific integrin/receptors that are overexpressed specifically on the tumor cell surface, resulting in minimizing dosage and reducing off-target effects. This review focuses on magnetic nanoparticle-based nonviral drug delivery systems with targeting moieties to deliver anticancer drugs, with an aim to provide suggestions on the development of SPIONs through discussion.

Fine-tuning the properties of the thrombin binding aptamer through cyclization: Effect of the 5'-3' connecting linker on the aptamer stability and anticoagulant activity

A small library of cyclic TBA analogues (named cycTBA I-IV), obtained by covalently connecting its 5'- and 3'-ends with flexible linkers, has been synthesized with the aim of improving its chemical and enzymatic stability, as well as its anticoagulant properties. Two chemical procedures have been exploited to achieve the desired cyclization, based on the oxime ligation method (providing cycTBA I and II) or on Cu(I)-assisted azide-alkyne cycloaddition (CuAAC) protocols (for cycTBA III and IV), leading to analogues containing circularizing linkers with different chemical nature and length, overall spanning from 22 to 48 atoms. The resulting cyclic TBAs have been characterized using a variety of biophysical methods (UV, CD, gel electrophoresis, SE-HPLC analyses) and then tested for their serum resistance and anticoagulant activity under in vitro experiments. A fine-tuning of the length and flexibility of the linker allowed identifying a cyclic analogue, cycTBA II, with improved anticoagulant activity, associated with a dramatically stabilized G-quadruplex structure (ΔT_m = +17 °C) and a 6.6-fold higher enzymatic resistance in serum compared to unmodified TBA.

Functional DNA Molecules Enable Selective and Stimuli-Responsive Nanoparticles for Biomedical Applications

Nanoparticles (NPs) have enormous potential to improve disease diagnosis and treatment due to their intrinsic electronic, optical, magnetic, mechanical, and physiological properties. To realize their full potential for nanomedicine, NPs must be biocompatible and targetable toward specific biomolecules to ensure selective sensing, imaging, and drug delivery in complex environments such as living cells, tissues, animals, and human bodies. In this Account, we summarize our efforts to impart specific biocompatibility and biorecognition functionality to NPs by developing strategies to integrate inorganic and organic NPs with functional DNA (fDNA), including aptamers, DNAzymes, and aptazymes to create fDNA-NPs. These hybrid NPs take advantage of fDNA's ability to either bind targets or catalyze reactions in the presence of targets selectively and utilize their unique physicochemical properties including small size, low immunogenicity, and ease of synthesis and chemical modification in comparison with other molecules such as antibodies. By integrating inorganic NPs such as gold NPs, quantum dots, and iron oxide nanoparticles with fDNA, we designed stimuli-responsive fDNA-NPs that exhibit target induced assembly and disassembly of NPs, resulting in a variety of colorimetric, fluorescent, and magnetic resonance imaging (MRI)-based sensors for diagnostic of a broad range of analytes. To impart both biocompatibility and selectivity on inorganic NPs for targeted bioimaging, we have demonstrated DNA-mediated surface functionalization, shape-controlled synthesis, and coordinative assembly of such NPs as specific bioprobes. A highlight is provided on the construction of fDNA-based nanoprobes with light-activatable sensing and imaging functions, which provides precise control of recognition properties of fDNA with high spatiotemporal resolution. To explore the potential of organic NPs for biosensing applications, we have developed an enzyme-responsive fDNA-liposome as a universal sensing platform compatible with diverse biological targets as well as different detection methods including fluorescence, MRI, or temperature, making possible point-of-care diagnostics. To expand the application regime of organic NPs, we collaborated with the Zimmerman group to prepare single-chain block copolymer-based NPs and incorporated it with a variety of functions, including monovalent DNA for assembly, tunable surface chemistry for cellular imaging, and coordinative Cu(II) sites for catalyzing intracellular click reactions, demonstrating the potential of using organic NPs to create promising fDNA-NP systems with programmable functionalities. Furthermore, we survey our recent endeavor in integration of cell-specific aptamers with different NPs for targeted drug delivery, showing that introducing stimuli-responsive properties into NPs that target tumor microenvironments would enable safer and more effective therapy for cancers. Finally, current challenges and future perspectives in fDNA-mediated engineering of NPs for biomedical applications are discussed.

