Aptamers and aptamer targeted delivery

Breaking Barriers: Nucleic Acid Aptamers in Gastrointestinal (GI) Cancers Therapy

Conventional cancer therapies can have significant adverse effects as they are not targeted to cancer cells and may damage healthy cells. Single-stranded oligonucleotides assembled in a particular architecture, known as aptamers, enable them to attach selectively to target areas. Usually, they are created by Systematic Evolution of Ligand by Exponential enrichment (SELEX), and they go through a rigorous pharmacological revision process to change their therapeutic half-life, affinity, and specificity. They could thus offer a viable substitute for antibodies in the targeted cancer treatment market. Although aptamers can be a better choice in some situations, antibodies are still appropriate for many other uses. The technique of delivering aptamers is simple and reasonable, and the time needed to manufacture them is relatively brief. Aptamers do not require animals or an immune response to be produced, in contrast to antibodies. When used as a medication, aptamers can directly suppress tumor cells. As an alternative, they can be included in systems for targeted drug delivery that administer medications specifically to tumor cells while reducing toxicity to healthy cells. The most recent and cutting-edge methods for treating gastrointestinal (GI) tract cancer with aptamers will be covered in this review, with a focus on targeted therapy as a means of conquering resistance to traditional medicines.

Advancement of targeted protein degradation strategies as therapeutics for undruggable disease targets

Targeted protein degradation (TPD) aids in developing novel bifunctional small-molecule degraders and eliminates proteins of interest. The TPD approach shows promising results in oncological, neurogenerative, cardiovascular and gynecological drug development. We provide an overview of technology advancements in TPD, including molecular glues, proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimeras, antibody-based PROTAC, GlueBody PROTAC, autophagy-targeting chimera, autophagosome-tethering compound, autophagy-targeting chimera and chaperone-mediated autophagy-based degraders. Here we discuss the development and evolution of the TPD field, the variety of proteins that PROTACs target and the biological repercussions of their degradation. We particularly highlight the recent improvements in TPD research that utilize autophagy or the endolysosomal pathway, which enables the targeting of undruggable targets.

Novel Detection of Nasty Bugs, Prevention Is Better than Cure

Hospital-acquired infections (HAIs) are a growing concern around the world. They contribute to increasing mortality and morbidity rates and are an economic threat. All hospital patients have the potential to contract an HAI, but those with weakened or inferior immune systems are at highest risk. Most hospital patients will contract at least one HAI, but many will contract multiple ones. Bacteria are the most common cause of HAIs and contribute to 80-90% of all HAIs, with Staphylococcus aureus, Clostridium difficile, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae accounting for the majority. Each of these bacteria are highly resistant to antibiotics and can produce a protective film, known as a biofilm, to further prevent their eradication. It has been shown that by detecting and eradicating bacteria in the environment, infection rates can be reduced. The current methods for detecting bacteria are time consuming, non-specific, and prone to false negatives or false positives. Aptamer-based biosensors have demonstrated specific, time-efficient and simple detection, highlighting the likelihood that they could be used in a similar way to detect HAI-causing bacteria.

Aptamers used for biosensors and targeted therapy

Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX

SUMMARY

High-throughput sequencing can enhance the analysis of aptamer libraries generated by the Systematic Evolution of Ligands by EXponential enrichment. Robust analysis of the resulting sequenced rounds is best implemented by determining a ranked consensus of reads following the processing by multiple aptamer detection algorithms. While several such approaches have been developed to this end, their installation and implementation is problematic. We developed AptCompare, a cross-platform program that combines six of the most widely used analytical approaches for the identification of RNA aptamer motifs and uses a simple weighted ranking to order the candidate aptamers, all driven within the same GUI-enabled environment. We demonstrate AptCompare's performance by identifying the top-ranked candidate aptamers from a previously published selection experiment in our laboratory, with follow-up bench assays demonstrating good correspondence between the sequences' rankings and their binding affinities.

AVAILABILITY AND IMPLEMENTATION

The source code and pre-built virtual machine images are freely available at https://bitbucket.org/shiehk/aptcompare.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cell-SELEX-Based Identification of a Human and Mouse Cross-Reactive Endothelial Cell-Internalizing Aptamer

Increased interest and insights gained by researchers on the roles of endothelial cells in the pathophysiology of cancer, inflammatory, and cardiovascular diseases have led to the design of pharmacological interventions aimed at the endothelium lining in the diseased sites. Toward this end, we used established brain microvascular endothelial cell lines mouse (bEND3), human (hCMEC/D3), and Toggle Cell-SELEX to identify a species cross-reactive, endothelial cell-internalizing aptamer R11-3. This 2'F-modified RNA aptamer is specific for endothelial cells as no internalization was seen with cells of nonendothelial origin. R11-3 was truncated in size, and its potential in endothelial targeted therapeutics was established using VEGFR2 targeting long interfering RNA (liRNA) aptamer chimera. Due to its specificity for both mouse and human endothelial cells, we believe that this aptamer not only fits for development of endothelial targeted drug development for human diseases but is also suitable for preclinical evaluation in mice.

Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers

Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.

