Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX

Targeting complement component 5a promotes vascular integrity and limits airway remodeling

Increased microvascular dilatation and permeability is observed during allograft rejection. Because vascular integrity is an important indicator of transplant health, we have sought to limit injury to blood vessels by blocking complement activation. Although complement component 3 (C3) inhibition is known to be vasculoprotective in transplantation studies, we recently demonstrated the paradoxical finding that, early in rejection, C3(-/-) transplant recipients actually exhibit worse microvascular injury than controls. In the genetic absence of C3, thrombin-mediated complement component 5 (C5) convertase activity leads to the generation of C5a (anaphylatoxin), a promoter of vasodilatation and permeability. In the current study, we demonstrated that microvessel thrombin deposition is significantly increased in C3(-/-) recipients during acute rejection. Thrombin colocalization with microvessels is closely associated with remarkably elevated plasma levels of C5a, vasodilatation, and increased vascular permeability. Administration of NOX-D19, a specific C5a inhibitor, to C3(-/-) recipients of airway transplants significantly improved tissue oxygenation, limited microvascular leakiness, and prevented airway ischemia, even in the absence of conventional T-cell-directed immunosuppression. As C3 inhibitors enter the clinics, the simultaneous targeting of this thrombin-mediated complement activation pathway and/or C5a itself may confer significant clinical benefit.

Use of RNA in drug design

This is a review of RNA as a target for small molecules (ribosomes, riboswitches, regulatory RNAs) and RNA-derived oligonucleotides as tools (antisense/small interfering RNA, ribozymes, aptamers/decoy RNA and microRNA). This review highlights the present state of research using RNA as a drug target or as a potential drug candidate and explains at which stage and to what extent rational design could eventually be involved. Special attention has been paid to the recent potential clinical applications of RNA either as drugs or drug targets. The review deals mainly with mechanistic approaches rather than with physicochemical or computational aspects of RNA-based drug design.

Advances in aptamer screening and small molecule aptasensors

It has been 20 years since aptamer and SELEX (systematic evolution of ligands by exponential enrichment) were described independently by Andrew Ellington and Larry Gold. Based on the great advantages of aptamers, there have been numerous isolated aptamers for various targets that have actively been applied as therapeutic and analytical tools. Over 2,000 papers related to aptamers or SELEX have been published, attesting to their wide usefulness and the applicability of aptamers. SELEX methods have been modified or re-created over the years to enable aptamer isolation with higher affinity and selectivity in more labor- and time-efficient manners, including automation. Initially, most of the studies about aptamers have focused on the protein targets, which have physiological functions in the body, and their applications as therapeutic agents or receptors for diagnostics. However, aptamers for small molecules such as organic or inorganic compounds, drugs, antibiotics, or metabolites have not been studied sufficiently, despite the ever-increasing need for rapid and simple analytical methods for various chemical targets in the fields of medical diagnostics, environmental monitoring, food safety, and national defense against targets including chemical warfare. This review focuses on not only recent advances in aptamer screening methods but also its analytical application for small molecules.

Aptamer binding and neutralization of β1-adrenoceptor autoantibodies: basics and a vision of its future in cardiomyopathy treatment

Autoantibodies directed against the second extracellular receptor loop of the β(1) receptor (β(1)-ECII-AABs) that belong to the superfamily of G protein-coupled receptors have been frequently found in patients with idiopathic dilated cardiomyopathy, Chagas' cardiomyopathy, and peripartum cardiomyopathy and have been clearly evidenced to be related to disease pathogenesis. Consequently, specific proteins or peptides used as binders in immunoapheresis or as in vivo neutralizers of β(1)-ECII-AABs have been suggested for patient treatment. Aptamers, which are target specifically selected short single- or double-stranded RNA or DNA sequences, are a recently introduced new molecule class applicable to bind and neutralize diverse molecule species, including antibodies. This article reviews selection technologies and characteristics of aptamers with respect to a single-stranded DNA aptamer recently identified as having a very high affinity against β(1)-ECII-AABs. The potential of this aptamer for the elimination of β(1)-ECII-AABs and in vivo neutralization is critically analyzed in view of its potential for future use in cardiomyopathy treatment.