Electrochemical aptasensor based on conductive supramolecular polymer hydrogels for thrombin detection with high selectivity

Herein, we synthesized a kind of conductive supramolecular polymer hydrogel (CSPH) based on polyaniline (PANI) which can not only improve the conductivity but also promote antifouling performance of the aptasensor for the specific recruitment of thrombin (TB) from complex samples. With the electrochemical copolymerization of aniline (AN) and 3-aminophenylboronic acid (ABA) on glassy carbon electrode (GCE), the electrode was then inserted into the polyvinyl alcohol (PVA) solution to obtain robust CSPH through boric acid groups incorporated onto PANI to cause gelation of PVA solution, owing to the hydrophilicity of CSPH and nearly electrical neutrality, the modified electrode is antifouling without integration of other antifouling materials. A sandwich-type electrochemical aptasensor was constructed on the CSPH based electrode interfaces. Thrombin aptamer 1 (TBA1) were modified on the CSPH through amide bond, and thrombin aptamer 2 modified magnetic nanoparticles (MNP-TBA2) are used as signal amplification probes, the aptasensor has good sensitivity with a linear range from 1 pmol/L to 10 nmol/L and has a detection limit down to 0.64 pmol/L. The strategy of utilizing eletropolymerization of CSPH films to undergo highly selective thrombin recognition is, of course, readily extended to a broad range of targets in the real samples, and the recovery was ranging from 95.2% to 106.3% and RSDs varying from 2.3% to 4.5%.

Stability Is Not Everything: The Case of the Cyclisation of a Thrombin-Binding Aptamer

With the aim of developing a new approach to obtain improved aptamers, a cyclic thrombin-binding aptamer (TBA) analogue (cycTBA) has been prepared by exploiting a copper(I)-assisted azide-alkyne cycloaddition. The markedly increased serum resistance and exceptional thermal stability of the G-quadruplex versus TBA were associated with halved thrombin inhibition, which suggested that some flexibility in the TBA structure was necessary for protein recognition.

Therapeutic nanoplatforms and delivery strategies for neurological disorders

The major neurological disorders found in a central nervous system (CNS), such as brain tumors, Alzheimer's diseases, Parkinson's diseases, and Huntington's disease, have led to devastating outcomes on the human public health. Of these disorders, early diagnostics remains poor, and no treatment has been successfully discovered; therefore, they become the most life-threatening medical burdens worldwide compared to other major diseases. The major obstacles for the drug discovery are the presence of a restrictive blood-brain barrier (BBB), limiting drug entry into brains and undesired neuroimmune activities caused by untargeted drugs, leading to irreversible neuronal damages. Recent advances in nanotechnology have contributed to the development of novel nanoplatforms and effective delivering strategies to improve the CNS disorder treatment while less disturbing brain systems. The nanoscale drug carriers, including liposomes, dendrimers, viral capsids, polymeric nanoparticles, silicon nanoparticles, and magnetic/metallic nanoparticles, enable the effective drug delivery penetrating across the BBB, the aforementioned challenges in the CNS. Moreover, drugs encapsulated by the nanocarriers can reach further deeper into targeting regions while preventing the degradation. In this review, we classify novel disease hallmarks incorporated with emerging nanoplatforms, describe promising approaches for improving drug delivery to the disordered CNS, and discuss their implications for clinical practice.

Activatable magnetic resonance nanosensor as a potential imaging agent for detecting and discriminating thrombosis

The early detection and accurate characterization of life-threatening diseases such as cardiovascular disease and cancer are critical to the design of treatment. Knowing whether or not a thrombus in a blood vessel is new (fresh) or old (constituted) is very important for physicians to decide a treatment protocol. We have designed smart MRI nano-sensors that can detect, sense and report the stage or progression of cardiovascular diseases such as thrombosis. The nanosensors were functionalized with fibrin-binding peptide to specifically target thrombus and were also labelled with fluorescent dye to enable optical imaging. We have demonstrated that our nanosensors were able to switch between the T1 and T2 signal depending on thrombus age or the presence or absence of thrombin at the thrombus site. The developed nanosensors appeared to be non-toxic when tested with Chinese Hamster Ovarian cells within the tested concentrations. The working principle demonstrated in this study can be applied to many other diseases such as cancer.