Functional calcium phosphate composites in nanomedicine

Calcium phosphate (CaP) materials have many peculiar and intriguing properties. In nature, CaP is found in nanostructured form embedded in a soft proteic matrix as the main mineral component of bones and teeth. The extraordinary stoichiometric flexibility, the different stabilities exhibited by its different forms as a function of pH and the highly dynamic nature of its surface ions, render CaP one of the most versatile materials for nanomedicine. This review summarizes some of the guidelines so far emerged for the synthesis of CaP composites in aqueous media that endow the material with tailored crystallinity, morphology, size, and functional properties. First, we introduce very briefly the areas of application of CaP within the nanomedicine field. Then through some selected examples, we review some synthetic routes where the presence of functional units (small templating molecules like surfactants, or oligomers and polymers) assists the synthesis and at the same time impart the functionality or the responsiveness desired for the end-application of the material. Finally, we illustrate two examples from our laboratory, where CaP is decorated by biologically active polymers or prepared within a thermo- and magneto-responsive hydrogel, respectively.

Aptamer-Drug Conjugates of Active Metabolites of Nucleoside Analogs and Cytotoxic Agents Inhibit Pancreatic Tumor Cell Growth

Aptamer-drug conjugates (ApDCs) have the potential to improve the therapeutic index of traditional chemotherapeutic agents due to their ability to deliver cytotoxic drugs specifically to cancer cells while sparing normal cells. This study reports on the conjugation of cytotoxic drugs to an aptamer previously described by our group, the pancreatic cancer RNA aptamer P19. To this end, P19 was incorporated with gemcitabine and 5-fluorouracil (5-FU), or conjugated to monomethyl auristatin E (MMAE) and derivative of maytansine 1 (DM1). The ApDCs P19-dFdCMP and P19-5FdUMP were shown to induce the phosphorylation of histone H2AX on Ser139 (γ-H2AX) and significantly inhibited cell proliferation by 51%-53% in PANC-1 and by 54%-34% in the gemcitabine-resistant pancreatic cancer cell line AsPC-1 (p ≤ 0.0001). P19-MMAE and P19-DM1 caused mitotic G2/M phase arrest and inhibited cell proliferation by up to 56% in a dose-dependent manner when compared to the control group (p ≤ 0.001). In addition, the cytotoxicity of P19-MMAE and P19-DM1 in normal cells and the control human breast cancer cell line MCF7 was minimal. These results suggest that this approach may be useful in decreasing cytotoxic side effects in non-tumoral tissue.

A Cholecystokinin B Receptor-Specific DNA Aptamer for Targeting Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinomas (PDACs) constitutively express the G-protein-coupled cholecystokinin B receptor (CCKBR). In this study, we identified DNA aptamers (APs) that bind to the CCKBR and describe their characterization and targeting efficacy. Using dual SELEX selection against “exposed” CCKBR peptides and CCKBR-expressing PDAC cells, a pool of DNA APs was identified. Further downselection was based on predicted structures and properties, and we selected eight APs for initial characterizations. The APs bound specifically to the CCKBR, and we showed not only that they did not stimulate proliferation of PDAC cell lines but rather inhibited their proliferation. We chose one AP, termed AP1153, for further binding and localization studies. We found that AP1153 did not activate CCKBR signaling pathways, and three-dimensional Confocal microscopy showed that AP1153 was internalized by PDAC cells in a receptor-mediated manner. AP1153 showed a binding affinity of 15 pM. Bioconjugation of AP1153 to the surface of fluorescent NPs greatly facilitated delivery of NPs to PDAC tumors in vivo. The selectivity of this AP-targeted NP delivery system holds promise for enhanced early detection of PDAC lesions as well as improved chemotherapeutic treatments for PDAC patients.

Aptamer-miRNA-212 Conjugate Sensitizes NSCLC Cells to TRAIL

TNF-related apoptosis-inducing ligand (TRAIL) is a promising antitumor agent for its remarkable ability to selectively induce apoptosis in cancer cells, without affecting the viability of healthy bystander cells. The TRAIL tumor suppressor pathway is deregulated in many human malignancies including lung cancer. In human non-small cell lung cancer (NSCLC) cells, sensitization to TRAIL therapy can be restored by increasing the expression levels of the tumor suppressor microRNA-212 (miR-212) leading to inhibition of the anti-apoptotic protein PED/PEA-15 implicated in treatment resistance. In this study, we exploited a previously described RNA aptamer inhibitor of the tyrosine kinase receptor Axl (GL21.T) expressed on lung cancer cells, as a means to deliver miR-212 into human NSCLC cells expressing Axl. We demonstrate efficient delivery of miR-212 following conjugation of the miR to GL21.T (GL21.T-miR212 chimera). We show that the chimera downregulates PED and restores TRAIL-mediate cytotoxicity in cancer cells. Importantly, treatment of Axl+ lung cancer cells with the chimera resulted in (i) an increase in caspase activation and (ii) a reduction of cell viability in combination with TRAIL therapy. In conclusion, we demonstrate that the GL21.T-miR212 chimera can be employed as an adjuvant to TRAIL therapy for the treatment of lung cancer.