Challenges and opportunities for small molecule aptamer development

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

Challenges and opportunities for small molecule aptamer development

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

Strategies for the discovery of therapeutic aptamers

IMPORTANCE OF THE FIELD

Therapeutic aptamers are synthetic, structured oligonucleotides that bind to a very broad range of targets with high affinity and specificity. They are an emerging class of targeting ligand that show great promise for treating a number of diseases. A series of aptamers currently in various stages of clinical development highlights the potential of aptamers for therapeutic applications.

AREAS COVERED IN THIS REVIEW

This review covers in vitro selection of oligonucleotide ligands, called aptamers, from a combinatorial library using the Systematic Evolution of Ligands by Exponential Enrichment process as well as the other known strategies for finding aptamers against various targets.

WHAT THE READER WILL GAIN

Readers will gain an understanding of the highly useful strategies for successful aptamer discovery. They may also be able to combine two or more of the presented strategies for their aptamer discovery projects.

TAKE HOME MESSAGE

Although many processes are available for discovering aptamers, it is not easy to discover an aptamer candidate that is ready to move toward pharmaceutical drug development. It is also apparent that there have been relatively few therapeutic advances and clinical trials undertaken due to the small number of companies that participate in aptamer development.

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.

Challenges and opportunities for small molecule aptamer development

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

RNA aptamers: a review of recent trends and applications

RNA aptamers, small oligonucleotides derived by an in-vitro selection process called SELEX (Systematic Evolution of Ligands by EXperimental enrichment), are important candidates for therapeutic and diagnostic applications. RNA aptamers have high affinity and specificity for their target molecules. In this review, we describe methods for generating RNA aptamers (the SELEX technique and modified SELEX processes) and therapeutic applications for diseases such as neovascular age-related macular degeneration (AMD), inflammatory diseases, and obesity. We also analyze the social networks among researchers and organizations (universities, research institutes, firms, etc.) that are active in the pursuit of aptamer-based therapeutic approaches. This study provides relevant information on recent research trends in RNA aptamers.

Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects

In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.

RNA aptamer evolution: two decades of SELEction

Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First developed in 1990, the SELEX process has become a powerful tool to select structured oligonucleotides for the recognition of targets, starting with small molecules, going through protein complexes until whole cells. SELEX has also evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. This review is an historical follow-up of SELEX method over the two decades since its first appearance.

Chimeric aptamers in cancer cell-targeted drug delivery

Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe₃O₄) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities.

Finding aptamers and small ribozymes in unexpected places

The discovery of the catalytic properties of RNAs was a milestone for our view of how life emerged and forced us to reformulate many of our dogmas. The urge to grasp the whole spectrum of potential activities of RNA molecules stimulated two decades of fervent research resulting in a deep understanding of RNA-based phenomena. Most ribozymes were discovered by serendipity during the analysis of chemical processes, whereas RNA aptamers were identified through meticulous design and selection even before their discovery in nature. The desire to obtain aptamers led to the development of sophisticated technology and the design of efficient strategies. With the new notion that transcriptomes cover a major part of genomes and determine the identity of cells, it is reasonable to speculate that many more aptamers and ribozymes are awaiting their discovery in unexpected places. Now, in the genomic era with the development of powerful bioinformatics and sequencing methods, we are overwhelmed with tools for studying the genomes of all living and possibly even extinct organisms. Genomic SELEX (systematic evolution of ligands by exponential enrichment) coupled with deep sequencing and sophisticated computational analysis not only gives access to unexplored parts of sequenced genomes but also allows screening metagenomes in an unbiased manner.

A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase

This article describes a method for selecting single-stranded DNA (ssDNA) molecules that bind with high-affinity aptamers to specific target proteins. This SELEX (systematic evolution of ligands by exponential enrichment) method is similar to other "primer-free" approaches where the random sequence ssDNA starting pool has no fixed sequences at the 5' and 3' termini. Therefore, there are no predetermined sequences that could bias selection. Like other SELEX methods, repeated cycles (typically 5-15) of selection and then amplification and reselection are used. The method differs from other primer-free approaches in that the key step for regenerating new material for subsequent rounds is ligation of the selected ssDNA to a defined sequence oligonucleotide using thermostable RNA ligase. Under specific conditions, this ligase ligated 30-nt random sequence ssDNA (5'-N(30)-3') to a specified 20-nt ssDNA with approximately 50% efficiency. Efficiency was improved to approximately 90% by the addition of a single T residue to the 3' end (5'-N(29)T-3'). High efficiency in this step is critical, especially early in the procedure because any selected material that is not ligated is lost. In this study, human immunodeficiency virus reverse transcriptase was used as the target protein, but the method could be applied to essentially any protein.