Preparation and characterization of an aptamer-functionalized solid-phase microextraction fiber and its application in the selective monitoring of adenosine phosphates with liquid chromatography and tandem mass spectrometry

An aptamer with adenosine triphosphate as a ligand was immobilized onto the surface of a porous-polymer-coated fiber to obtain an aptamer-functionalized porous-polymer-coated solid-phase microextraction fiber. The fiber was observed with a crosslinked and porous morphological surface structure. It shows specific selectivity to adenosine triphosphate with a selectivity coefficient of 22.1 compared to the scrambled oligonucleotide functionalized fiber, and the selectivity factors over other analogues and reference compounds were from 6.1 to 77.5. When the fiber-based solid-phase microextraction was coupled with liquid chromatography and tandem mass spectrometry, detection limits of 2.7, 29, and 34 μg/L were achieved for adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate, respectively. The spiking recoveries of 77.6-91.9% were achieved for trace adenosine phosphates in human serum sample. Furthermore, the fibers showed high stability and good reusability and could be used over 50 times for the real serum sample pretreatment without remarkable performance reduction.

DNA Aptamer-Based Activatable Probes for Photoacoustic Imaging in Living Mice

DNA aptamers are a powerful class of molecules for sensing targets, but have been limited when applied to imaging in living animals because most aptamer probes are fluorescence-based, which limits imaging penetration depth. Photoacoustic (PA) imaging emerged as an alternative to MRI and X-ray tomography in biomedical imaging, due to its ability to afford high-resolution images at depths in the cm range. Despite its promise, PA imaging is limited by a lack of strategies to design selective and activatable probes for targets. To overcome this limitation, we report design and demonstration of PA probes based on DNA aptamers that can hybridize to DNA strands conjugated to a near-infrared fluorophore/quencher pair (IRDye 800CW/IRDye QC-1) with efficient contact quenching. Binding of the target triggered a release of the DNA strand with the quencher and thus relief of the contact quenching, resulting in a change of the PA signal ratio at 780/725 nm. Using thrombin as a model, a relationship was established between the thrombin concentrations and the PA ratio, with a dynamic range of 0-1000 nM and a limit of detection of 112 nM. Finally, in vivo PA imaging studies showed that the PA ratio increased significantly 45 min after injection of thrombin but not with injection of PBS as a vehicle control, demonstrating the first aptamer-based activatable PA probe for advanced molecular imaging in living mice. Since in vitro selection can obtain aptamers selective for many targets, the design demonstrated can be applied for PA imaging of a number of targets.

Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery

Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.

Fluorescent Thrombin Binding Aptamer-Tagged Nanoparticles for an Efficient and Reversible Control of Thrombin Activity

Progress in understanding and treatment of thrombotic diseases requires new effective methods for the easy, rapid, and reversible control of coagulation processes. In this framework, the use of aptamers, and particularly of the thrombin binding aptamer (TBA), has aroused strong interest, due to its enormous therapeutic potential, associated with a large number of possible applications in biotechnological and bioanalytical fields. Here, we describe a new TBA analogue (named tris-mTBA), carrying three different pendant groups: a dansyl residue at the 3'- and a β-cyclodextrin moiety at the 5'-end-providing a host-guest system which exhibits a marked fluorescence enhancement upon TBA G-quadruplex folding-and a biotin tag, allowing the attachment of the aptamer onto biocompatible streptavidin-coated silica nanoparticles (NPs) of 50 nm hydrodynamic diameter (Sicastar). The use of nanoparticles for the in vivo delivery of TBA, expected to induce per se increased nuclease resistance and improved pharmacokinetic properties of this oligonucleotide, offers as an additional advantage the possibility to exploit multivalency effects, due to the presence of multiple copies of TBA on a single scaffold. In addition, the selected fluorescent system allows monitoring both the presence of TBA on the functionalized NPs and its correct folding upon immobilization, also conferring enhanced enzymatic resistance and bioactivity. The anticoagulant activity of the new tris-mTBA, free or conjugated to Sicastar NPs, was evaluated by dynamic light scattering experiments. Highly effective and reversible inhibition of thrombin activity toward fibrinogen was found for the free tris-mTBA and especially for the tris-mTBA-conjugated NPs, demonstrating great potential for the biomedical control of blood clotting.

