In vitro selection and characterization of cellulose-binding RNA aptamers using isothermal amplification

Selection of Plastic-Binding DNA Aptamers for Microplastics Detection

Plastics are critical materials for modern technological applications, yet environmental contamination by microplastics has become a growing concern. In this study, DNA aptamers were isolated for two of the most abundant plastic materials: polyvinylchloride (PVC) and polystyrene (PS). These aptamers contain approximately 90 % cytosine and thymine but only 10 % purine content. Among them, the PVC-1 aptamer binds to PVC with a six-fold higher capacity than a random sequenced DNA. Among the tested plastic materials, PVC and PS exhibited the highest specific binding capacity. Using fluorophore-labeled PVC-1 aptamer, PS/PVC microplastics as low as 1 mg were detected, and the aptamer was selective for microplastics over other environmentally relevant materials, such as silica. Molecular dynamics simulations indicated that the aptamer attempted to maximize contact with the plastic surface for adsorption. This plastic-binding aptamer is expected to find applications in environmental monitoring and has fundamental implications for surface-binding aptamers.

Advances in Microfluidic Paper-Based Analytical Devices (µPADs): Design, Fabrication, and Applications

Microfluidic Paper-based Analytical Devices (µPADs) have emerged as a new class of microfluidic systems, offering numerous advantages over traditional microfluidic chips. These advantages include simplicity, cost-effectiveness, stability, storability, disposability, and portability. As a result, various designs for different types of assays are developed and investigated. In recent years, µPADs are combined with conventional detection methods to enable rapid on-site detection, providing results comparable to expensive and sophisticated large-scale testing methods that require more time and skilled personnel. The application of µPAD techniques is extensive in environmental quality control/analysis, clinical diagnosis, and food safety testing, paving the way for on-site real-time diagnosis as a promising future development. This review focuses on the recent research advancements in the design, fabrication, material selection, and detection methods of µPADs. It provides a comprehensive understanding of their principles of operation, applications, and future development prospects.

Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency

The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.

Aptamers Selected for Recognizing Amyloid β-Protein-A Case for Cautious Optimism

Aptamers are versatile oligonucleotide ligands used for molecular recognition of diverse targets. However, application of aptamers to the field of amyloid β-protein (Aβ) has been limited so far. Aβ is an intrinsically disordered protein that exists in a dynamic conformational equilibrium, presenting time-dependent ensembles of short-lived, metastable structures and assemblies that have been generally difficult to isolate and characterize. Moreover, despite understanding of potential physiological roles of Aβ, this peptide has been linked to the pathogenesis of Alzheimer disease, and its pathogenic roles remain controversial. Accumulated scientific evidence thus far highlights undesirable or nonspecific interactions between selected aptamers and different Aβ assemblies likely due to the metastable nature of Aβ or inherent affinity of RNA oligonucleotides to β-sheet-rich fibrillar structures of amyloidogenic proteins. Accordingly, lessons drawn from Aβ–aptamer studies emphasize that purity and uniformity of the protein target and rigorous characterization of aptamers’ specificity are important for realizing and garnering the full potential of aptamers selected for recognizing Aβ or other intrinsically disordered proteins. This review summarizes studies of aptamers selected for recognizing different Aβ assemblies and highlights controversies, difficulties, and limitations of such studies.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10¹⁴ random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization

Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.

Preparation of λN-GST fusion protein for affinity immobilization of RNA

Affinity purification of in vitro transcribed RNA is becoming an attractive alternative to purification using standard denaturing gel electrophoresis. Affinity purification is particularly advantageous because it can be performed in a few hours under non-denaturing conditions. However, the performance of affinity purification methods can vary tremendously depending on the RNA immobilization matrix. It was previously shown that RNA immobilization via an optimized λN-GST fusion protein bound to glutathione-Sepharose resin allows affinity purification of RNA with very high purity and yield. This Chapter outlines the experimental procedure employed to prepare the λN-GST fusion protein used for RNA immobilization in successful affinity purifications of RNA. It describes the details of protein expression and purification as well as routine quality control analyses.

The sweet and sour of serological glycoprotein tumor biomarker quantification

Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.

Binding sugars: from natural lectins to synthetic receptors and engineered neolectins

The large diversity and complexity of glycan structures together with their crucial role in many biological or pathological processes require the development of new high-throughput techniques for analyses. Lectins are classically used for characterising, imaging or targeting glycoconjugates and, when printed on microarrays, they are very useful tools for profiling glycomes. Development of recombinant lectins gives access to reliable and reproducible material, while engineering of new binding sites on existing scaffolds allows tuning of specificity. From the accumulated knowledge on protein-carbohydrate interactions, it is now possible to use nucleotide and peptide (bio)synthesis for producing new carbohydrate-binding molecules. Such a biomimetic approach can also be addressed by boron chemistry and supra-molecular chemistry for the design of fully artificial glycosensors.