Calcitonin gene-related peptide receptor antagonists for migraine

IMPORTANCE OF THE FIELD

Migraine is a highly prevalent disabling condition, and the current treatment options are not satisfactory. The role of calcitonin gene-related peptide (CGRP) in migraine pathophysiology is well established. CGRP receptor antagonists address this new target and have the potential to improve therapy for both responders and non-responders to previous options.

AREAS COVERED IN THIS REVIEW

This review describes CGRP, its receptors and their role in the pathophysiology of migraine. CGRP receptor antagonists are a recent development; all reported antagonists are reported in chronological order. The experimental evidence, as well as all clinical trials since the first proof-of-concept study in 2004, is discussed.

WHAT THE READER WILL GAIN

An overview of the CGRP system and why it provides an attractive drug target for headache. The main focus is on the currently presented CGRP receptor antagonists and clinical evidence for this new therapeutic option.

TAKE HOME MESSAGE

CGRP receptor antagonists will provide an additional and valuable therapeutic option for the treatment of headaches.

Primer-free aptamer selection using a random DNA library

Aptamers are highly structured oligonucleotides (DNA or RNA) that can bind to targets with affinities comparable to antibodies (1). They are identified through an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX) to recognize a wide variety of targets, from small molecules to proteins and other macromolecules (2-4). Aptamers have properties that are well suited for in vivo diagnostic and/or therapeutic applications: Besides good specificity and affinity, they are easily synthesized, survive more rigorous processing conditions, they are poorly immunogenic, and their relatively small size can result in facile penetration of tissues. Aptamers that are identified through the standard SELEX process usually comprise approximately 80 nucleotides (nt), since they are typically selected from nucleic acid libraries with approximately 40 nt long randomized regions plus fixed primer sites of approximately 20 nt on each side. The fixed primer sequences thus can comprise nearly approximately 50% of the library sequences, and therefore may positively or negatively compromise identification of aptamers in the selection process (3), although bioinformatics approaches suggest that the fixed sequences do not contribute significantly to aptamer structure after selection (5). To address these potential problems, primer sequences have been blocked by complementary oligonucleotides or switched to different sequences midway during the rounds of SELEX (6), or they have been trimmed to 6-9 nt (7, 8). Wen and Gray (9) designed a primer-free genomic SELEX method, in which the primer sequences were completely removed from the library before selection and were then regenerated to allow amplification of the selected genomic fragments. However, to employ the technique, a unique genomic library has to be constructed, which possesses limited diversity, and regeneration after rounds of selection relies on a linear reamplification step. Alternatively, efforts to circumvent problems caused by fixed primer sequences using high efficiency partitioning are met with problems regarding PCR amplification (10). We have developed a primer-free (PF) selection method that significantly simplifies SELEX procedures and effectively eliminates primer-interference problems (11, 12). The protocols work in a straightforward manner. The central random region of the library is purified without extraneous flanking sequences and is bound to a suitable target (for example to a purified protein or complex mixtures such as cell lines). Then the bound sequences are obtained, reunited with flanking sequences, and re-amplified to generate selected sub-libraries. As an example, here we selected aptamers to S100B, a protein marker for melanoma. Binding assays showed Kd s in the 10(-7) - 10(-8) M range after a few rounds of selection, and we demonstrate that the aptamers function effectively in a sandwich binding format.

Aptamer-based molecular recognition for biosensor development

Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.

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.

In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules

It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids.

Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories

Aptamers that are selected in vitro from random pools of DNA or RNA molecules by SELEX (Systematic evolution of ligands by exponential enrichment) technique have been extensively explored for analytical and biomedical applications. Although many aptamers with high affinity and specificity against specific ligands have been reported, there is still a lack of well characterized DNA aptamers. Here we report the selection of a group of aptamer candidates (85 mer) against streptavidin. Through comparing the predicted secondary structures of all the candidates, a conservative bulge-hairpin structure section (about 29 mer) was found, and then it was determined to be the binding motif to streptavidin. This binding motif was further discovered to also exist in streptavidin-binding aptamers (SBAs) selected by three other laboratories using different methods. The primary sequences of this secondary structure motif are very different, only several nucleotides in the loop and bulge area are critical for binding and other nucleotides are variable. The streptavidin binding of all the SBAs could be competed by biotin implying that they bind to the same site on streptavidin. These results suggest that the evolution of SBA is predominated by specific groups on streptavidin. The highly variable sequence composition of streptavidin-binding aptamer would make the design of aptameric sensor or device based on streptavidin more flexible and easy.