Controlled in-cell activation of RNA therapeutics using bond-cleaving bio-orthogonal chemistry

In vitro exogenous activation of siRNA nanodrug using bio-orthogonal de-click chemistry.

Temporal control of siRNA activation is a major challenge for RNAi-based therapeutics. The majority of the reported siRNA delivery systems rely on environmental factors, such as differences in extracellular and intracellular redox potential, ATP concentration, or pH to activate an siRNA payload. However dynamic endogenous environments are far too complex to rely on for controllable siRNA release and can result in premature siRNA activation prior to reaching the intended biological target. In addition, there are uncertainties about timing, degree and rate of the siRNA activation with spontaneous release approaches. Herein we describe a bio-orthogonal chemistry approach to address this important challenge. With our approach we were able achieve two major goals: complete siRNA inactivation upon immobilization of the payload on the surface of iron oxide nanoparticles and controlled in-cell activation with the addition of a small non-toxic chemical trigger after sufficient cellular uptake of the nanoparticles was confirmed. We have demonstrated our in-cell activation approach using two siRNAs against green fluorescent protein (GFP) and cyclin dependent kinase 8 (CDK8) in GFP expressing MDA-MB-231 cell line. We anticipate that this methodology will potentially advance the clinical translation of RNAi-based therapeutics, as the described bio-orthogonal chemistry can be generalized for any siRNA of choice.

Effect of ligand on particle size and morphology of nanostructures synthesized by thermal decomposition of coordination compounds

Thermal decomposition of organometallic and various coordination compounds are known as general method to synthesize a wide range of nanostructures including metals, metal oxides and sulfides. Herein, in order to coordinate metals and prepare suitable precursor - due to the efficient role of precursor on the particle size and morphology of products - appropriate ligands will be introduced.

Recent Advances on Magnetic Relaxation Switching Assay-Based Nanosensors

Magnetic relaxation switching assay (MRSw)-based nanosensors respond to the changes of transverse relaxation time (T₂) of water molecules resulted from the analyte-induced aggregation and disaggregation of magnetic nanoparticles (MNPs). This strategy has been widely applied to the detections of various substrates from heavy metal ions to organic pollutants, proteins, nucleic acids, bacteria and viruses, and specific cells. Compared with other nanosensors, MRSw-based nanosensors not only are free from the background interferences, signal bleaching, and quenching but also overcome light scattering from samples without pretreatments. Therefore, MRSw-based nanosensors have been developed as real-time and on-site detection platforms for environmental protection, food safety, and risk assessment. This review summarizes the latest developments of the principles, the applicable magnetic nanoparticles, and the exploited environmental and biological applications of MRSw-based nanosensors.

Theranostic DNAzymes

DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.