Modular Assembly of Cell-targeting Devices Based on an Uncommon G-quadruplex Aptamer

Aptamers are valuable tools that provide great potential to develop cost-effective diagnostics and therapies in the biomedical field. Here, we report a novel DNA aptamer that folds into an unconventional G-quadruplex structure able to recognize and enter specifically into human Burkitt's lymphoma cells. We further optimized this aptamer to a highly versatile and stable minimized version. The minimized aptamer can be easily equipped with different functionalities like quantum dots, organic dyes, or even a second different aptamer domain yielding a bi-paratopic aptamer. Although the target molecule of the aptamer remains unknown, our microscopy and pharmacological studies revealed that the aptamer hijacks the clathrin-mediated endocytosis pathway for its cellular internalization. We conclude that this novel class of aptamers can be used as a modular tool to specifically deliver different cargoes into malignant cells. This work provides a thorough characterization of the aptamer and we expect that our strategy will pave the path for future therapeutic applications.

Aptamers: new arrows to target dendritic cells

Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the "systematic evolution of ligands by exponential enrichment" (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.

Biocompatible cationic lipids for the formulation of liposomal DNA vectors

Ethylphosphocholine lipids are highly biocompatible cationic amphiphiles that can be used for the formulation of liposomal DNA vectors, with negligible toxic effects on cells and organisms. Here we report the characterization of EDPPC (1,2-dipalmitoyl-sn-glycero-O-ethyl-3-phosphocholine chloride) liposomes, containing two different zwitterionic helper lipids, POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine). Depending on the nature of the helper lipid, a phase separation in the bilayer is found at room temperature, where domains enriched in the cationic component coexist in a relatively large temperature range with regions where the zwitterionic lipids are predominant. We studied DNA complexation, the internal structure of lipoplexes and their docking and fusogenic ability with model target bilayers. The structural and functional modifications caused by DNA binding were studied using Dynamic Light Scattering (DLS), zeta potential, and small and wide angle X-ray scattering (SAXS-WAXS) measurements, while the interaction with membranes was assessed by using Giant Unilamellar Vesicles (GUVs) as model target bilayers. The results presented establish a connection between the physicochemical properties of lipid bilayers, and in particular of lipid demixing, with the phase state of the complexes and their ability to interact with model membranes.

Screening of DNA aptamers against myoglobin using a positive and negative selection units integrated microfluidic chip and its biosensing application

An aptamer screening method using a positive and negative selection units integrated microfluidic chip was introduced. Here, myoglobin (Myo), one of the early markers to increase after acute myocardial infarction, was used as the model. After 7-round selection, the aptamers, which exhibited dissociation constants (K(d)) in the nanomolar range (from 4.93 to 6.38 nM), were successfully obtained using a positive and negative selection units integrated microfluidic chip. The aptamer with the highest affinity (K(d) = 4.93 nM) was then used for the fabrication of a label-free supersandwich electrochemical biosensor for Myo detection based on target-induced aptamer displacement. The detection limit of this aptamer-based electrochemical biosensor was 10 pM, which was significantly lower than that of those previous antibody-based biosensors for Myo detection. This work may not only develop a strategy for screening aptamer but also offer promising alternatives to the traditional analytical and immunological methods for Myo detection.

Aptamer-targeted antigen delivery

Effective therapeutic vaccines often require activation of T cell-mediated immunity. Robust T cell activation, including CD8 T cell responses, can be achieved using antibodies or antibody fragments to direct antigens of interest to professional antigen presenting cells. This approach represents an important advance in enhancing vaccine efficacy. Nucleic acid aptamers present a promising alternative to protein-based targeting approaches. We have selected aptamers that specifically bind the murine receptor, DEC205, a C-type lectin expressed predominantly on the surface of CD8α⁺ dendritic cells (DCs) that has been shown to be efficient at facilitating antigen crosspresentation and subsequent CD8⁺ T cell activation. Using a minimized aptamer conjugated to the model antigen ovalbumin (OVA), DEC205-targeted antigen crosspresentation was verified in vitro and in vivo by proliferation and cytokine production by primary murine CD8⁺ T cells expressing a T cell receptor specific for the major histocompatibility complex (MHC) I-restricted OVA_257–264 peptide SIINFEKL. Compared with a nonspecific ribonucleic acid (RNA) of similar length, DEC205 aptamer-OVA-mediated antigen delivery stimulated strong proliferation and production of interferon (IFN)-γ and interleukin (IL)-2. The immune responses elicited by aptamer-OVA conjugates were sufficient to inhibit the growth of established OVA-expressing B16 tumor cells. Our results demonstrate a new application of aptamer technology for the development of effective T cell-mediated vaccines.

Use of oligonucleotide aptamer ligands to modulate the function of immune receptors

The paucity of costimulation at the tumor site compromises the ability of tumor-specific T cells to eliminate the tumor. The recent U.S. Food and Drug Administration approval of ipilumimab, an antibody that blocks the inhibitory action of CTLA-4, and clinical trials targeting 4-1BB and PD-1 or PD-L1, have underscored the therapeutic potential of using immunomodulatory antibodies to stimulate protective immunity in human patients. Nonetheless, systemic administration of immunomodulatory antibodies has been associated with dose-limiting autoimmune pathologies, conceivably reflecting also the activation of resident autoreactive T cells. Arguably, targeting immunomodulatory ligands to the disseminated tumor lesions of the patient would reduce such drug-associated toxicities. We have recently developed a new class of inhibitory (CTLA-4) and agonistic (4-1BB and OX-40) ligands composed of short oligonucleotide (ODN) aptamers that exhibited bioactivities comparable or superior to that of antibodies. To reduce toxicity, the immunomodulatory aptamers were targeted to the tumor by conjugation to a second aptamer that bound to a product expressed on the surface of the tumor cell, the targeting aptamer, generating a bispecific aptamer conjugate analogous to bispecific antibodies. In a proof-of-concept study in mice, we have shown that an agonistic 4-1BB-binding aptamer conjugated to a prostate-specific membrane antigen (PSMA)-binding aptamer led to the inhibition of PSMA-expressing tumors, was more effective than, and synergized with, vaccination, and exhibited a superior therapeutic index compared with nontargeted costimulation with 4-1BB antibodies or 4-1BB aptamers. The cell-free chemically synthesized ODN aptamers offer significant advantages over antibodies in terms of synthesis, cost, as well as conjugation chemistry needed to generate bispecific ligand fusions.