Primer-free aptamer selection using a random DNA library

Aptamers are high-affinity oligonucleotides which can be selected from large random libraries by systematic evolution of ligands by exponential enrichment (SELEX) protocols, with affinities and specificities comparable or better than antibodies. The SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere (with false positives and negatives) with the selection process. Here we present a primer-free protocol using a random DNA library.

The chemical biology of aptamers

Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.

Inhibition of calcitonin gene-related peptide function: a promising strategy for treating migraine

The neuropeptide calcitonin gene-related peptide (CGRP) is implicated in the underlying pathology of migraine. Serum levels of CGRP, which are elevated during a migraine attack, have been reported to return to normal with alleviation of pain. In addition, CGRP administration has been shown to cause a migraine-like headache in susceptible individuals. Importantly, CGRP receptors are found on many cell types within the trigeminovascular system that are thought to play important roles in controlling inflammatory and nociceptive processes. Based on these findings, it was proposed that blockage of CGRP receptor function and, hence, the physiological effects of CGRP would be effective in aborting a migraine attack. This review will summarize key preclinical data that support the therapeutic potential of using CGRP receptor antagonists or molecules that bind CGRP within the context of current neurovascular theories on migraine pathology.

The shorter the better: reducing fixed primer regions of oligonucleotide libraries for aptamer selection

Oligonucleotide aptamers are highly structured DNA or RNA molecules, or modified versions thereof, that can bind to targets with specific affinities comparable to antibodies. They are identified through an in vitro selection process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment) to recognize a wide variety of targets, from small molecules to proteins, and from cultured cells to whole organisms. Aptamers possess a number of desirable properties, such as ease of synthesis, stability, robustness, and lack of immunogenicity. Standard SELEX libraries require two primers, one on each side of a central random domain, to amplify the target-bound sequences via PCR or RT-PCR. However, these primer sequences cause non-specific binding by their nature, and have been reported to lead to large numbers of false-positive binding sequences, or to interfere with binding of sequences within the random regions. This review is focused on methods which have been developed to eliminate fixed primer interference during the SELEX process.

CGRP function-blocking antibodies inhibit neurogenic vasodilatation without affecting heart rate or arterial blood pressure in the rat

BACKGROUND AND PURPOSE

Calcitonin gene-related peptide (CGRP) receptor antagonists effectively abort migraine headache and inhibit neurogenic vasodilatation in humans as well as rat models. Monoclonal antibodies typically have long half-lives, and we investigated whether or not function-blocking CGRP antibodies would inhibit neurogenic vasodilatation with a long duration of action and therefore be a possible approach to preventive therapy of migraine. During chronic treatment with anti-CGRP antibodies, we measured cardiovascular function, which might be a safety concern of CGRP inhibition.

EXPERIMENTAL APPROACH

We used two rat blood flow models that measure electrically stimulated vasodilatation in the skin or in the middle meningeal artery (MMA). These vasomotor responses are largely dependent on the neurogenic release of CGRP from sensory afferents. To assess cardiovascular function during chronic systemic anti-CGRP antibody treatment, we measured heart rate and blood pressure in conscious rats.

KEY RESULTS

Treatment with anti-CGRP antibodies inhibited skin vasodilatation or the increase in MMA diameter to a similar magnitude as treatment with CGRP receptor antagonists. Although CGRP antibody treatment had a slower onset of action than the CGRP receptor antagonists, the inhibition was still evident 1 week after dosing. Chronic treatment with anti-CGRP antibodies had no detectable effects on heart rate or blood pressure.

CONCLUSIONS AND IMPLICATIONS

We showed for the first time that anti-CGRP antibodies exert a long lasting inhibition of neurogenic vasodilatation in two different rat models of arterial blood flow. We have provided strong preclinical evidence that anti-CGRP antibody may be a suitable drug candidate for the preventive treatment of migraine.