Combinatorial Screening of DNA Aptamers for Molecular Imaging of HER2 in Cancer

HER2, a cell membrane protein overexpressed in many types of cancers, is correlated with poor diagnosis, suboptimal treatment outcome, and low survival rate. Multiple HER2-targeted drugs have been developed for the treatment of HER2-overexpressing tumor, which can in turn down-regulate HER2 expression. It is thus significant to profile HER2 expression for cancer prognosis, patient stratification, and monitoring therapy response. Aptamers, a class of single-stranded DNA/RNA (ssDNA/ssRNA) ligands, are promising for molecular biomarker imaging. Aptamers typically have strong binding affinity, high selectivity, batch-to-batch reproducibility, and low toxicity, and systemically injected aptamers often have high tumor-to-background ratio within a short time. However, current aptamers have been mostly screened in vitro, and these aptamers may lose binding ability in vivo due to conformational change under physiological environments. Here, a DNA library was combinatorially screened in vitro and in vivo, to select HER2-targeting DNA aptamers, termed Heraptamers, and labeled with ¹⁸F for positron emission tomography (PET) imaging of HER2 in ovarian cancer. Specifically, using systematic evolution of ligands by exponential enrichment (SELEX), Heraptamer candidates were first selected and validated in vitro using HER2 extracellular domain (ECD) and HER2-positive SKOV3 cancer cells; then, aptamer candidates were modified with alkyne, radiolabeled with ¹⁸F using azide-functionalized precursors by click chemistry, and screened in SKOV3-tumor-bearing mice using PET. Two aptamers, Heraptamer1 and Heraptamer2, reached high tumor uptake ratios within as short as 1 h. At 1.5 h post injection, the tumor uptake ratio of these two aptamers was up to 0.5%ID/g (injection dose/gram tissue), with tumor-to-muscle ratio of 4.55 ± 1.63 in SKOV3 tumor. In contrast, these aptamers have low uptake ratios in control MDA-MB-231 tumors. These preclinical studies showed that Heraptamers are promising for specific HER2 imaging.

A significant enhancement of color transition from an on-off type achromatic colorimetric nanosensor for highly sensitive multi-analyte detection with the naked eye

Here, we report the development of an achromatic nanoparticle-based colorimetric sensor (achromatic nanosensor) with an on-off type color change that significantly enhances the color transition and increases the sensitivity of the sensor for naked-eye inspection. The achromatic nanosensor was prepared via a modified CMYK (CRYK) subtractive color model by combining DNA-functionalized gold nanoparticles (AuNPs-DNA), silver nanoparticles (AgNPs-DNA), and gold nanorods (AuNRs-DNA). The initially black-colored achromatic nanosensor not only allowed multiplexed detection by generating target-specific diverse color changes, but also improved the recognition of color changes by the naked eye. Thus, this on-off type color change enabled analysis near the limit of detection (LOD) with the naked eye. In addition, we developed a new image processing method adapted for this achromatic sensor. By quantifying the saturation value of the color images of the achromatic sensor, we could significantly amplify the color signal of the samples, which is difficult to achieve with general colorimetric sensors. The practical application of this achromatic nanosensor for biomarker detection was demonstrated with thrombin and platelet-derived growth factor (PDGF) in human blood plasma. These results provide a new sensing platform that is applicable to most NP-based colorimetric sensing systems for a wide range of applications, including biomolecular diagnosis, chemical pollutant sensing, environmental monitoring, etc.

A novel nanosensor composed of aptamer bio-dots and gold nanoparticles for determination of thrombin with multiple signals

Thrombin is a crucial multifunctional enzyme involved in many physiological and pathological processes. Its detection is of great importance. In this work, a novel bio-dots nanosensor for detection of thrombin with colorimetric, fluorometric and light-scattering signals is developed. This nanosensor is composed of thrombin-binding aptamer bio-dots (TBA-dots) and gold nanoparticles (AuNPs), where TBA-dots serve as fluorometric reporter and AuNPs function as multiple roles as colorimetric reporter, light scattering reporter and fluorescence quencher. TBA-dots retain inherent structures of aptamer to specifically interact with thrombin and simultaneously induce the aggregation of AuNPs. The mechanism of the sensing system is based on distance-dependent aggregation of AuNPs and fluorescence resonance energy transfer (FRET). The nanosensor needs no further surface functionalization required for the as-prepared bio-dots and AuNPs, which provides a sensitive method for the selective detection of thrombin with a detection limit as low as 0.59nM. In addition, it provides a brand new perspective for bio-dots and its potential use in bioanalysis.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

Multimodal Detection of a Small Molecule Target Using Stimuli-Responsive Liposome Triggered by Aptamer-Enzyme Conjugate

