Inhibitory RNA ligand to reverse transcriptase from feline immunodeficiency virus

The Application of Aptamer and Research Progress in Liver Disease

Aptamers, as a kind of small-molecule nucleic acid, have attracted much attention since their discovery. Compared with biological reagents such as antibodies, aptamers have the advantages of small molecular weight, low immunogenicity, low cost, and easy modification. At present, aptamers are mainly used in disease biomarker discovery, disease diagnosis, treatment, and targeted drug delivery vectors. In the process of screening and optimizing aptamers, it is found that there are still many problems need to be solved such as the design of the library, optimization of screening conditions, the truncation of screened aptamer, and the stability and toxicity of the aptamer. In recent years, the incidence of liver-related diseases is increasing year by year and the treatment measures are relatively lacking, which has attracted the people's attention in the application of aptamers in liver diseases. This article mainly summarizes the research status of aptamers in disease diagnosis and treatment, especially focusing on the application of aptamers in liver diseases, showing the crucial significance of aptamers in the diagnosis and treatment of liver diseases, and the use of Discovery Studio software to find the binding target and sequence of aptamers, and explore their possible interaction sites.

Aptamers, antibody scFv, and antibody Fab' fragments: An overview and comparison of three of the most versatile biosensor biorecognition elements

The choice of biosensing elements is crucial for the development of the optimal biosensor. Three of the most versatile biosensing elements are antibody single-chain Fv fragments (scFv), antibody fragment-antigen binding (Fab') units, and aptamers. This article provides an overview of these three biorecognition elements with respects to their synthesis/engineering, various immobilization techniques, and examples of their use in biosensors. Furthermore, the final section of the review compares and contrasts their characteristics (time/cost of development, ease and variability of immobilization, affinity, stability) illustrating their advantages and disadvantages. Overall, scFv fragments are found to display the highest customizability (i.e. addition of functional groups, immobilizing peptides, etc.) due to recombinant synthesis techniques. If time and cost are an issue in the development of the biosensor, Fab' fragments should be chosen as they are relatively cheap and can be developed quickly from whole antibodies (several days). However, if there are sufficient funds and time is not a factor, aptamers should be utilized as they display the greatest affinity towards their target analytes and are extremely stable (excellent biosensor regenerability).

Aptamer-mediated nanoparticle interactions: from oligonucleotide-protein complexes to SELEX screens

Aptamers are oligonucleotides displaying specific binding properties for a predetermined target. They can be easily immobilized on various surfaces such as nanoparticles. Functionalized particles can then be used to various aims. We took advantage of the AlphaScreen(®) technology for monitoring aptamer-mediated interactions. A particle bearing an aptamer contains a photosensitizer whereas another type of particle contains a chemiluminescer. Irradiation causes the formation of singlet oxygen species in the photosensitizer-containing bead that in turn activates the chemiluminescer. Luminescence emission can be observed if the two types of beads are in close proximity (<200 nm). This is achieved when the cognate ligand of the aptamer is grafted onto the chemiluminescer-containing bead. Using this technology we have screened oligonucleotide libraries and monitored aptamer-protein interactions. This constitutes the basis for aptamer-based analytical assays.

Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance

BACKGROUND

Reverse transcriptase is an indispensable enzyme for real-time reverse transcriptase (RT)-PCR, a standard method in molecular diagnostics for detection and quantification of defined RNA molecules. The prevention of non-specific products due to elongation of misprimed oligonucleotides by the enzyme at temperatures beneath the specific annealing temperature is one of the biggest challenges in real-time RT-PCR.In the present study, an aptamer directed against the reverse transcriptase was analyzed for its potential to attain a temperature-dependent reverse transcriptase ("hot start" RT).

FINDINGS

The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). Results with aptamer revealed a reduced RT activity at low temperatures while achieving full activity at the specific annealing temperature of 55 °C. Sensitivity (limit of detection (LoD) 95 %) of the MERS-CoV assay was increased by about two times in the presence of aptamer.

CONCLUSIONS

The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays.