Real-time imaging of protein internalization using aptamer conjugates

Angiogenin is a potent angiogenic factor that is known to play an important role in tumor angiogenesis. In this paper, we investigate the cellular internalization of angiogenin conjugated with its highly specific aptamer. By using fluorophore-labeled aptamer and confocal laser scanning microscopy, we have developed a novel and simple method by which to visualize the real-time process of angiogenin internalization. Specifically, when aptamer-angiogenin conjugates were added into cell cultures, conjugates could be selectively bound to HUVE cells (human umbilical vein endothelial cells) and MCF-7 cells (human breast cancer cells). Nuclear staining and Z-axis scanning studies demonstrated that the aptamer-angiogenin conjugates were internalized to intracellular organelles, and dynamic confocal imaging studies indicated that the conjugates were quickly internalized. These results provide the first evidence that a fluorophore-labeled aptamer can be used as a fluorescent probe to visualize the spatiotemporal process of protein internalization in real time.

Effect of LHRH-PE40 on target cells via LHRH receptors

OBJECTIVE

To detect the effect and cytotoxicity of luteinizing hormone-releasing hormone-Pseudomonas aeruginosa exotoxin 40 (LHRH-PE40) on target cells using LHRH receptors (LHRHR).

METHODS

The affinity of LHRH-PE40 and LHRH binding to LHRHR on the membrane surface of target cells were measured by enzyme linked immunosorbent assay. Morphological observations with light microscope were used to analyze its receptor pathway, with Spiegelmer, and cytotoxicity. IC(50) values of LHRH-PE40, which caused 50% inhibition of tumor cell growth were evaluated by MTT assay. The target cells were exposed to LHRH-PE40 and its cytotoxicity was analyzed by scanning and transmission electron microscopies, agarose gel electrophoresis, and flow cytometry.

RESULTS

LHRH-PE40 killed target cells by LHRHR pathway. The morphological changes in these cells showed decreased cell size, cytoplasmic membrane blebbing, and chromatin condensation and margination. At a certain concentration and time point, HeLa cells were also induced to undergo programmed cell death.

CONCLUSION

LHRH-PE40 induced target cells apoptosis via LHRHR.

Minimal primer and primer-free SELEX protocols for selection of aptamers from random DNA libraries

Standard systematic evolution of ligands by exponential enrichment (SELEX) protocols require libraries that contain two primers, one on each side of a central random domain, which allow amplification of target-bound sequences via PCR or RT-PCR. However, these primer sequences cause nonspecific binding by their nature (generally adding about 20 nt on each end of the random sequence of about 30-40 nt), and can result in large numbers of false-positive binding sequences and/or interfere with good binding random sequences. Here, we have developed two DNA-based methods that reduce and/or eliminate the primer sequences from the target-binding step, thus reducing or eliminating the interference caused by the primer sequences. In these methods, the starting selection libraries contain a central random sequence that is: (i) flanked by only 2 nt on each side (minimal primer); or (ii) flanked only by either a 2- or 0-nt overhand on the 3' end (primer-free). These methods allow primer regeneration and re-elimination after and before selection, are fast and simple, and don't require any chemical modifications for selection in a variety of conditions. Further, the selection rounds are performed with DNA oligomers, which are generally employed as end product aptamers.

Methods for selection of aptamers to protein targets

Aptamers are synthetic single-stranded RNA or DNA molecules capable of specific binding to other target molecules. In this review, the main aptamer properties are considered and methods for selection of aptamers against various protein targets are described. Special attention is given to the methods for directed selection of aptamers, which allow one to obtain ligands with specified properties.

Electrochemical biochips for protein analysis

Proteins bear important functions for most life processes. It is estimated that the human proteome comprises more than 250,000 proteins. Over the last years, highly sophisticated and powerful instruments have been developed that allow their detection and characterization with great precision and sensitivity. However, these instruments need well-equipped laboratories and a well-trained staff. For the determination of proteins in a hospital, in a doctor's office, or at home, low-budget protein analysis methods are needed that are easy to perform. In addition, for a proteomic approach, highly parallel measurements with small sample sizes are required. Biochips are considered as promising tools for such applications. The following chapter describes electrochemical biochips for protein analysis that use antibodies or aptamers as recognition elements.

In-vitro and in-vivo antagonistic action of an anti-amylin Spiegelmer

The anorectic and dipsogenic effects of the pancreatic hormone amylin are mediated by the area postrema and the subfornical organ. We tested the effectiveness of a new amylin antagonist, a so-called RNA Spiegelmer, by electrophysiological in-vitro recordings from the rat subfornical organ and by immunohistological c-Fos studies in the area postrema. Amylin's excitatory effect on subfornical organ neurons was blocked by the anti-amylin Spiegelmer. Peripheral administration 5 h prior to amylin also suppressed the amylin-induced activation (c-Fos expression) in the area postrema. The biostable anti-amylin Spiegelmer may be therapeutically beneficial in conditions associated with high plasma amylin levels, such as cancer anorexia occurring during certain pancreatic tumors.

