The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer

Selection and characterization of DNA aptamers targeting the surface Borrelia protein CspZ with high-throughput cross-over SELEX

Lyme borreliosis (LB) is the most prevalent tick-borne illness, with an estimated 700 000 cases annually in the United States and Europe. The LB diagnosis based on a two-tiered serology remains controversial due to its indirect nature and low sensitivity during the early stage of the disease. Aptamers are single-stranded DNA or RNA oligonucleotides that exhibit high selectivity and specificity for their target due to their unique three-dimensional structure. By applying cross-over-SELEX process, an enrichment of DNA oligonucleotide sequences against a surface protein of Borrelia, named CspZ, has been performed and monitored using absorbance at 260 nm, melting curves and NGS analyses. Beyond sequence enrichment, oligonucleotides binding to CspZ were observed during the selection rounds by Dot Blot and beads assays. Thirteen unique and highly redundant oligonucleotide sequences were further characterized using multiple approaches such as Dot Blot, BioLayer Interferometry and Surface Plasmon Resonance. The selected aptamers showed KD values from tens of nanomolar to the micromolar range by BLI and SPR. Two aptamers, Apta9 and Apta10, characterized by flow cytometry and epifluorescence microscopy, were able to specifically recognize Borrelia burgdorferi sensu stricto. This strategy holds promise for the development of an improved diagnostic assay.

Aptamer-Assisted DNA SELEX: Dual-Site Targeting of a Single Protein

Heterobivalent fusion aptamers that target a single protein show significant promise for studying protein-protein interactions. However, a major challenge is finding two distinct aptamers that can simultaneously recognize the same protein. In this study, we used a novel technique called Aptamer-Assisted DNA SELEX (AADS) to isolate two distinct aptamers capable of recognizing different sites on the programmed death-ligand 1 (PD-L1) protein. Initially, Aptamer 1 (P1C2) was identified by using conventional DNA SELEX targeting the PD-L1 protein. Subsequently, Aptamer 2 (P1CSC) was obtained via AADS, which was designed to bind to the PD-L1/P1C2 complex. After confirming that both aptamers could simultaneously recognize the PD-L1 protein, we engineered fusion aptamers by optimizing their orientation and linker sequences, resulting in the creation of the optimized fusion aptamer, P1CSC-T7-P1C1. Our fusion aptamer targeting PD-L1 demonstrated remarkable specificity and affinity, effectively inhibiting PD-1/PD-L1 interactions at both the protein and cellular levels. These findings highlight the potential of fusion aptamers via AADS as powerful tools for targeting the PD-L1 protein and cancer cells (A549 cells). This represents a significant advancement in aptamer-based molecular recognition and has the potential to drive innovation as a versatile method for targeting a wide range of proteins.

DNA Nanotags for Multiplexed Single-Particle Electron Microscopy and In Situ Electron Cryotomography

DNA nanostructures present new opportunities as Nanotags for electron microscopy (EM) imaging, leveraging their high programmability, unique shapes, biomolecule conjugation capability, and stability compatible with standard cryogenic sample preparation protocols. This perspective highlights the potential of DNA Nanotags to enable high-throughput multiplexed EM analysis and facilitate in situ particle identification for cryogenic electron tomography (cryo-ET). Meanwhile, applying Nanotags in live-cell environments requires the efficient cellular uptake of intact structures and successful cytosolic migration. Promising strategies such as employing direct cytosolic delivery platforms and expressing RNA-based Nanotags in situ are discussed, while more systematic studies are needed to fully understand the intracellular trafficking and achieve precise localization of DNA Nanotags.

A Label-Free Aptasensor for the Detection of Sulfaquinoxaline Using AuNPs and Aptamer in Water Environment

Sulfaquinoxaline (SQX) is widely utilized in aquaculture and animal husbandry due to its broad antimicrobial spectrum and low cost. However, it is difficult to degrade, and there are relevant residues in the aquatic environment, which could be harmful to both the ecological environment and human health. As a new recognition molecule, the aptamer can be recognized with SQX with high affinity and specificity, and the aptamer is no longer adsorbed to AuNPs after binding to SQX, which weakens the catalytic effect of AuNPs. Consequently, an aptasensor for the detection of SQX was successfully developed. This aptasensor exhibits a linear range of 40-640 ng/mL, with a detection limit of 36.95 ng/mL, demonstrating both sensitivity and selectivity. The recoveries of this aptasensor in water samples ranged from 90 to 109.9%, which was quite in line with high-performance liquid chromatography. These findings suggest that the aptasensor is a valuable tool for detecting SQX in aqueous environmental samples.

Selection of aptamers using β-1,3-glucan recognition protein-tagged proteins and curdlan beads

RNA aptamersare nucleic acids that are obtained using the systematic evolution of ligands by exponential enrichment (SELEX) method. When using conventional selection methods to immobilize target proteins on matrix beads using protein tags, sequences are obtained that bind not only to the target proteins but also to the protein tags and matrix beads. In this study, we performed SELEX using β-1,3-glucan recognition protein (GRP)-tags and curdlan beads to immobilize the acute myeloid leukaemia 1 (AML1) Runt domain (RD) and analysed the enrichment of aptamers using high-throughput sequencing. Comparison of aptamer enrichment using the GRP-tag and His-tag suggested that aptamers were enriched using the GRP-tag as well as using the His-tag. Furthermore, surface plasmon resonance analysis revealed that the aptamer did not bind to the GRP-tag and that the conjugation of the GRP-tag to RD weakened the interaction between the aptamer and RD. The GRP-tag could have acted as a competitor to reduce weakly bound RNAs. Therefore, the affinity system of the GRP-tagged proteins and curdlan beads is suitable for obtaining specific aptamers using SELEX.

An AuNPs-Based Fluorescent Sensor with Truncated Aptamer for Detection of Sulfaquinoxaline in Water

Herein, we developed a novel truncation technique for aptamer sequences to fabricate highly sensitive aptasensors based on molecular docking and molecular dynamics simulations. The binding mechanism and energy composition of the aptamer/sulfaquinoxaline (SQX) complexes were investigated. We successfully obtained a new SQX-specific aptamer (SBA28-1: CCCTAGGGG) with high affinity (K_d = 27.36 nM) and high specificity determined using graphene oxide. This aptamer has a unique stem-loop structure that can bind to SQX. Then, we fabricated a fluorescence aptasensor based on SBA28-1, gold nanoparticles (AuNPs), and rhodamine B (RhoB) that presented a good linear range of 1.25–160 ng/mL and a limit of detection of 1.04 ng/mL. When used to analyze water samples, the aptasensor presented acceptable recovery rates of 93.1–100.1% and coefficients of variation (CVs) of 2.2–10.2%. In conclusion, the fluorescence aptasensor can accurately and sensitively detect SQX in water samples and has good application prospects.