The World Health Organization has declared the outbreak of a novel coronavirus (SARS-CoV-2 or 2019-nCoV) as a global pandemic. However, the mechanisms behind the coronavirus infection are not yet fully understood, nor are there any targeted treatments or vaccines. In this study, we identified high-binding-affinity aptamers targeting SARS-CoV-2 RBD, using an ACE2 competition-based aptamer selection strategy and a machine learning screening algorithm. The Kd values of the optimized CoV2-RBD-1C and CoV2-RBD-4C aptamers against RBD were 5.8 nM and 19.9 nM, respectively. Simulated interaction modeling, along with competitive experiments, suggests that two aptamers may have partially identical binding sites at ACE2 on SARS-CoV-2 RBD. These aptamers present an opportunity for generating new probes for recognition of SARS-CoV-2 and could provide assistance in the diagnosis and treatment of SARS-CoV-2 while providing a new tool for in-depth study of the mechanisms behind the coronavirus infection.

Discovery of Aptamers Targeting the Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein.

Surface functional groups strongly affect the properties of carbon dots (CDs). Amino, carboxy, and hydroxy groups are most commonly encountered in CDs, and they can be introduced via covalent and noncovalent modification. This article (with 116 refs.) reviews the progress made in the past few years. Following an introduction into the field, a large section covers methods for covalent modification (via amide coupling reactions, silylation, and other reactions including esterification, sulfonylation and copolymerization). Next section reviews methods for noncovalent modifications (π interactions, complexation/chelation, and electrostatic interactions). The resulting modified CDs are powerful nanomaterials for targeting and extracting analytes, and in drug release. The modification of the surface also affects fluorescence quantum yields, complexation capacity, the color of fluorescence, and their quenching capability. Current challenges are critically assessed in the concluding section.

Surface modification and chemical functionalization of carbon dots: a review

Aptamers evolved from live cells as effective molecular probes for cancer study

The COVID-19 pandemic caused by SARS-CoV-2 is threating global health. Inhibiting interaction of the receptor-binding domain of SARS-CoV-2 S protein (SRBD ) and human ACE2 receptor is a promising treatment strategy. However, SARS-CoV-2 neutralizing antibodies are compromised by their risk of antibody-dependent enhancement (ADE) and unfavorably large size for intranasal delivery. To avoid these limitations, we demonstrated an aptamer blocking strategy by engineering aptamers' binding to the region on SRBD that directly mediates ACE2 receptor engagement, leading to block SARS-CoV-2 infection. With aptamer selection against SRBD and molecular docking, aptamer CoV2-6 was identified and applied to prevent, compete with, and substitute ACE2 from binding to SRBD . CoV2-6 was further shortened and engineered as a circular bivalent aptamer CoV2-6C3 (cb-CoV2-6C3) to improve the stability, affinity, and inhibition efficacy. cb-CoV2-6C3 is stable in serum for more than 12âh and can be stored at room temperature for more than 14âdays. Furthermore, cb-CoV2-6C3 binds to SRBD with high affinity (Kd =0.13ânM) and blocks authentic SARS-CoV-2 virus with an IC50 of 0.42ânM.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202100225

Aptamer Blocking Strategy Inhibits SARS-CoV-2 Virus Infection.

Development of DNA aptamers using Cell-SELEX

A new carbon dot (CD)-based nanoprobe for the ratiometric fluorescence detection of DNA was constructed in this work. Thiazole orange (TO), a specific organic small molecular probe toward DNA, is covalently linked to the surface of CDs, acting as the recognition element and the fluorescence response unit. In the absence of DNA, the nanoprobe only emitted the blue fluorescence of CDs, whereas TO was almost nonfluorescent. Upon addition of DNA, a turn-on emission at 530 nm appeared and gradually enhanced along with the increasing of the target DNA, whereas the fluorescence of CDs was unchanged, which realized the ratiometric detection of the target DNA. The CD-TO nanoprobe showed good selectivity to parallel G-quadruplex (G4) and double-stranded (ds) DNA over antiparallel G4 and single-stranded DNA. Moreover, the ratiometric fluorescence nanoprobe exhibited high sensitivity for ssab (a dsDNA) and c-myc (a parallel G4) with a low detection limit of 0.90 and 3.31 nM, respectively. Additionally, the G4/hemin peroxidase activity inhibition experiment demonstrated that CD-TO bound to the G4s through the end-stacking mode.

Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA.

Neurite outgrowth is the critical step of nervous development. Molecular probes against neurites are essential for evaluation of the nervous system development, compound neurotoxicity, and drug efficacy on nerve regeneration. To obtain a neurite probe, we developed a neurite-SELEX strategy and generated a DNA aptamer, yly12, that strongly binds neurites. The molecular target of yly12 was identified to be neural cell adhesion molecule L1 (L1CAM), a surface antigen expressed in normal nervous system and various cancers. Here, yly12 was successfully applied to image the three-dimensional network of neurites between live cells, as well as the neurite fibers on normal brain tissue section. This aptamer was also found to have an inhibitory effect on neurite outgrowth between cells. Given the advantages of aptamers, yly12 hold great potential as a molecular tool in the field of neuroscientific research. The high efficiency of neurite-SELEX suggests that SELEX against a subcellular structure instead of the whole ...

Imaging of Neurite Network with an Anti-L1CAM Aptamer Generated by Neurite-SELEX.

The pH of mitochondria (pHm) is crucial in physiological processes. Here, we report a new mitochondria-targeted ratiometric pH-sensitive fluorescent probe for monitoring the mitochondrial pH change...

A Mitochondria-Targeted Ratiometric Fluorescent pH Probe

G-quadruplex (G4) forming sequences commonly exist in the genome and are closely related to gene regulation and expression. Development of a fluorescent probe that can specifically recognize G4 is ...

Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA

We present a novel microbead-based detection platform as a simple and universal strategy for simultaneous determination of multiple biomolecules. This platform is composed of streptavidin coated uniform-sized polystyrene microbeads, dye and biotin-labeled ssDNA or aptamer probes, and quencher-labeled complementary sequences. By this method, upon target binding to the probes, quencher strand dissociation is triggered, which results in fluorescence reactivation of the microbead linked probes. The fluorescence variation is readily monitored by flow cytometry and with a high sensitivity. Explicitly, this microbead-based detection platform shows a high sensitivity for target DNA with a detection limit as low as 0.20 nM, alongside good selectivity from one-base mismatched DNA. This novel platform also shows good selectivity and high sensitivity for protein detection when aptamer is used as a probe. The detection limit for lysozyme is as low as 8.56 nM. Moreover, simultaneous detection of multiple targets has been achieved via incorporating different dye-labeled probes on the microbeads concurrently. We have also applied this developed strategy to the detection of target DNA in human serum. This strategy can be easily extended to other targets through simple probe and quencher variation.

Dihua Shangguan

Papers

Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA.

Imaging of Neurite Network with an Anti-L1CAM Aptamer Generated by Neurite-SELEX.

A Mitochondria-Targeted Ratiometric Fluorescent pH Probe

Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA

Microbead-Based Platform for Multiplex Detection of DNA and Protein.