Nucleic acid aptamers for targeting of shRNA-based cancer therapeutics

Aptamers are nucleic acid ligands which have been validated to bind to epitopes with a specificity similar to that of monoclonal antibodies. Aptamers have been primarily investigated for their direct function in terms of inhibition of protein targets; however, recent evidence gives reason to actively explore aptamers as targeting moieties for delivery of anticancer therapeutics. Many aptamers have been developed to bind to extracellular membrane domains of proteins overexpressed on cancer cells and have the potential to be modified for use in targeting cancer therapeutics. The use of DNA vector-based short hairpin RNA (shRNA) for RNA interference (RNAi) is a precise means for the disruption of target gene expression but its clinical usage in cancer is limited by obstacles related to delivery into cancer cells. Nucleic acid aptamers are attractive candidates for targeting of shRNA therapies. Their small size, ease of production and modification, and high specificity are valued attributes in comparison to other targeting moieties currently being tested. Here we review the development of aptamers directed to PSMA, Nucleolin, HER-3, RET, TN-C, and MUC1 and focus on their potential for use in targeting of shRNA-based cancer therapeutics.

Advances in SELEX and application of aptamers in the central nervous system

SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a screening technique that involves the progressive selection of highly specific ligands by repeated rounds of partition and amplification from a large combinatorial nucleic acid library. The products of the selection are called aptamers, which are short single stranded DNA or RNA molecules, binding with high affinity, attributed to their specific three-dimensional shapes, to a large variety of targets, ranging from small molecules to complex mixtures. Various improvement of the original SELEX method described in 1990 have been obtained recently, such as capillary electrophoresis SELEX, Toggle-SELEX, Tailored-SELEX, Photo-SELEX, and others. These new variants greatly shorten time of selection and improve aptamer affinity and specificity. Such aptamers have great potential as detecting and/or diagnostic reagents. Furthermore, some aptamers specifically inhibit biological functions of targeted proteins, and are considered as potent therapeutic lead structures evaluated in preclinical disease models. Recently, one aptamer has been approved by Food and Drug Administration of US for treating age-related macular degeneration. This review presents recent advances in the field of SELEX with special emphasis on applications of aptamers as analytical, diagnostic and therapeutic tools in the central nervous system.

Aptamers: molecular tools for analytical applications

Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.

SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands

SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.

Effect of two novel CGRP-binding compounds in a closed cranial window rat model

We investigated the in vivo effects of two novel calcitonin gene-related peptide (CGRP) binding molecules in the genuine closed cranial window model in the rat. The RNA-Spiegelmer (NOX-C89) and the monoclonal CGRP antibody are CGRP scavengers and might be used as an alternative to CGRP-receptor antagonists in the treatment of migraine. Rats were anaesthetized and a closed cranial window established. Changes in dural and pial artery diameter and mean arterial blood pressure were measured simultaneously. Infusion of the RNA-Spiegelmer or the CGRP antibody alone had no effect on the arteries or the mean arterial blood pressure. We then used a bolus of 0.3 microg/kg CGRP (n=6) or electrical stimulation (25 V, 5 Hz, 1 ms pulse width and of 10 s of duration) (n=6) to induce dilatation of dural and pial arteries (mediated via CGRP-receptors). Pre-treatment with the RNA-Spiegelmer inhibited CGRP-induced vasodilatation of the dural artery (from 38+/-17% to 7+/-3%) and the pial artery (from 14+/-1% to 3+/-2%) (P<0.05). The RNA-Spiegelmer, however, did not significantly inhibit dilatation induced by electrical stimulation (P>0.05). The CGRP antibody caused a significant reduction of the dural artery diameter caused by intravenous CGRP-infusion (from 23+/-5% to 12+/-3%) (P<0.05), but did not inhibit dilatation caused by electrical stimulation (P>0.05). In conclusion, the CGRP scavengers effectively inhibited the effect of circulating CGRP but do not modify the effect of electrical stimulation and the consequent liberation of CGRP from perivascular sensory nerve fibres.

SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways

Systematic Evolution of Ligands by EXponential enrichment (SELEX) is an experimental procedure that allows extraction, from an initially random pool of oligonucleotides, of the oligomers with a desired binding affinity for a given molecular target. The procedure can be used to infer the strongest binders for a given DNA or RNA binding protein, and the highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic and therapeutic applications. Recently, important new modifications of the SELEX protocol have been proposed. In particular, a modification of the standard SELEX procedure allows generating a dataset from which protein-DNA interaction parameters can be determined with unprecedented accuracy. Another variant of SELEX allows investigating interactions of a protein with nucleic-acid fragments derived from the entire genome of an organism. We review here different SELEX-based methods, with particular emphasis on the experimental design and on the applications aimed at inferring protein-DNA interactions. In addition to the experimental issues, we also review relevant methods of data analysis, as well as theoretical modeling of SELEX.

Inhibitory effect of BIBN4096BS, CGRP(8-37), a CGRP antibody and an RNA-Spiegelmer on CGRP induced vasodilatation in the perfused and non-perfused rat middle cerebral artery

BACKGROUND AND PURPOSE

A new concept for the inhibition of CGRP signalling has been developed by interaction with the CGRP molecule per se by using a CGRP antibody or a CGRP binding RNA-Spiegelmer (NOX-C89). We have compared these CGRP scavengers with two known receptor antagonists (CGRP8-37 and BIBN4096BS) on CGRP-induced relaxations in the rat middle cerebral artery (MCA). Furthermore, the role of the endothelial barrier has been studied.

EXPERIMENTAL APPROACH

We used the luminally perfused MCA in an arteriograph, pressurized to 85 mm Hg and myograph studies of isolated ring segments of the MCA.

KEY RESULTS

In myograph studies and in the perfusion system during abluminal application, alphaCGRP and betaCGRP induced concentration-dependent dilatation of the MCA. Given luminally neither peptide was significantly vasodilator. Adrenomedullin and amylin induced weak dilatations. In myograph experiments, relaxation induced by alphaCGRP was prevented by the four CGRP blockers (CGRP8-37, BIBN4096BS, the CGRP antibody and NOX-C89.). In abluminal perfusion experiments, the relaxant response to alphaCGRP was prevented by these agents to a varying degree. Dilatation induced by abluminal application of alphaCGRP was inhibited by luminal CGRP8-37 but not by luminal BIBN4096BS, CGRP antibody or NOX-C89.

CONCLUSIONS AND IMPLICATIONS

alpha or betaCGRP acted on smooth muscle cell CGRP receptors in rat MCA and were effectively prevented from reaching these receptors by the endothelial barrier. The CGRP blockers significantly inhibited alphaCGRP induced relaxation but were also prevented from reaching the CGRP receptors by the arterial endothelium.

A mathematical analysis of SELEX

Systematic evolution of ligands by exponential enrichment (SELEX) is a procedure by which a mixture of nucleic acids that vary in sequence can be separated into pure components with the goal of isolating those with specific biochemical activities. The basic idea is to combine the mixture with a specific target molecule and then separate the target-NA complex from the resulting reaction. The target-NA complex is then separated by mechanical means (for example by filtration), the NA is then eluted from the complex, amplified by polymerase chain reaction (PCR) and the process repeated. After several rounds, one should be left with a pool of [NA] that consists mostly of the species in the original pool that best binds to the target. In Irvine et al. [Irvine, D., Tuerk, C., Gold, L., 1991. SELEXION, systematic evolution of nucleic acids by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 222, 739-761] a mathematical analysis of this process was given. In this paper we revisit Irvine et al. [Ibid]. By rewriting the equations for the SELEX process, we considerably reduce the labor of computing the round to round distribution of nucleic acid fractions. We also establish necessary and sufficient conditions for the SELEX process to converge to a pool consisting solely of the best binding nucleic acid to a fixed target in a manner that maximizes the percentage of bound target. The assumption is that there is a single nucleic acid binding site on the target that permits occupation by not more than one nucleic acid. We analyze the case for which there is no background loss (no support losses and no free [NA] left on the support). We then examine the case in which such there are such losses. The significance of the analysis is that it suggests an experimental approach for the SELEX process as defined in Irvine et al. [Ibid] to converge to a pool consisting of a single best binding nucleic acid without recourse to any a priori information about the nature of the binding constants or the distribution of the individual nucleic acid fragments.