RNA aptamers and their therapeutic and diagnostic applications

RNA Aptamers refer to RNA oligonulceotides that are capable of binding to specific targets with high affinity and specificity. Through a process called Systematic Evolution of Ligands by EXponential enrichment (SELEX), a number of RNA aptamers have been identified against various targets including organic compounds, nucleotides, proteins and even whole cells and organisms. RNA aptamers have proven to be of high therapeutic and diagnostic value with recent FDA approval of the first aptamer drug and additional ones in the clinical pipelines. It has also been found to be a particularly useful tool for cell-type specific delivery of other RNA therapeutics like siRNA. All these establish RNA aptamers as one of the pivotal tools of the emerging RNA nanotechnology field in the fight against human diseases including cancer, viral infections and other diseases. This article summarizes the current advancement in the identification of RNA aptamers and also provides some examples of their therapeutic and diagnostic applications.

Emerging molecular targets for brain repair after stroke

The field of neuroprotection generated consistent preclinical findings of mechanisms of cell death but these failed to be translated into clinics. The approaches that combine the modulation of the inhibitory environment together with the promotion of intrinsic axonal outgrowth needs further work before combined therapeutic strategies will be transferable to clinic trials. It is likely that only when some answers have been found to these issues will our therapeutic efforts meet our expectations. Stroke is a clinically heterogeneous disease and combinatorial treatments require much greater work in pharmacological and toxicological testing. Advances in genetics and results of the Whole Human Genome Project (HGP) provided new unknown information in relation to stroke. Genetic factors are not the only determinants of responses to some diseases. It was recognized early on that "epigenetic" factors were major players in the aetiology and progression of many diseases like stroke. The major players are microRNAs that represent the best-characterized subclass of noncoding RNAs. Epigenetic mechanisms convert environmental conditions and physiological stresses into long-term changes in gene expression and translation. Epigenetics in stroke are in their infancy but offer great promise for better understanding of stroke pathology and the potential viability of new strategies for its treatment.

Promising new assays and technologies for the diagnosis and management of infectious diseases

In the first decade of the 21st century, we have seen the completion of the human genome project and marked progress in the human microbiome project. The vast amount of data generated from these efforts combined with advances in molecular and biomedical technologies have led to the development of a multitude of assays and technologies that may be useful in the diagnosis and management of infectious diseases. Here, we identify several new assays and technologies that have recently come into clinical use or have potential for clinical use in the near future. The scope of this review is broad and includes topics such as the serum marker procalcitonin, gene expression profiling, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and nucleic acid aptamers. Principles that underlie each assay or technology, their clinical applications, and potential strengths and limitations are addressed.

MicroPET/SPECT/CT imaging of small animal models of disease

For the greater part of the last century, basic science research has been limited to in vitro studies of cellular processes and ex vivo tissue examination from suitable animal models of disease. In the last three decades, however, new techniques have been developed that permit the imaging of live animals using X-rays, radiotracer emissions, magnetic resonance signals, sound waves and optical fluorescence, and bioluminescence. The objective of this review is to provide a broad overview of common animal imaging modalities, with a focus on positron emission tomography (PET), single photon emission computed tomography (SPECT), and computed tomography (CT). Important examples, benefits, and limits of microPET/SPECT/CT technologies in current use, and their central role in improving our understanding of biological behavior and in facilitating the development of treatments from bench to bedside are included.

RNAi-based nanomedicines for targeted personalized therapy

RNA interference (RNAi) has just made it through the pipeline to clinical trials. However, in order for RNAi to serve as an ideal personalized therapeutics and be clinically approved-safe, specific, and potent strategies must be devised for efficient delivery of RNAi payloads to specific cell types, which despite the immense potential, remains a challenge. Through evaluating the recent reported studies in this field, we introduce the progress in designing targeted nano-scaled strategies that are anticipated to overcome the delivery drawbacks and along with the exciting "omics" discipline to personalize RNAi-based therapeutics.

Aptamer-dendrimer bioconjugate: a nanotool for therapeutics, diagnosis, and imaging

INTRODUCTION

Aptamers hold great promise as molecular tool in biomedical applications due to the therapeutic utility exhibited by their target specificity and sensitivity. Although current development of aptamer is hindered by its probable in vivo degradation, inefficient immobilization on probe surface, and generation of low detection signal, bioconjugation with nanomaterials can feasibly solve these problems. Nanostructures such as dendrimers, with multivalency and nonimmunogenicity, bioconjugated with aptamers have opened newer vistas for better pharmaceutical applications of aptamers.

