SELEX and dynamic combinatorial chemistry interplay for the selection of conjugated RNA aptamers

Discovery of selective monosaccharide receptors via dynamic combinatorial chemistry

The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly and screening of virtual libraries of receptors, with the use of ITC and NMR to validate the hits and molecular modelling to understand the binding mechanisms. We discovered a minimalistic receptor, 1F (N-benzyl-L-phenylalanine), with considerable affinity for fructose (Ka = 1762 M-1) and remarkable selectivity (>50-fold) over other common monosaccharides. The approach accelerates the discovery process of receptors for saccharides.

Access to 1'-Amino Carbocyclic Phosphoramidite to Enable Postsynthetic Functionalization of Oligonucleotides

We report a synthesis of a carbocyclic, abasic RNA phosphoramidite decorated with an amino functionality. The building block was efficiently incorporated into an RNA oligonucleotide in a site-specific manner, followed by deprotection to a free amino group. The amino moiety could be further derivatized as exemplified with fluorescein N-hydroxysuccinimide ester. Hence, this convertible building block may provide access to a variety of RNA oligonucleotides via postsynthetic amino group functionalization. In particular, providing a vector toward nucleobase replacements.

Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents

The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.

Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides

In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.

Aptamers targeting cell surface proteins

High affinity binders targeting specific cell surface proteins are vital for development of basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acid aptamers have potential as binding molecules for cell surface proteins, because they form distinct structures that have high affinity and specificity for a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX). Among advantages of this method, purified and complex heterogeneous targets, such as bacteria, viruses, and whole-living cells, can be used for selection of aptamers. Moreover, SELEX allows generation of cell-surface-specific aptamers without prior knowledge of expression profiles in target cells. Therefore, the technology has been widely used as a valid and feasible method to generate aptamers binding to cell surface proteins with intact structure. Herein, this review summarizes and updates iconic SELEX technologies that target membrane proteins.

Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target

Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established.

In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies

Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.

Protein-Directed Dynamic Combinatorial Chemistry: A Guide to Protein Ligand and Inhibitor Discovery

Protein-directed dynamic combinatorial chemistry is an emerging technique for efficient discovery of novel chemical structures for binding to a target protein. Typically, this method relies on a library of small molecules that react reversibly with each other to generate a combinatorial library. The components in the combinatorial library are at equilibrium with each other under thermodynamic control. When a protein is added to the equilibrium mixture, and if the protein interacts with any components of the combinatorial library, the position of the equilibrium will shift and those components that interact with the protein will be amplified, which can then be identified by a suitable biophysical technique. Such information is useful as a starting point to guide further organic synthesis of novel protein ligands and enzyme inhibitors. This review uses literature examples to discuss the practicalities of applying this method to inhibitor discovery, in particular, the set-up of the combinatorial library, the reversible reactions that may be employed, and the choice of detection methods to screen protein ligands from a mixture of reversibly forming molecules.

Aptasensors for viral diagnostics

•

We discuss progress in aptamer-based detection of viruses.

•

We consider the use of aptasensors for point-of-care diagnostics of viruses.

•

Aptamers have distinct advantages over antibodies for virus recognition.

•

There is strong demand for multiplexed diagnostic measurement of pathogens.

Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.

Generation of Aptamers with an Expanded Chemical Repertoire

The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs).

A Versatile Approach Towards Nucleobase-Modified Aptamers

A novel and versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of nucleobase-modified aptamers with unprecedented recognition properties. Reintroduction of the modification after enzymatic replication gives broad access to many chemical modifications. This wide applicability, which is not limited to a single modification, will rapidly advance the application of in vitro selection approaches beyond what is currently feasible and enable the generation of aptamers to many targets that have so far not been addressable.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

In vitro selection using modified or unnatural nucleotides

Incorporation of modified nucleotides into in vitro RNA or DNA selections offers many potential advantages, such as the increased stability of selected nucleic acids against nuclease degradation, improved affinities, expanded chemical functionality, and increased library diversity. This unit provides useful information and protocols for in vitro selection using modified nucleotides. It includes a discussion of when to use modified nucleotides; protocols for evaluating and optimizing transcription reactions, as well as confirming the incorporation of the modified nucleotides; protocols for evaluating modified nucleotide transcripts as template in reverse transcription reactions; protocols for the evaluation of the fidelity of modified nucleotides in the replication and the regeneration of the pool; and a protocol to compare modified nucleotide pools and selection conditions.