Selection-by-function: efficient enrichment of cathepsin E inhibitors from a DNA library

A method for efficient enrichment of protease inhibitors out of a DNA library was developed by introducing SF-link technology. A two-step selection strategy was designed consisting of the initial enrichment of aptamers based on binding function while the second enrichment step was based on the inhibitory activity to a protease, cathepsin E (CE). The latter was constructed by covalently linking of a biotinylated peptide substrate to each of the ssDNA molecule contained in the preliminarily selected DNA library, generating 'SF-link'. Gradual enrichment of inhibitory DNAs was attained in the course of selection. One molecule, SFR-6-3, showed an IC(50) of around 30 nM, a K(d) of around 15 nM and high selectivity for CE. Sequence and structure analysis revealed a C-rich sequence without any guanine and possibly an i-motif structure, which must be novel to be found in in vitro-selected aptamers. SF-link technology, which is novel as the screening technology, provided a remarkable enrichment of specific protease inhibitors and has a potential to be further developed.

Aptamers come of age - at last

Nucleic-acid aptamers have the molecular recognition properties of antibodies, and can be isolated robotically for high-throughput applications in diagnostics, research and therapeutics. Unlike antibodies, however, they can be chemically derivatized easily to extend their lifetimes in biological fluids and their bioavailability in animals. The first aptamer-based clinical drugs have recently entered service. Meanwhile, active research programmes have identified a wide range of anti-viral aptamers that could form the basis for future therapeutics.

In vitro selection using a dual RNA library that allows primerless selection

High affinity target-binding aptamers are identified from random oligonucleotide libraries by an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Since the SELEX process includes a PCR amplification step the randomized region of the oligonucleotide libraries need to be flanked by two fixed primer binding sequences. These primer binding sites are often difficult to truncate because they may be necessary to maintain the structure of the aptamer or may even be part of the target binding motif. We designed a novel type of RNA library that carries fixed sequences which constrain the oligonucleotides into a partly double-stranded structure, thereby minimizing the risk that the primer binding sequences become part of the target-binding motif. Moreover, the specific design of the library including the use of tandem RNA Polymerase promoters allows the selection of oligonucleotides without any primer binding sequences. The library was used to select aptamers to the mirror-image peptide of ghrelin. Ghrelin is a potent stimulator of growth-hormone release and food intake. After selection, the identified aptamer sequences were directly synthesized in their mirror-image configuration. The final 44 nt-Spiegelmer, named NOX-B11-3, blocks ghrelin action in a cell culture assay displaying an IC₅₀ of 4.5 nM at 37°C.

Inhibition of stimulated meningeal blood flow by a calcitonin gene-related peptide binding mirror-image RNA oligonucleotide

Calcitonin gene-related peptide (CGRP) released from trigeminal afferents is known to play an important role in the control of intracranial blood flow. In a rat preparation with exposed cranial dura mater, periods of electrical stimulation induce increases in meningeal blood flow. These responses are due to arterial vasodilatation mediated in part by the release of CGRP. In this preparation, the effect of a CGRP-binding mirror-image oligonucleotide (Spiegelmer NOX-C89) was examined. Spiegelmer NOX-C89 applied topically at concentrations between 10(-7) and 10(-5) M to the exposed dura mater led to a dose-dependent inhibition of the electrically evoked blood flow increases. The highest dose reduced the mean increases in flow to 56% of the respective control levels. A nonfunctional control Spiegelmer (not binding to CGRP) was ineffective in changing blood flow increases. Intravenous injection of NOX-C89 (5 mg kg(-1)) reduced the evoked blood flow increases to an average of 65.5% of the control. The basal blood flow was not changed by any of the applied substances. In addition, an ex vivo preparation of the hemisected rat skull was used to determine CGRP release from the cranial dura mater caused by antidromic activation of meningeal afferents. In this model, 10(-6) M of NOX-C89 reduced the evoked CGRP release by about 50%. We conclude that increases in meningeal blood flow due to afferent activation can be reduced by sequestering the released CGRP and thus preventing it from activating vascular CGRP receptors. Moreover, the Spiegelmer NOX-C89 may inhibit CGRP release from meningeal afferents. Therefore, the approach to interfere with the CGRP/CGRP receptor system by binding the CGRP may open a new opportunity for the therapy of diseases that are linked to excessive CGRP release such as some forms of primary headaches.