Development of a novel ssDNA aptamer targeting neutrophil gelatinase-associated lipocalin and its application in clinical trials

Structurally Different Yet Functionally Similar: Aptamers Specific for the Ebola Virus Soluble Glycoprotein and GP1,2 and Their Application in Electrochemical Sensing

The Ebola virus glycoprotein (GP) gene templates several mRNAs that produce either the virion-associated transmembrane protein or one of two secreted glycoproteins. Soluble glycoprotein (sGP) is the predominant product. GP1 and sGP share an amino terminal sequence of 295 amino acids but differ in quaternary structure, with GP1 being a heterohexamer with GP2 and sGP a homodimer. Two structurally different DNA aptamers were selected against sGP that also bound GP1,2. These DNA aptamers were compared with a 2'FY-RNA aptamer for their interactions with the Ebola GP gene products. The three aptamers have almost identical binding isotherms for sGP and GP1,2 in solution and on the virion. They demonstrated high affinity and selectivity for sGP and GP1,2. Furthermore, one aptamer, used as a sensing element in an electrochemical format, detected GP1,2 on pseudotyped virions and sGP with high sensitivity in the presence of serum, including from an Ebola-virus-infected monkey. Our results suggest that the aptamers interact with sGP across the interface between the monomers, which is different from the sites on the protein bound by most antibodies. The remarkable similarity in functional features of three structurally distinct aptamers suggests that aptamers, like antibodies, have preferred binding sites on proteins.

SERS based Y-shaped aptasensor for early diagnosis of acute kidney injury

Considering the pivotal role of biomarkers in plasma, the development of biomarker specific sensing platforms is of great significance to achieve accurate diagnosis and monitor the occurrence and progress in acute kidney injury (AKI). In this paper, we develop a promising surface-enhanced Raman scattering-based aptasensor for duplex detection of two protein biomarkers in AKI. Exploiting the base-pairing specificity of nucleic acids to form a Y-shaped self-assembled aptasensor, the MGITC labelled gold nanoparticles will be attached to the surface of magnetic beads. In the presence of specific AKI-related biomarkers, the gold nanoparticles will detach from magnetic beads into the supernatant, thus leading to a SERS signal increase, which can be used for the highly sensitive analysis of target biomarkers. In addition, the limit of detection calculated for each biomarker indicates that the SERS-based aptasensor can well meet the detection requirements in clinical applications. Finally, the generality of this sensor in the early diagnosis of AKI is confirmed by using a rat model and spiked plasma samples. This sensing platform provides a facile and general route for sensitive SERS detection of AKI-related biomarkers, which offers great promising utility for in vitro and accurate practical bioassay in AKI early diagnosis.

We develop a promising SERS-based aptasensor for duplex detection of protein biomarkers in AKI. The development of biomarker specific sensors is of great significance to achieving accurate diagnosis and monitoring the occurrence and progress of AKI.

Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury

Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.

Machine learning guided aptamer refinement and discovery

Aptamers are single-stranded nucleic acid ligands that bind to target molecules with high affinity and specificity. They are typically discovered by searching large libraries for sequences with desirable binding properties. These libraries, however, are practically constrained to a fraction of the theoretical sequence space. Machine learning provides an opportunity to intelligently navigate this space to identify high-performing aptamers. Here, we propose an approach that employs particle display (PD) to partition a library of aptamers by affinity, and uses such data to train machine learning models to predict affinity in silico. Our model predicted high-affinity DNA aptamers from experimental candidates at a rate 11-fold higher than random perturbation and generated novel, high-affinity aptamers at a greater rate than observed by PD alone. Our approach also facilitated the design of truncated aptamers 70% shorter and with higher binding affinity (1.5 nM) than the best experimental candidate. This work demonstrates how combining machine learning and physical approaches can be used to expedite the discovery of better diagnostic and therapeutic agents.

Current aptamer discovery approaches are unable to probe the complete space of possible sequences. Here, the authors use machine learning to facilitate the development of DNA aptamers with improved binding affinities, and truncate them without significantly compromising binding affinity.