Aptamer Puns

Hey guys! I don't know if this post is ok for this sub but I am just feeling really isolated and out of place because I'm the only one doing anything remotely like this in my entire institute right now and I'm basically self guided on the whole project and I'm wondering if there's anyone else in the group who's doing this cos I'd really like to not feel alone and pointless...?

Currently, the broad use of monovalent aptamers in oncology faces challenges, including insufficient recognition and internalization caused by finite unitary receptors, as well as confined recognition spectrum. Herein, we describe the development of a dual-targeting circular aptamer (DTCA) that can recognize two different biomarkers on living cells to augment aptamer-receptor interactions, thus allowing the enhanced recognition event to occur. This improvement not only boosts binding and internalization abilities, but also expands the recognition spectrum for different leukemia cells. Moreover, the stability of DTCA in serum can be significantly improved by an enzyme-promoted terminal ligation strategy. The chemical incorporation of 5-fluorodeoxyuridine into DTCA resulted in a pharmaceutically functional aptamer that exhibited excellent selectivity, as demonstrated by its high cytotoxicity against target cancer cells, but not to normal cells. The superiority of our newly developed strategy was further highlighted by its precise tumor imaging capability.

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A place for members of r/aptamer to chat with each other

We describe a tumor-targeting yet enhanced chemotherapy, which is enabled by nanomicelles self-assembled from multivalent aptamer drug conjugates. Co-self-assembly with a multivalent PEG-conjugated drug analogue reaches an optimal complementation between the blood circulation and tumor-targeting ability of the nanomicelles, which augments the antitumor immune responses of the checkpoint blockade.

Abstract

A tumor-targeting enhanced chemotherapy, enabled by aptamer-drug conjugate nanomicelles, is reported that boosts antitumor immune responses. Multivalent aptamer drug conjugate (ApMDC), an amphiphilic telodendrimer consisting of a hydrophilic aptamer and a hydrophobic monodendron anchored with four anticancer drugs by acid-labile linkers, was designed and synthesized. By co-self-assembly with an ApMDC analogue, in which aptamer is replaced with polyethylene glycol, the surface aptamer density of these nanomicelles can be screened to reach an optimal complementation between blood circulation and tumor-targeting ability. Optimized nanomicelles can enhance immunogenic cell death of tumor cells, which strikingly augments the tumor-specific immune responses of the checkpoint blockade in immunocompetent tumor-bearing mice. ApMDC nanomicelles represent a robust platform for structure–function optimization of drug conjugates and nanomedicines.

https://ift.tt/2RXaAwj

Journal of the American Chemical SocietyDOI: 10.1021/jacs.1c02929

Jinqi Deng, Fei Tian, Chao Liu, Yuan Liu, Shuai Zhao, Ting Fu, Jiashu Sun, and Weihong Tan

https://ift.tt/3tjAPdl

SP6 is a DNA aptamer binding to the SARS‐CoV‐2 spike glycoprotein and inhibits pseudovirus infection of cells. As the aptamer does not interfere with the CoV‐2S ACE2 receptor binding domain, it provides an RBD‐independent mechanism of virus inhibition.

Abstract

The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS‐CoV‐2 (CoV2‐S) binds to the human angiotensin‐converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2‐S. The aptamer does not bind to the RBD of CoV2‐S and does not block the interaction of CoV2‐S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS‐CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.

https://ift.tt/3tO40WM

Advantages of aptamers and SELEX in diverse research fields are summarized in this Minireview, along with some limitations and possible solutions to them. Furthermore described are future perspectives for aptamer modification with a near‐infinite number of molecular‐modulating elements that will result in more powerful tools in bioscience.

Abstract

The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.

https://ift.tt/3a5HdLU

Journal of the American Chemical SocietyDOI: 10.1021/jacs.1c03013

Zhiyong Huang, Dan Wang, Cheng-Yu Long, Shen-Huan Li, Xue-Qiang Wang, and Weihong Tan

https://ift.tt/3v7OzZA

I have searched for the information about how aptamer binds RNA but couldn’t find anything useful. Does it form complementary pairs with the RNA, or just noncovalent interactions?