Chitosan-graphene oxide based aptasensor for the impedimetric detection of lysozyme

An impedimetric detection of lysozyme (LYS) was performed for the first time in this study at the surface of chitosan-graphene oxide (CHIT-GO) modified sensor based on the specific interaction process between DNA aptamer and its cognate protein, LYS. The amino linked DNA aptamer (APT) was covalently immobilized without using any chemical agents onto the surface of pencil graphite electrode (PGE). These PGEs are inexpensive and simple to use, and thus, they can be furtherly developed for a single-use application in a portable protein chip device. The electrochemical impedance spectroscopy (EIS) technique was used herein to analyze (i) the surface characterization of unmodified PGE and CHIT-GO modified PGE, and also (ii) the interaction between APT and LYS. The limit of detection (DL) was found as 0.38 μg/mL (equals to 28.53 nM). This impedimetric LYS aptasensor exhibited a higher selectivity toward thrombin and bovine serum albumin, even in the mixture samples.

Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, "UCAA-motif" RNA Aptamers

RNA aptamers that bind the reverse transcriptase (RT) of human immunodeficiency virus (HIV) compete with nucleic acid primer/template for access to RT, inhibit RT enzymatic activity in vitro, and suppress viral replication when expressed in human cells. Numerous pseudoknot aptamers have been identified by sequence analysis, but relatively few have been confirmed experimentally. In this work, a screen of nearly 100 full-length and >60 truncated aptamer transcripts established the predictive value of the F1Pk and F2Pk pseudoknot signature motifs. The screen also identified a new, nonpseudoknot motif with a conserved unpaired UCAA element. High-throughput sequence (HTS) analysis identified 181 clusters capable of forming this novel element. Comparative sequence analysis, enzymatic probing and RT inhibition by aptamer variants established the essential requirements of the motif, which include two conserved base pairs (AC/GU) on the 5′ side of the unpaired UCAA. Aptamers in this family inhibit RT in primer extension assays with IC₅₀ values in the low nmol/l range, and they suppress viral replication with a potency that is comparable with that of previously studied aptamers. All three known anti-RT aptamer families (pseudoknots, the UCAA element, and the recently described “(6/5)AL” motif) are therefore suitable for developing aptamer-based antiviral gene therapies.

Biorecognition on graphene: physical, covalent, and affinity immobilization methods exhibiting dramatic differences

The preparation of biorecognition layers on the surface of a sensing platform is a very crucial step for the development of sensitive and selective biosensors. Different protocols have been used thus far for the immobilization of biomolecules onto various electrode surfaces. In this work, we investigate how the protocol followed for the immobilization of a DNA aptamer affects the performance of the fabricated thrombin aptasensor. Specifically, the differences in selectivity and optimum amount of immobilized aptamer of the fabricated aptasensors adopting either physical, covalent, or affinity immobilization were compared. It was discovered that while all three methods of immobilization uniformly show a similar optimum amount of immobilized aptamer, physical, and covalent immobilization methods exhibit higher selectivity than affinity immobilization. Hence, it is believed that our findings are very important in order to optimize and improve the performance of graphene-based aptasensors.

Development of DNA aptamers using Cell-SELEX

In the past two decades, high-affinity nucleic acid aptamers have been developed for a wide variety of pure molecules and complex systems such as live cells. Conceptually, aptamers are developed by an evolutionary process, whereby, as selection progresses, sequences with a certain conformation capable of binding to the target of interest emerge and dominate the pool. This protocol, cell-SELEX (systematic evolution of ligands by exponential enrichment), is a method that can generate DNA aptamers that can bind specifically to a cell type of interest. Commonly, a cancer cell line is used as the target to generate aptamers that can differentiate that cell type from other cancers or normal cells. A single-stranded DNA (ssDNA) library pool is incubated with the target cells. Nonbinding sequences are washed off and bound sequences are recovered from the cells by heating cell-DNA complexes at 95 degrees C, followed by centrifugation. The recovered pool is incubated with the control cell line to filter out the sequences that bind to common molecules on both the target and the control, leading to the enrichment of specific binders to the target. Binding sequences are amplified by PCR using fluorescein isothiocyanate-labeled sense and biotin-labeled antisense primers. This is followed by removal of antisense strands to generate an ssDNA pool for subsequent rounds of selection. The enrichment of the selected pools is monitored by flow cytometry binding assays, with selected pools having increased fluorescence compared with the unselected DNA library. The procedure, from design of oligonucleotides to enrichment of the selected pools, takes approximately 3 months.