DCC in the development of nucleic acid targeted and nucleic acid inspired structures

Nucleic acids were one of the first biological targets explored with DCC, and research into the application has continued to yield novel and useful structures for sequence- and structure-selective recognition of oligonucleotides. This chapter reviews major developments in DNA- and RNA-targeted DCC, including methods under development for the conversion of DCC-derived lead compounds into probe molecules suitable for studies in vitro and in vivo. Innovative applications of DCC for the discovery of new materials based on nucleic acids and new methods for the modification of nucleic acid structure and function are also discussed.

Advances in binder identification and characterisation: the case of oligonucleotide aptamers

Aptamers represent an important class of synthetic protein binders useful for proteome-wide applications. The identification and characterisation of such molecules have been greatly facilitated by the development of Systematic Evolution of Ligands by Exponential Amplification (SELEX). Since then numerous advances and alternatives to improve efficient aptamer discovery have been reported. In the present manuscript we discuss the recent advances performed around the SELEX approach that may help to expand the availability of new aptamers and the subsequent applications that may be developed.

Identification of ligands for the Tau exon 10 splicing regulatory element RNA by using dynamic combinatorial chemistry

We describe the use of dynamic combinatorial chemistry (DCC) to identify ligands for the stem-loop structure located at the exon 10-5'-intron junction of Tau pre-mRNA, which is involved in the onset of several tauopathies including frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). A series of ligands that combine the small aminoglycoside neamine and heteroaromatic moieties (azaquinolone and two acridines) have been identified by using DCC. These compounds effectively bind the stem-loop RNA target (the concentration required for 50% RNA response (EC(50)): 2-58 μM), as determined by fluorescence titration experiments. Importantly, most of them are able to stabilize both the wild-type and the +3 and +14 mutated sequences associated with the development of FTDP-17 without producing a significant change in the overall structure of the RNA (as analyzed by circular dichroism (CD) spectroscopy), which is a key factor for recognition by the splicing regulatory machinery. A good correlation has been found between the affinity of the ligands for the target and their ability to stabilize the RNA secondary structure.

Targeting Nucleic Acids using Dynamic Combinatorial Chemistry

Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.

Automation in the high-throughput selection of random combinatorial libraries--different approaches for select applications

Automation in combination with high throughput screening methods has revolutionised molecular biology in the last two decades. Today, many combinatorial libraries as well as several systems for automation are available. Depending on scope, budget and time, a different combination of library and experimental handling might be most effective. In this review we will discuss several concepts of combinatorial libraries and provide information as what to expect from these depending on the given context.

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.

In vitro selection using modified or unnatural nucleotides

The use of modified nucleotides in an RNA or DNA pool to be used for in vitro selection offers many potential advantages, such as the increased stability of the selected nucleic acid against nuclease degradation. This unit provides useful information and protocols for in vitro selection using modified nucleotides. It includes a discussion of when to use modified nucleotides; protocols for preparing a modified RNA pool and verifying its suitability for in vitro selection; and protocols for selecting and amplifying a functionally enriched pool.

Dynamic combinatorial chemistry: on the road to fulfilling the promise

Dynamic combinatorial chemistry makes use of reversible reactions between functionalised monomeric building blocks to generate a mixture of products (dimers or oligomers) under thermodynamic equilibrium. This system reorganises upon addition of a target so that species that bind to, and are therefore stabilised by the target, are favourably formed and are thus amplified. Since the mid-1990's, dynamic combinatorial chemistry has been successfully applied to the identification/selection of ion receptors, enzyme inhibitors, catalysts, materials and nucleic acid ligands. Although it is now established as a powerful tool with broad applications some intrinsic limitations appeared when working on systems of increasing complexity. We present here the most recent advances in the field of dynamic combinatorial chemistry that have been developed to overcome these limitations and explore new areas of application.

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.

Chemical Biology is

Chemical Biology is a relatively new field, and as such is not yet simply or succinctly defined. It includes such a wide range of fundamental problems that this commentary could only include just a few snapshots of potential areas of interest. Overarching themes and selected recent successes and ideas in chemical biology are described to illustrate broadly the scope of the field, but should not be taken as exhaustive. The Chemical Biology Section of Chemistry Central Journal is pleased to receive manuscripts describing research into all and any aspects of the subject.