AREAS COVERED

This review covers brief overview of aptamers and dendrimers, with specific focus on recent progresses of aptamer-dendrimer (Apt-D) bioconjugate in areas of targeted drug delivery, diagnosis, and molecular imaging along with the discussion on the currently available conjugates, using their in vitro and in vivo results.

EXPERT OPINION

The novel Apt-D bioconjugates have led to advances in targeting cancer cell, have amplified biosensing, and offered in vivo cell imaging. Because of the unique properties and applications, Apt-D bioconjugate propose an exciting future. However, further research in synthesis of new target-specific aptamers and their conjugation with dendrimers is required to establish full potential of Apt-D bioconjugate.

Inhibition of HIV-1 protease expression in T cells owing to DNA aptamer-mediated specific delivery of siRNA

Targeted delivery is a promising way to improve the safety and efficiency of siRNA delivery. We show that a DNA aptamer could be used to deliver siRNA into CD4(+) T cells specifically. The DNA aptamer was obtained from the conversion of a reported RNA aptamer that binds to CD4 protein on the surface of T cells. It was covalently conjugated to the sense strand of the siRNA targeting HIV-1 protease (HIV-PR). The resulting DNA aptamer-siRNA chimera could specifically enter into CD4(+) T cells and efficiently knock down the expression of exogenous HIV-PR gene. This study provides the first evidence that the DNA aptamer with intrinsic stability has a greater potential to be used for siRNA delivery.

Hybrid compounds: from simple combinations to nanomachines

The combination of two different and independently acting compounds into one covalently linked hybrid compound can convey synergy from the effects of both independently acting moieties to the new composite compound, leading to a pharmacological potency greater than the sum of each individual moiety's potencies. Here, we review a variety of such hybrid compounds, which can consist of various functional parts, molecular recognition or subcellular targeting moieties, or combinations thereof, acting either simultaneously or sequentially. Such moieties within a hybrid compound can consist of a variety of substance classes, including small organic molecules, polypeptides or nucleic acids identified either via rational molecular design or selection from libraries. Precedent for hybrid compounds comes from naturally occurring proteins and small molecules, such as botulinum toxin and bleomycin, which are secreted by micro-organisms. We review the high degree of suitability of hybrid compounds for the treatment of multifactorial diseases by simultaneously hitting several targets along an identified disease pathway. Examples are hybrid compounds against Alzheimer's disease, against the cancer-relevant phosphoinisitide-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and epidermal growth factor signaling cascade, or in antimalarial therapy via simultaneous hitting of different mechanisms of hemozoin formation. Molecular recognition by peptides or aptamers (recognition-specific RNA or peptide sequences) can be combined with the transport of small molecule β-sheet breakers or toxins, or targeting to ubiquitin-dependent proteolysis. The vision of molecular nanomachines is currently realized in sequentially acting modular nanotransporters, consisting of four modules including a target, a membrane and nuclear translocation sequence, as well as a drug attachment domain. Through the rational combination of existing drugs and the synergy of their effects, a rapid amplification of their potency may be achieved, greatly accelerating drug development. A further enhancement of simultaneous multitarget action is enabled through the design of multifunctional hybrid drugs with sequential effects that make these hybrid molecules resemble intelligent nanomachines.

Immobilized smart RNA on graphene oxide nanosheets to specifically recognize and adsorb trace peptide toxins in drinking water

The contaminations of peptide toxins in drinking water lead directly to sickness and even death in both humans and animals. A smart RNA as aptamer is covalently immobilized on graphene oxide to form a polydispersed and stable RNA-graphene oxide nanosheet. RNA-graphene oxide nanosheets can resist nuclease and natural organic matter, and specifically adsorb trace peptide toxin (microcystin-LR) in drinking water. The adsorption data fit the pseudo-second-order kinetics and the Langmuir isotherm model. The adsorption capacity of RNA-graphene oxide nanosheets decreases at extreme pH, temperature, ionic strength and natural organic matter, but it is suitable to adsorb trance pollutants in contaminated drinking water. Compared with other chemical and biological sorbents, RNA-graphene oxide nanosheets present specific and competitive adsorption, and are easily synthesized and regenerated. Aptamer (RNA) covalently immobilized on graphene oxide nanosheets is a potentially useful tool in recognizing, enriching and separating small molecules and biomacromolecules in the purification of contaminated water and the preparation of samples.

Aptasensor for ampicillin using gold nanoparticle based dual fluorescence-colorimetric methods

A gold nanoparticle based dual fluorescence-colorimetric method was developed as an aptasensor to detect ampicillin using its single-stranded DNA (ssDNA) aptamer, which was discovered by a magnetic bead-based SELEX technique. The selected aptamers, AMP4 (5'-CACGGCATGGTGGGCGTCGTG-3'), AMP17 (5'-GCGGGCGGTTGTATAGCGG-3'), and AMP18 (5'-TTAGTTGGGGTTCAGTTGG-3'), were confirmed to have high sensitivity and specificity to ampicillin (K(d), AMP7 = 9.4 nM, AMP17 = 13.4 nM, and AMP18 = 9.8 nM, respectively). The 5'-fluorescein amidite (FAM)-modified aptamer was used as a dual probe for observing fluorescence differences and color changes simultaneously. The lower limits of detection for this dual method were a 2 ng/mL by fluorescence and a 10 ng/mL by colorimetry for ampicillin in the milk as well as in distilled water. Because these detection limits were below the maximum residue limit of ampicillin, this aptasensor was sensitive enough to detect antibiotics in food products, such as milk and animal tissues. In addition, this dual aptasensor will be a more accurate method for antibiotics in food products as it concurrently uses two detection methods: fluorescence and colorimetry.

