Distinguishing closely related amyloid precursors using an RNA aptamer

G-quadruplex formation in RNA aptamers selected for binding to HIV-1 capsid

HIV-1 capsid protein (CA) is essential for viral replication and interacts with numerous host factors to facilitate successful infection. Thus, CA is an integral target for the study of virus-host dynamics and therapeutic development. The multifaceted functions of CA stem from the ability of CA to assemble into distinct structural components that come together to form the mature capsid core. Each structural component, including monomers, pentamers, and hexamers, presents a variety of solvent-accessible surfaces. However, the structure-function relationships of these components that facilitate replication and virus-host interactions have yet to be fully elucidated. A major challenge is the genetic fragility of CA, which precludes the use of many common methods. To overcome these constraints, we identified CA-targeting aptamers with binding specificity for either the mature CA hexamer lattice alone or both the CA hexamer lattice and soluble CA hexamer. To enable utilization of these aptamers as molecular tools for the study of CA structure-function relationships in cells, understanding the higher-order structures of these aptamers is required. While our initial work on a subset of aptamers included predictive and qualitative biochemical characterizations that provided insight into aptamer secondary structures, these approaches were insufficient for determining more complex non-canonical architectures. Here, we further clarify aptamer structural motifs using focused, quantitative biophysical approaches, primarily through the use of multi-effective spectroscopic methods and thermodynamic analyses. Aptamer L15.20.1 displayed particularly strong, unambiguous indications of stable RNA G-quadruplex (rG4) formation under physiological conditions in a region of the aptamer also previously shown to be necessary for CA-aptamer interactions. Non-canonical structures, such as the rG4, have distinct chemical signatures and interfaces that may support downstream applications without the need for complex modifications or labels that may negatively affect aptamer folding. Thus, aptamer representative L15.20.1, containing a putative rG4 in a region likely required for aptamer binding to CA with probable function under cellular conditions, may be a particularly useful tool for the study of HIV-1 CA.

FaptaSyme: A Strategy for Converting a Monomer/Oligomer-Nonselective Aptameric Sensor into an Oligomer-Selective One

Aptameric sensors can bind molecular targets and produce output signals, a phenomenon that is used in bioassays. In some cases, it is important to distinguish between monomeric and oligomeric forms of a target. Here, we propose a strategy to convert a monomer/oligomer-nonselective sensor into an oligomer-selective sensor. We designed an aptazyme that produced a high fluorescent output in the presence of oligomeric α-synuclein (a molecular marker of Parkinson's disease) but not its monomeric form. The strategy is potentially useful in the design of point-of-care tests for the diagnosis of neurodegenerative diseases.

Selection of DNA Aptamer That Blocks the Fibrillogenesis of a Proteolytic Amyloidogenic Fragment of β2 m

Dialysis-related amyloidosis (DRA) is a severe complication of hemodialysis that results in progressive destruction of bones and joints. Elevated concentrations of the β₂ -microglobulin (β₂ m) level in the serum of subjects on hemodialysis promote the formation of amyloid fibrils in osteoarticular tissues. β₂ m lacking the N-terminal six residues of the mature protein (ΔN6β₂ m) constitutes 25-30% of β₂ m in ex vivo DRA amyloid. Unlike full-length wild-type β₂ m, ΔN6β₂ m forms amyloid fibrils at neutral pH in vitro. However, the role of ΔN6β₂ m in DRA is, at present, poorly understood. In the present study, we screened novel phosphorothioate-modified aptamers directed against ΔN6β₂ m using combinatorial chemistry in vitro. We identified 11 ΔN6β₂ m aptamers; among the identified aptamers, clone #2, #8, and #10 aptamers had higher binding affinity to ΔN6β₂ m than the others. Biolayer interferometry analysis revealed that K_D values of clone #2, #8, and #10 aptamers were 56, 23, and 44 nM, respectively. Furthermore, the clone #8 aptamer inhibited fibril formation in a dose-dependent manner, as assessed by Thioflavin T fluorescence assay. Fibrils formed from ΔN6β₂ m bind to Congo red, displaying changes in the absorbance spectrum of the dye characteristic of binding to amyloid fibrils, which was completely blocked by treatment with clone #8 aptamer. These results suggest the potential of ΔN6β₂ m aptamers as tools for elucidating co-assembly mechanisms in amyloid formation.

Amyloid plaques beyond Aβ: a survey of the diverse modulators of amyloid aggregation

Aggregation of the amyloid-β (Aβ) peptide is strongly correlated with Alzheimer's disease (AD). Recent research has improved our understanding of the kinetics of amyloid fibril assembly and revealed new details regarding different stages in plaque formation. Presently, interest is turning toward studying this process in a holistic context, focusing on cellular components which interact with the Aβ peptide at various junctures during aggregation, from monomer to cross-β amyloid fibrils. However, even in isolation, a multitude of factors including protein purity, pH, salt content, and agitation affect Aβ fibril formation and deposition, often producing complicated and conflicting results. The failure of numerous inhibitors in clinical trials for AD suggests that a detailed examination of the complex interactions that occur during plaque formation, including binding of carbohydrates, lipids, nucleic acids, and metal ions, is important for understanding the diversity of manifestations of the disease. Unraveling how a variety of key macromolecular modulators interact with the Aβ peptide and change its aggregation properties may provide opportunities for developing therapies. Since no protein acts in isolation, the interplay of these diverse molecules may differentiate disease onset, progression, and severity, and thus are worth careful consideration.

A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity

The balance between protein folding and misfolding is a crucial determinant of amyloid assembly. Transient intermediates that are sparsely populated during protein folding have been identified as key players in amyloid aggregation. However, due to their ephemeral nature, structural characterization of these species remains challenging. Here, using the power of nonuniformly sampled NMR methods we investigate the folding pathway of amyloidogenic and nonamyloidogenic variants of β2-microglobulin (β2m) in atomic detail. Despite folding via common intermediate states, we show that the decreased population of the aggregation-prone ITrans state and population of a less stable, more dynamic species ablate amyloid formation by increasing the energy barrier for amyloid assembly. The results show that subtle changes in conformational dynamics can have a dramatic effect in determining whether a protein is amyloidogenic, without perturbation of the mechanism of protein folding.

Trends in aptamer selection methods and applications

Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.