We developed a new approach to selectively modify native proteins in their biological environment using electrophilic, covalent aptamers. These aptamers are generated through introduction of a proximity‐driven electrophile at specific nucleic acid sites. Using thrombin as a proof‐of‐concept, we demonstrate that covalent aptamers can selectively transfer a variety of functional handles and/or irreversibly crosslink to the target protein. This approach offers broad programmability and high target specificity. Furthermore, it addresses issues common to aptamers such as instability towards endogenous nucleases and residence times during target engagement. Covalent aptamers are new tools that enable specific protein modification and sensitive protein detection. Moreover, they provide prolonged, nuclease‐resistant enzyme inhibition.

https://ift.tt/3vyGZrK

Journal of the American Chemical SocietyDOI: 10.1021/jacs.1c02016

Yu Yang, Jun Xu, Yang Sun, Liuting Mo, Bo Liu, Xiaoshu Pan, Zhuang Liu, and Weihong Tan

https://ift.tt/3hPCiGg

Structural transition metal ions: Post‐transition/transition metal ions can induce, through their coordination to nucleobases, substantial DNA destabilization. We exploited such property for elaborating fluorescent aptamer probes that switch between inert, metal ion‐complexed and active, target‐bound states. This very simple structural switching strategy was applied to the homogeneous‐phase detection of small organics using diversely structured aptamers.

Abstract

We introduced an aptamer switch design that relies on the ability of post‐transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb2+, Cd2+) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.

https://ift.tt/30XlVOm

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 (S RBD) 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 the limitations of neutralizing antibodies, we proposed and demonstrated an aptamer blocking strategy by engineering aptamers’ binding to the region on S RBD that directly mediates ACE2 receptor engagement, leading to block SARS‐CoV‐2 infection. With aptamer selection against S RBD and molecular docking, aptamer CoV2‐6 was identified and successfully applied to prevent, compete, and substitute ACE2 from binding to S RBD protein. CoV2‐6 was further shortened and engineered as a circular bivalent apamer CoV2‐6C3 (cb‐CoV2‐6C3) to improve the stability, affinity, and inhibition efficacy. With its circular form, cb‐CoV2‐6C3 aptamer was found to be stable in serum for more than 12 hours and can be stored at room temperature for more than 14 days. The circular bivalent aptamer binds to S RBD with high affinity (Kd of 0.13 nM) and blocks authentic SARS‐CoV‐2 virus with a half‐maximal inhibitory concentration of 0.42 nM. With its excellent affinity, stability, safety and programmability, our aptamer showed its capability to inhibit SARS‐CoV‐2 infection, suggesting aptamer blocking strategy as a new direction for developing therapeutic agents against COVID‐19 and other emerging infectious diseases.

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Aptamers, oligonucleotide‐based recognition elements isolated from random libraries, have several favorable attributes for biosensing. This Review examines state‐of‐the‐art methods and advances in the isolation and characterization of small‐molecule‐binding aptamers and their use in various biosensors. Factors limiting aptamer‐based sensors and potential solutions to these issues are also discussed.

Abstract

Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor‐intensive to develop aptamer‐based sensors for small‐molecule detection. Here, we review the challenges and advances in the isolation and characterization of small‐molecule‐binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer–target binding and structure. Afterwards, we discuss various small‐molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer‐based small‐molecule sensors for real‐world applications.

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Synthetic ssDNA aptamers containing a conserved sequence motif that specifically targets the receptor‐binding domain (RBD) of the SARS‐CoV‐2 spike have the capacity to neutralize the virus and prevent host cell infection in vitro, suggesting a new therapeutic approach to treat COVID‐19.