Release of photoactivatable drugs from plasmonic nanoparticles for targeted cancer therapy

Chemotherapy is an important modality in cancer treatment. The major challenges of recent works are to improve drug loading, increase selectivity to target cells, and control the precise release of drugs. In the present study, we devised a smart drug carrier, an aptamer/hairpin DNA-gold nanoparticle (apt/hp-Au NP) conjugate for targeted delivery of drugs. The DNA aptamer sgc8c, which possesses strong affinity for protein tyrosine kinase 7 (PTK7), abundantly expressed on the surface of CCRF-CEM (T-cell acute lymphoblastic leukemia) cells, was assembled onto the surface of Au NPs. The repeated d(CGATCG) sequence within the hpDNA on the Au NP surface was used for the loading of the anticancer drug doxorubicin (Dox). After optimization, 25 (±3) sgc8c and 305 (±9) Dox molecules were successfully loaded onto the AuNP (13 nm) surface. The binding capability of apt/hp-Au NP conjugates toward targeted cells was investigated by flow cytometry and atomic absorption spectroscopy, which showed that the aptamer-functionalized nanoconjugates were selective for targeting of cancer cells. A cell toxicity (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, MTT) assay also demonstrated that these drug-loaded nanoconjugates could kill targeted cancer cells more effectively than nontargeted (control) cells. Most importantly, when illuminated with plasmon-resonant light (532 nm), Dox:nanoconjugates displayed enhanced antitumor efficacy with few side effects. The marked release of Dox from these nanoconjugates in living cells was monitored by increasing fluorescence signals upon light exposure. In vitro studies confirmed that aptamer-functionalized hp-Au NPs can be used as carriers for targeted delivery of drugs with remote control capability by laser irradiation with high spatial/temporal resolution.

An RNA aptamer that specifically binds pancreatic adenocarcinoma up-regulated factor inhibits migration and growth of pancreatic cancer cells

Previously, we reported that a novel secretory protein, pancreatic adenocarcinoma up-regulated factor (PAUF), which is highly expressed in pancreatic cancer and mediates the growth and metastasis of pancreatic cancer cells. In this study, we generated and characterized a 2'-fluoropyrimidine modified RNA aptamer (P12FR2) directed against human PAUF. P12FR2 binds specifically to human PAUF with an estimated apparent K(D) of 77nM. P12FR2 aptamer inhibits PAUF-induced migration of PANC-1, human pancreatic cancer cells, in a wound healing assay. Moreover, intraperitoneal injection of P12FR2 decreased tumor growth by about 60% in an in vivo xenograft model with CFPAC-1 pancreatic cancer cells, without causing a loss of weight in the treated mice. Taken together, we propose here that PAUF-specific RNA aptamer, P12FR2, has the potential to be effective in the therapy of human pancreatic cancer.

Highly efficient enzymatic synthesis of 3'-deoxyapionucleic acid (apioNA) having the four natural nucleobases

The synthesis of the 3'-deoxyapionucleoside 3''-triphosphates (apioNTPs) having the four natural nucleobases and their enzymatic incorporation into a DNA-DNA primer-template have been tried. Therminator DNA polymerase was shown to incorporate these apioNTPs effectively giving 43mer DNA-apioNA chimera.

HAPIscreen, a method for high-throughput aptamer identification

Background

Aptamers are oligonucleotides displaying specific binding properties for a predetermined target. They are selected from libraries of randomly synthesized candidates through an in vitro selection process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment) alternating selection and amplification steps. SELEX is followed by cloning and sequencing of the enriched pool of oligonucleotides to enable comparison of the selected sequences. The most represented candidates are then synthesized and their binding properties are individually evaluated thus leading to the identification of aptamers. These post-selection steps are time consuming and introduce a bias to the expense of poorly amplified binders that might be of high affinity and are consequently underrepresented. A method that would circumvent these limitations would be highly valuable.

Results

We describe a novel homogeneous solution-based method for screening large populations of oligonucleotide candidates generated from SELEX. This approach, based on the AlphaScreen^® technology, is carried out on the exclusive basis of the binding properties of the selected candidates without the needs of performing a priori sequencing. It therefore enables the functional identification of high affinity aptamers. We validated the HAPIscreen (High throughput APtamer Identification screen) methodology using aptamers targeted to RNA hairpins, previously identified in our laboratory. We then screened pools of candidates issued from SELEX rounds in a 384 well microplate format and identify new RNA aptamers to pre-microRNAs.