Nanomaterials which can respond to external stimuli have attracted considerable attention due to their potential applications in sensing and biomedicine. One of the most promising classes of such materials is the stimuli-responsive liposome that can release its contents in response to a specific target. Despite recent progress, development of liposomes responsive to small molecular targets remains a challenge, due to the difficulty in designing the transduction process to link between target binding and triggered release, even though small molecular metabolites play important roles in many biological processes. Herein, we demonstrate a combination of an aptamer (apt) for target recognition and enzyme phosphatidylcholine 2-acetylhydrolase (PLA2) for rupture of liposome. As a proof-of-concept, cocaine molecules were used to trigger the release of the enzyme. The exposure to DNA-PLA2 conjugates induced the rupture of liposome containing uranin and gadopentetic acid (Gd-DTPA), allowing multimodal fluorescent and MRI detection of cocaine. The strategy demonstrated in this work can be generally applied to other imaging modalities by loading different imaging agents, as well as other targets by using different functional DNAs.

Applications of aptamers in targeted imaging: state of the art

Aptamers are single-stranded oligonucleotides with high affinity and specificity to the target molecules or cells, thus they can serve as an important category of molecular targeting ligand. Since their discovery, aptamers have been rapidly translated into clinical practice. The strong target affinity/selectivity, cost-effectivity, chemical versatility and safety of aptamers are superior to traditional peptides- or proteins-based ligands which make them unique choices for molecular imaging. Therefore, aptamers are considered to be extremely useful to guide various imaging contrast agents to the target tissues or cells for optical, magnetic resonance, nuclear, computed tomography, ultrasound and multimodality imaging. This review aims to provide an overview of aptamers' advantages as targeting ligands and their application in targeted imaging. Further research in synthesis of new types of aptamers and their conjugation with new categories of contrast agents is required to develop clinically translatable aptamer-based imaging agents which will eventually result in improved patient care.

Gold-Coated Superparamagnetic Nanoparticles for Single Methyl Discrimination in DNA Aptamers

Au- and iron-based magnetic nanoparticles (NPs) are promising NPs for biomedical applications due to their unique properties. The combination of a gold coating over a magnetic core puts together the benefits from adding the magnetic properties to the robust chemistry provided by the thiol functionalization of gold. Here, the use of Au-coated magnetic NPs for molecular detection of a single methylation in DNA aptamer is described. Binding of α-thrombin to two aptamers conjugated to these NPs causes aggregation, a phenomenon that can be observed by UV, DLS and MRI. These techniques discriminate a single methylation in one of the aptamers, preventing aggregation due to the inability of α-thrombin to recognize it. A parallel study with gold and ferromagnetic NPs is detailed, concluding that the Au coating of FexOy NP does not affect their performance and that they are suitable as complex biosensors. These results prove the high detection potency of Au-coated SPIONs for biomedical applications especially for DNA repair detection.

Aptamer-based biosensors for biomedical diagnostics

Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.

Superparamagnetic iron oxide nanoparticles for in vivo molecular and cellular imaging

In the last decade, the biomedical applications of nanoparticles (NPs) (e.g. cell tracking, biosensing, magnetic resonance imaging (MRI), targeted drug delivery, and tissue engineering) have been increasingly developed. Among the various NP types, superparamagnetic iron oxide NPs (SPIONs) have attracted considerable attention for early detection of diseases due to their specific physicochemical properties and their molecular imaging capabilities. A comprehensive review is presented on the recent advances in the development of in vitro and in vivo SPION applications for molecular imaging, along with opportunities and challenges.

Overcoming the concentration-dependence of responsive probes for magnetic resonance imaging

In magnetic resonance imaging, contrast agents are molecules that increase the contrast-to-noise ratio of non-invasively acquired images. The information gained from magnetic resonance imaging can be increased using responsive contrast agents that undergo chemical changes, and consequently changes to contrast enhancement, for example in response to specific biomarkers that are indicative of diseases. A major limitation with modern responsive contrast agents is concentration-dependence that requires the concentration of contrast agent to be known: an extremely challenging task in vivo. Here, we review advances in several strategies aimed at overcoming the concentration-dependent nature of responsive contrast agents.

Sequence-selective binding of oligonucleotides to superparamagnetic cobalt ferrite nanoparticles: a new way to fabricate functional nanoconjugates

The interaction between homo-oligonucleotides and unmodified superparamagnetic cobalt ferrite nanoparticles has been investigated.