Using aptamers to visualize and capture cancer cells

Since diseased cells exist in exceedingly low concentration at the early stage of cancer, highly sensitive imaging and detection methods are required. By improving the methods for capturing and visualizing cancer cells, clinicians can diagnose metastatic relapse, stratify patients for therapeutic purposes, monitor response to drugs and therapies, and track tumor progression. Therefore, using advanced biotechnological and analytical methods combined with cell-SELEX (systematic evolution of ligands by exponential enrichment)-based aptamers, we improved the capture and visualization of diseased cells in a manner that is inexpensive, simple, sensitive, and fast. This multiplexed cancer detection platform therefore improves our control over a range of clinical exigencies, including cancer diagnosis, therapeutic modalities, and drug delivery systems.

Nucleic acid aptamers for biosensors and bio-analytical applications

Oligonucleotides were once considered only functional as molecules for the storage of genetic information. However, the discovery of RNAzymes, and later, DNAzymes, unravelled the innate potential of oligonucleotides in many other biological applications. In the last two decades, these applications have been further expanded through the introduction of Systematic Evolution of Ligands by EXponential enrichment (SELEX) which has generated, by repeated rounds of in vitro selection, a type of molecular probe termed aptamers. Aptamers are oligonucleic acid (or peptide) molecules that can bind to various molecular targets and are viewed as complements to antibodies. Aptamers have found applications in many areas, such as bio-technology, medicine, pharmacology, microbiology, and analytical chemistry, including chromatographic separation and biosensors. In this review, we focus on the use of aptamers in the development of biosensors. Coupled with their ability to bind a variety of targets, the robust nature of oligonucleotides, in terms of synthesis, storage, and wide range of temperature stability and chemical manipulation, makes them highly suitable for biosensor design and engineering. Among the many design strategies, we discuss three general paradigms that have appeared most frequently in the literature: structure-switching, enzyme-based, and aptazyme-based designs.

Mapping of RNA-protein interactions

RNA-protein interactions are important biological events that perform multiple functions in all living organisms. The wide range of RNA interactions demands diverse conformations to provide contacts for the selective recognition of proteins. Various analytical procedures are presently available for quantitative analyses of RNA-protein complexes, but analytical-based mapping of these complexes is essential to probe specific interactions. In this overview, interactions of functional RNAs and RNA-aptamers with target proteins are discussed by means of mapping strategies.

Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): a comparison of their molecular and biochemical properties

This chapter reviews most of the biochemical data on reverse transcriptases (RTs) of retroviruses, other than those of HIV-1 and murine leukemia virus (MLV) that are covered in detail in other reviews of this special edition devoted to reverse transcriptases. The various RTs mentioned are grouped according to their retroviral origins and include the RTs of the alpharetroviruses, lentiviruses (both primate, other than HIV-1, and non-primate lentiviruses), betaretroviruses, deltaretroviruses and spumaretroviruses. For each RT group, the processing, molecular organization as well as the enzymatic activities and biochemical properties are described. Several RTs function as dimers, primarily as heterodimers, while the others are active as monomeric proteins. The comparisons between the diverse properties of the various RTs show the common traits that characterize the RTs from all retroviral subfamilies. In addition, the unique features of the specific RTs groups are also discussed.

Antiviral aptamers

Aptamers are rare nucleic acid ligands, which can be concocted in the laboratory from the randomized pool of molecules by affinity and amplification processes. Aptamers have several properties as they can be applied complementarily to antibodies and have several advantages over antibodies. In the past, several aptamers have been selected with a view to develop antiviral agents for therapeutic applications. This review summarizes potent antiviral aptamers and their strategies to prevent the viral replication.

Aptamers in the virologists' toolkit

Aptamers are artificial nucleic acid ligands that can be generated in vitro against a wide range of molecules, including the gene products of viruses. Aptamers are isolated from complex libraries of synthetic nucleic acids by an iterative, cell-free process that involves repetitively reducing the complexity of the library by partitioning on the basis of selective binding to the target molecule, followed by reamplification. For virologists, aptamers have potential uses as tools to help to analyse the molecular biology of virus replication, as a complement to the more familiar monoclonal antibodies. They also have potential applications as diagnostic biosensors and in the development of antiviral agents. In recent years, these two promising avenues have been explored increasingly by virologists; here, the progress that has been made is reviewed.

Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication

Nucleic acid aptamers to HIV-1 reverse transcriptase (RT) are potent inhibitors of DNA polymerase function in vitro, and they have been shown to inhibit viral replication when expressed in cultured T-lymphoid lines. We monitored RT inhibition by five RNA pseudoknot RNA aptamers in a series of biochemical assays designed to mimic discrete steps of viral reverse transcription. Our results demonstrate potent aptamer inhibition (IC50 values in the low nanomolar range) of all RT functions assayed, including RNA- and DNA-primed DNA polymerization, strand displacement synthesis, and polymerase-independent RNase H activity. Additionally, we observe differences in the time dependence of aptamer inhibition. Polymerase-independent RNase H activity is the most resistant to long term aptamer suppression, and RNA-dependent DNA polymerization is the most susceptible. Finally, when DNA polymerization was monitored in the presence of an RNA aptamer in combination with each of four different small molecule inhibitors, significant synergy was observed between the aptamer and the two nucleoside analog RT inhibitors (azidothymidine triphosphate or ddCTP), whereas two non-nucleoside analog RT inhibitors showed either weak synergy (efavirenz) or antagonism (nevirapine). Together, these results support a model wherein aptamers suppress viral replication by cumulative inhibition of RT at every stage of genome replication.

Mutations that confer resistance to template-analog inhibitors of human immunodeficiency virus (HIV) type 1 reverse transcriptase lead to severe defects in HIV replication

We isolated two template analog reverse transcriptase (RT) inhibitor-resistant mutants of human immunodeficiency virus (HIV) type 1 RT by using the DNA aptamer, RT1t49. The mutations associated, N255D or N265D, displayed low-level resistance to RT1t49, while high-level resistance could be observed when both mutations were present (Dbl). Molecular clones of HIV that contained the mutations produced replication-defective virions. All three RT mutants displayed severe processivity defects. Thus, while biochemical resistance to the DNA aptamer RT1t49 can be generated in vitro via multiple mutations, the overlap between the aptamer- and template-primer-binding pockets favors mutations that also affect the RT-template-primer interaction. Therefore, viruses with such mutations are replication defective. Potent inhibition and a built-in mechanism to render aptamer-resistant viruses replication defective make this an attractive class of inhibitors.

Aptamers: An Emerging Class of Molecules That Rival Antibodies in Diagnostics

Antibodies, the most popular class of molecules providing molecular recognition needs for a wide range of applications, have been around for more than three decades. As a result, antibodies have made substantial contributions toward the advancement of diagnostic assays and have become indispensable in most diagnostic tests that are used routinely in clinics today. The development of the systematic evolution of ligands by exponential enrichment (SELEX) process, however, made possible the isolation of oligonucleotide sequences with the capacity to recognize virtually any class of target molecules with high affinity and specificity. These oligonucleotide sequences, referred to as “aptamers”, are beginning to emerge as a class of molecules that rival antibodies in both therapeutic and diagnostic applications. Aptamers are different from antibodies, yet they mimic properties of antibodies in a variety of diagnostic formats. The demand for diagnostic assays to assist in the management of existing and emerging diseases is increasing, and aptamers could potentially fulfill molecular recognition needs in those assays. Compared with the bellwether antibody technology, aptamer research is still in its infancy, but it is progressing at a fast pace. The potential of aptamers may be realized in the near future in the form of aptamer-based diagnostic products in the market. In such products, aptamers may play a key role either in conjunction with, or in place of, antibodies. It is also likely that existing diagnostic formats may change according to the need to better harness the unique properties of aptamers.

Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element

We have extracted from a random population of about 10(9) oligodeoxynucleotides a series of 21-mers that are able to bind to a folded DNA 76-mer used as a template for in vitro transcription of the TAR element of the retrovirus HIV-1, by the T7 RNA polymerase. Five aptastrucs, that is, aptamers able to bind to the structure, out of 15 analyzed sequences, share the consensus motif 5'-PyGGG(TG)PyC, complementary in part to a weak double-stranded region of the target. (The parentheses indicate that either T or G is missing in one of these aptastrucs.) A dissociation constant of about 3 microM was evaluated by electrophoretic mobility shift assay for the winner sequence. Interactions between the aptastruc and the target sequences involve more than Watson-Crick base pairing of the consensus octamer. The binding is chemistry dependent. Phosphorothioate oligodeoxyribonucleotides and 2'-O-methyl oligoribonucleotides derived from the selected aptastrucs exhibit a weak if any affinity for the target.