Affinity purification of RNA using an ARiBo tag

The increased awareness of the importance of RNA in biology, illustrated by the recent attention given to RNA interference research and applications, has spurred structural and functional investigations of RNA. For these studies, the traditional purification method for in vitro transcribed RNA is denaturing polyacrylamide gel electrophoresis. However, gel-based procedures denature the RNA and can be very tedious and time-consuming. Thus, several alternative schemes have been developed for fast non-denaturing purification of RNA transcribed in vitro. In a recent report, a quick affinity purification procedure was developed for RNAs transcribed with a 3'-ARiBo tag and shown to provide RNA with exceptionally high purity and yield. The ARiBo tag contains the λboxB RNA and the glmS ribozyme, allowing immobilization on GSH-Sepharose resin via a λN-GST fusion protein and elution by activation of the glmS ribozyme with glucosamine-6-phosphate. This Chapter outlines the experimental details for affinity batch purification of RNAs using ARiBo tags. Although the procedure was originally developed for purification of a stable purine riboswitch mutant, it is demonstrated here for purification of the terminal loop of the let-7g precursor miRNA, an important target of the pluripotency factor Lin28.

Protonation of base pairs in RNA: context analysis and quantum chemical investigations of their geometries and stabilities

Base pairs involving protonated nucleobases play important roles in mediating global macromolecular conformational changes and in facilitation of catalysis in a variety of functional RNA molecules. Here we present our attempts at understanding the role of such base pairs by detecting possible protonated base pairs in the available RNA crystal structures using BPFind software, in their specific structural contexts, and by the characterization of their geometries, interaction energies, and stabilities using advanced quantum chemical computations. We report occurrences of 18 distinct protonated base pair combinations from a representative data set of RNA crystal structures and propose a theoretical model for one putative base pair combination. Optimization of base pair geometries was carried out at the B3LYP/cc-pVTZ level, and the BSSE corrected interaction energies were calculated at the MP2/aug-cc-pVDZ level of theory. The geometries for each of the base pairs were characterized in terms of H-bonding patterns observed, rmsd values observed on optimization, and base pair geometrical parameters. In addition, the intermolecular interaction in these complexes was also analyzed using Morokuma energy decomposition. The gas phase interaction energies of the base pairs range from -24 to -49 kcal/mol and reveal the dominance of Hartree-Fock component of interaction energy constituting 73% to 98% of the total interaction energy values. On the basis of our combined bioinformatics and quantum chemical analysis of different protonated base pairs, we suggest resolution of structural ambiguities and correlate their geometric and energetic features with their structural and functional roles. In addition, we also examine the suitability of specific base pairs as key elements in molecular switches and as nucleators for higher order structures such as base triplets and quartets.

The ARiBo tag: a reliable tool for affinity purification of RNAs under native conditions

Although RNA-based biological processes and therapeutics have gained increasing interest, purification of in vitro transcribed RNA generally relies on gel-based methods that are time-consuming, tedious and denature the RNA. Here, we present a reliable procedure for affinity batch purification of RNA, which exploits the high-affinity interaction between the boxB RNA and the N-peptide from bacteriophage λ. The RNA of interest is synthesized with an ARiBo tag, which consists of an activatable ribozyme (the glmS ribozyme) and the λBoxB RNA. This ARiBo-fusion RNA is initially captured on Glutathione-Sepharose resin via a GST/λN-fusion protein, and the RNA of interest is subsequently eluted by ribozyme self-cleavage using glucosamine-6-phosphate. Several GST/λN-fusion proteins and ARiBo tags were tested to optimize RNA yield and purity. The optimized procedure enables one to quickly obtain (3 h) highly pure RNA (>99%) under native conditions and with yields comparable to standard denaturing gel-based protocols. It is widely applicable to a variety of RNAs, including riboswitches, ribozymes and microRNAs. In addition, it can be easily adapted to a wide range of applications that require RNA purification and/or immobilization, including isolation of RNA-associated complexes from living cells and high-throughput applications.

Bioactive paper provides a low-cost platform for diagnostics

Bioactive paper includes a range of potential paper-based materials that can perform analytical functions normally reserved for multi-well plates in the laboratory or for portable electronic devices. Pathogen detection is the most compelling application. Simple paper-based detection, not requiring hardware, has the potential to have impacts in society, ranging from the kitchen to disasters in the developing world. Bioactive-paper research is an emerging field with significant efforts in Canada, USA (Harvard), Finland and Australia. Following a brief introduction to the material and surface properties of paper, I review the literature. Some of the early work exploits the porosity of paper to generate paper-based microfluidics ("paperfluidics") devices. I exclude from this review printed electronic devices and plastics-supported devices.