Abstract

The receptor‐binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 spike (S) protein plays a central role in mediating the first step of virus infection to cause disease: virus binding to angiotensin‐converting enzyme 2 (ACE2) receptors on human host cells. Therefore, S/RBD is an ideal target for blocking and neutralization therapies to prevent and treat coronavirus disease 2019 (COVID‐19). Using a target‐based selection approach, we developed oligonucleotide aptamers containing a conserved sequence motif that specifically targets S/RBD. Synthetic aptamers had high binding affinity for S/RBD‐coated virus mimics (KD≈7 nM) and also blocked interaction of S/RBD with ACE2 receptors (IC50≈5 nM). Importantly, aptamers were able to neutralize S protein‐expressing viral particles and prevent host cell infection, suggesting a promising COVID‐19 therapy strategy.

https://ift.tt/2OXODfp

Exosomal glycoproteins play important roles in many physiological and pathological functions. However, the existing methods for studying glycosylation of exosomal proteins of interest are often cumbersome and affect the exosome integrity. Herein, we developed a dual labeling strategy based on a protein-specific aptamer tagging and metabolic glycan labeling for visualizing glycosylation of specific proteins on exosomes. The glycosylation of exosomal PD-L1 (exoPD-L1) was imaged in situ using intramolecular fluorescence resonance energy transfer (FRET) between fluorescent PD-L1 aptamers bound on exoPD-L1 and fluorescent tags on glycans introduced via metabolic glycan labeling. This method enables in situ visualization and biological function study of exosomal protein glycosylation. Through this strategy, exoPD-L1 glycosylation was confirmed for the first time to be required in interaction with PD-1 and participated in inhibiting of CD8+ T cell proliferation. In general, we have developed an efficient and non-destructive method to study the presence and function of exosomal protein-specific glycosylation in situ, which provides a powerful tool for exosomal glycoproteomics research.

https://ift.tt/3oTUksy

Journal of the American Chemical SocietyDOI: 10.1021/jacs.9b10460

Paola Amero, Ganesh L. R. Lokesh, Rajan R. Chaudhari, Roberto Cardenas-Zuniga, Thomas Schubert, Yasmin M. Attia□, Efigenia Montalvo-Gonzalez, Abdelrahman M. Elsayed▼, Cristina Ivan, Zhihui Wang, Vittorio Cristini, Vittorio de Franciscis⬡△, Shuxing Zhang, David E. Volk, Rahul Mitra, Cristian Rodriguez-Aguayo, Anil K. Sood, and Gabriel Lopez-Berestein

https://ift.tt/33KAuWN

SP6 is a DNA aptamer binding to the SARS‐CoV‐2 spike glycoprotein and inhibits pseudovirus infection of cells. As the aptamer does not interfere with the CoV‐2S ACE2 receptor binding domain, it provides an RBD‐independent mechanism of virus inhibition.

Abstract

The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS‐CoV‐2 (CoV2‐S) binds to the human angiotensin‐converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2‐S. The aptamer does not bind to the RBD of CoV2‐S and does not block the interaction of CoV2‐S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS‐CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.

https://ift.tt/3tO40WM

SP6 is a DNA aptamer binding to the SARS‐CoV‐2 spike glycoprotein and inhibits pseudovirus infection of cells. As the aptamer does not interfere with the CoV‐2S ACE2 receptor binding domain, it provides an RBD‐independent mechanism of virus inhibition.

Abstract

The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS‐CoV‐2 (CoV2‐S) binds to the human angiotensin‐converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2‐S. The aptamer does not bind to the RBD of CoV2‐S and does not block the interaction of CoV2‐S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS‐CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.

https://ift.tt/3tO40WM

Here, a tumor–targeting yet enhanced chemotherapy enabled by aptamer–drug conjugate nanomicelles is reported to boost antitumor immune responses. Aptamer–multivalent–drug conjugate (ApMDC), an amphiphilic telodendrimer consisting of a hydrophilic aptamer and a hydrophobic monodendron anchored with four anticancer drugs by acid–labile linkers, is designed and synthesized. By co–self–assembly with an ApMDC analogue, in which aptamer is replaced with polyethylene glycol, surface aptamer density of these nanomicelles can be screened to reach an optimal complementation between blood circulation and tumor–targeting ability. Optimized nanomicelles can enhance immunogenic cell death of tumor cells, which strikingly augments tumor–specific immune responses of checkpoint blockade in immunocompetent tumor–bearing mice. ApMDC nanomicelles represent a robust platform for structure–function optimization of drug conjugates and nanomedicines, suggesting an alternative to improve antitumor efficacy.

https://ift.tt/2RXaAwj