Conclusions

HAPIscreen, an Alphascreen^®-based methodology for the identification of aptamers is faster and less biased than current procedures based on sequence comparison of selected oligonucleotides and sampling binding properties of few individuals. Moreover this methodology allows for screening larger number of candidates. Used here for selecting anti-premiR aptamers, HAPIscreen can be adapted to any type of tagged target and is fully amenable to automation.

ssDNA aptamer-based column for simultaneous removal of nanogram per liter level of illicit and analgesic pharmaceuticals in drinking water

Aptamers are a new class of single-stranded DNA/RNA molecules selected from synthetic nucleic acid libraries for molecular recognition. Our group reports a novel aptamer column for the removal of trace (ng/L) pharmaceuticals in drinking water. In this study, cocaine and diclofenac were chosen as model molecules to test the aptamer column which presented high removal capacity, selectivity, and stability. The removal of pharmaceuticals was as high as 88-95%. The data of adsorption were fitted with Langmuir isotherm and a pseudo-second-order kinetic model. A thermodynamic experiment proved the adsorption processes were exothermic in spontaneity. The kinetics of aptamer was composed of three steps: activation, binding, and hybridization. The first step was the rate-controlling step. The adsorption system was divided into three parts: kinetic, mixed, and thermodynamic zones from 0% to 100% binding fraction of aptamer. Furthermore, the aptamer column was reusable and achieved strong removal efficiency from 4 to 30 °C at normal cation ion concentration (5-100 mg/L) for multipollutants without cross effects and secondary pollution. This work indicates that aptamer, as a new sorbent, can be used in the removal of persistent organic pollutants, biological toxins, and pathogenic bacteria from surface, drinking, and ground water.

Targeted chemoimmunotherapy using drug-loaded aptamer-dendrimer bioconjugates

We reported an innovative, targeted chemoimmuno drug-delivery system. Although chemoimmunotherapy, as an alternative to or in combination with conventional therapeutic systems, has been in the forefront of recent oncological research, as presently configured, such systems face several major obstacles for efficient clinical application. Here, we establish a novel nano-platform for effective chemoimmunotherapy designed to overcome the drawbacks of conventional cancer therapies, describing a delivery system based on a dendrimer and a single-strand DNA-A9 PSMA (prostate-specific membrane antigen) RNA aptamer hybrid. Employing these vehicles, we demonstrate the promising possibility of this chemoimmuno therapeutic system against prostate cancer in in vivo and in vitro models.

Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer

A selective kanamycin-binding single-strand DNA (ssDNA) aptamer (TGGGGGTTGAGGCTAAGCCGA) was discovered through in vitro selection using affinity chromatography with kanamycin-immobilized sepharose beads. The selected aptamer has a high affinity for kanamycin and also for kanamycin derivatives such as kanamycin B and tobramycin. The dissociation constants (K(d) [kanamycin]=78.8 nM, K(d) [kanamycin B]=84.5 nM, and K(d) [tobramycin]=103 nM) of the new aptamer were determined by fluorescence intensity analysis using 5'-fluorescein amidite (FAM) modification. Using this aptamer, kanamycin was detected down to 25 nM by the gold nanoparticle-based colorimetric method. Because the designed colorimetric method is simple, easy, and visible to the naked eye, it has advantages that make it useful for the detection of kanamycin. Furthermore, the selected new aptamer has many potential applications as a bioprobe for the detection of kanamycin, kanamycin B, and tobramycin in pharmaceutical preparations and food products.

Optimizing siRNA delivery to the genital mucosa

RNA interference (RNAi) describes a highly conserved pathway, present in eukaryotic cells, for regulating gene expression. Small stretches of double-stranded RNA, termed small interfering RNAs (siRNAs), utilize this pathway to bind homologous mRNA, resulting in site-specific mRNA cleavage and subsequent protein degradation. The ubiquitous presence of the RNAi machinery, combined with its specificity and efficacy, makes it an attractive mechanism for reducing aberrant gene expression in therapeutic settings. However, a major obstacle to utilizing RNAi in the clinic is siRNA delivery. Administered siRNAs must make contact with the appropriate cell types and, following internalization, gain access to the cytosol where the RNAi machinery resides. This must be achieved so that silencing is maximized, whilst minimizing any undesirable off-target effects. Recently, the utility of siRNAs as a microbicide, usually applied to the genital mucosa for preventing transmission of sexually transmitted diseases including HIV-1 and HSV-2, has been investigated. In this review we will describe these studies and discuss potential strategies for improving gene silencing.

The emerging role of epigenetics in stroke: II. RNA regulatory circuitry

Recent scientific advances have demonstrated the existence of extensive RNA-based regulatory networks involved in orchestrating nearly every cellular process in health and various disease states. This previously hidden layer of functional RNAs is derived largely from non-protein-coding DNA sequences that constitute more than 98% of the genome in humans. These non-protein-coding RNAs (ncRNAs) include subclasses that are well known, such as transfer RNAs and ribosomal RNAs, as well as those that have more recently been characterized, such as microRNAs, small nucleolar RNAs, and long ncRNAs. In this review, we examine the role of these novel ncRNAs in the nervous system and highlight emerging evidence that implicates RNA-based networks in the molecular pathogenesis of stroke. We also describe RNA editing, a related epigenetic mechanism that is partly responsible for generating the exquisite degrees of environmental responsiveness and molecular diversity that characterize ncRNAs. In addition, we discuss the development of future therapeutic strategies for locus-specific and genome-wide regulation of genes and functional gene networks through the modulation of RNA transcription, posttranscriptional RNA processing (eg, RNA modifications, quality control, intracellular trafficking, and local and long-distance intercellular transport), and RNA translation. These novel approaches for neural cell- and tissue-selective reprogramming of epigenetic regulatory mechanisms are likely to promote more effective neuroprotective and neural regenerative responses for safeguarding and even restoring central nervous system function.

Cell-specific aptamer-mediated targeted drug delivery

Nucleic acid aptamers are in vitro-selected small, single-stranded DNA or RNA oligonucleotides that can specifically recognize their target on the basis of their unique 3-dimensional structures. Recent advances in the development of escort aptamers to deliver and enhance the efficacy of other therapeutic agents have drawn enthusiasm in exploiting cell-type-specific aptamers as drug delivery vehicles. This review mainly focuses on the recent developments of aptamer-mediated targeted delivery systems. We also place particular emphasis on aptamers evolved against cell membrane receptors and possibilities for translation to clinical applications.

Improved cancer therapy and molecular imaging with multivalent, multispecific antibodies

Antibodies are highly versatile proteins with the ability to be used to target diverse compounds, such as radionuclides for imaging and therapy, or drugs and toxins for therapy, but also can be used unconjugated to elicit therapeutically beneficial responses, usually with minimal toxicity. This update describes a new procedure for forming multivalent and/or multispecific proteins, known as the dock-and-lock (DNL) technique. Developed as a procedure for preparing bispecific antibodies capable of binding divalently to a tumor antigen and monovalently to a radiolabeled hapten-peptide for pretargeted imaging and therapy, this methodology has the flexibility to create a number of other biologic agents of therapeutic interest. A variety of constructs, based on anti-CD20 and CD22 antibodies, have been made, with results showing that multispecific antibodies have very different properties from the respective parental monospecific antibodies. The technique is not restricted to antibody combination, but other biologics, such as interferon-alpha2b, have been prepared. These types of constructs not only allow small biologics to be sustained in the blood longer, but also to be selectively targeted. Thus, DNL technology is a highly flexible platform that can be used to prepare many different types of agents that could further improve cancer detection and therapy.

Receptor-targeted nanocarriers for therapeutic delivery to cancer

Efficient and site-specific delivery of therapeutic drugs is a critical challenge in clinical treatment of cancer. Nano-sized carriers such as liposomes, micelles, and polymeric nanoparticles have been investigated for improving bioavailability and pharmacokinetic properties of therapeutics via various mechanisms, for example, the enhanced permeability and retention (EPR) effect. Further improvement can potentially be achieved by conjugation of targeting ligands onto nanocarriers to achieve selective delivery to the tumour cell or the tumour vasculature. Indeed, receptor-targeted nanocarrier delivery has been shown to improve therapeutic responses both in vitro and in vivo. A variety of ligands have been investigated including folate, transferrin, antibodies, peptides and aptamers. Multiple functionalities can be incorporated into the design of nanoparticles, e.g., to enable imaging and triggered intracellular drug release. In this review, we mainly focus on recent advances on the development of targeted nanocarriers and will introduce novel concepts such as multi-targeting and multi-functional nanoparticles.

Aptamers as therapeutics

Aptamers are single-stranded oligonucleotides that fold into defined architectures and bind to targets such as proteins.

In binding proteins they often inhibit protein–protein interactions and thereby may elicit therapeutic effects such as antagonism.

Aptamers are discovered using SELEX (systematic evolution of ligands by exponential enrichment), a directed in vitro evolution technique in which large libraries of degenerate oligonucleotides are iteratively and alternately partitioned for target binding. They are then amplified enzymatically until functional sequences are identified by the sequencing of cloned individuals.

For most therapeutic purposes, aptamers are truncated to reduce synthesis costs, modified at the sugars and capped at their termini to increase nuclease resistance, and conjugated to polyethylene glycol or another entity to reduce renal filtration rates.

The first aptamer approved for a therapeutic application was pegaptanib sodium (Macugen; Pfizer/Eyetech), which was approved in 2004 by the US Food and Drug Administration for macular degeneration.

Eight other aptamers are currently undergoing clinical evaluation for various haematology, oncology, ocular and inflammatory indications.

Aptamers are ultimately chemically synthesized in a readily scalable process in which specific conjugation points are introduced with defined stereochemistry.

Unlike some protein therapeutics, aptamers do not elicit antibodies, and because aptamers generally contain sugars modified at their 2′-positions, Toll-like receptor-mediated innate immune responses are also abrogated.

As aptamers are oligonucleotides they can be readily assembled into supramolecular multi-component structures using hybridization.

Owing to the fact that binding to appropriate cell-surface targets can lead to internalization, aptamers can also be used to deliver therapeutic cargoes such as small interfering RNA.

Supramolecular assemblies of aptamers and delivery agents have already been demonstrated in vivo and may pave the way for further therapeutic strategies with this modality in the future.

Aptamers are oligonucleotide sequences that are capable of recognizing target proteins with an affinity and specificity rivalling that of antibodies. In this article, Keefe and colleagues discuss the development, properties and therapeutic potential of aptamers, highlighting those currently in the clinic.

Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Aptamers exhibit significant advantages relative to protein therapeutics in terms of size, synthetic accessibility and modification by medicinal chemistry. Despite these properties, aptamers have been slow to reach the marketplace, with only one aptamer-based drug receiving approval so far. A series of aptamers currently in development may change how nucleic acid therapeutics are perceived. It is likely that in the future, aptamers will increasingly find use in concert with other therapeutic molecules and modalities.