CRISPR-Mediated Isogenic Cell-SELEX Approach for Generating Highly Specific Aptamers Against Native Membrane Proteins

Rosch, Jonah C.; Neal, Emma H.; Balikov, Daniel A.; Rahim, Mohsin; Lippmann, Ethan S.

doi:10.1007/s12195-020-00651-y

Cited by 16 publications

(12 citation statements)

References 35 publications

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“…For example, we recently described a cell-SELEX strategy to generate aptamers that can discriminate membrane receptor homologs on the surface of living cells 35 , which could be extended here to preferentially target and retain multifaceted nucleic acid nanostructures within different tissue compartments. This strategy could be particularly powerful in solid tumors, where we have shown preferential penetration and gene silencing of albumin-binding nanocomplexes 8 , which could potentially be augmented by using aptamers that bind receptors that are overexpressed or mutated on the surface of the cancer cells.…”

Section: Discussionmentioning

confidence: 99%

Albumin-binding Aptamer Chimeras for Improved siRNA Bioavailability

et al. 2021

Preprint

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Short interfering RNAs (siRNAs) are potent nucleic acid-based drugs designed to target disease driving genes that may otherwise be undruggable with small molecules. However, the potential of administering therapeutic siRNA in vivo is limited by poor pharmacokinetic properties, including rapid renal clearance and nuclease degradation. Nanocarriers have traditionally been explored as means to overcome these challenges, but they have intrinsic downsides such as dose-limiting toxicity and synthetic complexity. Backpacking on natural carriers such as albumin, which is present at high concentration and has a long half-life in serum, is an effective way to modify pharmacokinetics of biologic drugs that otherwise have poor bioavailability. In this work, we sought to develop albumin-binding aptamer-siRNA chimeras to improve the bioavailability of siRNA. We used a Systematic Evolution of Ligands through Exponential Enrichment (SELEX) approach to obtain RNA aptamers with modified bases that bind albumin with high affinity. We then fused the aptamers directly to an siRNA to generate the chimera structure. These aptamer-siRNA chimeras are stable in serum, exhibit potent gene knockdown capabilities in vitro, and display extended circulation time in vivo. We suggest that this albumin-binding aptamer-siRNA chimera approach is a promising strategy for drug delivery applications.

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Section: Discussionmentioning

confidence: 99%

Albumin-binding Aptamer Chimeras for Improved siRNA Bioavailability

et al. 2021

Preprint

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“…RNA structure is a key determinant of its diverse biological functions. − Therefore, creating RNA molecules with specific structures and functions is of great value to research, where computational methods for modeling RNA secondary structures come in handy. Thus far, this approach has been utilized for synthetic biology and biotechnology applications to design RNA-based devices, including riboregulators, ,,− aptamers, − and CRISPR guides. − Current advanced approaches for in-silico RNA design rely on free energy minimization algorithms, which estimate the thermodynamic stability of different structures. − To enhance the prediction accuracy, some methods also incorporate experimental mapping data or structural conservation information from a set of homologous sequences. − Several prominent software tools have been developed for in-silico RNA design based on these approaches, including but not limited to NUPACK, RNAstructure, ViennaRNA, UNAfold, and the deep-learning framework. These tools offer a variety of features, such as analysis, prediction, comparison, and synthesis of nucleic acid structures and interactions, each with its own advantages and drawbacks.…”

Section: Modelingmentioning

confidence: 99%

RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics

Koksaldi,

Park,

Atilla

et al. 2024

ACS Synth. Biol.

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In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.

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“…Depending on the integration methods of SELEX, several SELEX methods have emerged for preferred aptamer selection, including cell-SELEX, microfluidic-SELEX, capillary electrophoresis-SELEX methods, etc. [ 62 , 63 ]. In our group, we obtained the aptamer specific against antibiotic penicillin (PenG) via graphene oxide (MAX)-SELEX method described in Figure 4 B [ 60 ].…”

Section: Mxene In Na Biosensorsmentioning

confidence: 99%

MXene-Based Nucleic Acid Biosensors for Agricultural and Food Systems

Wang

Gunasekaran

2022

Biosensors

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MXene is a two-dimensional (2D) nanomaterial that exhibits several superior properties suitable for fabricating biosensors. Likewise, the nucleic acid (NA) in oligomerization forms possesses highly specific biorecognition ability and other features amenable to biosensing. Hence the combined use of MXene and NA is becoming increasingly common in biosensor design and development. In this review, MXene- and NA-based biosensors are discussed in terms of their sensing mechanisms and fabrication details. MXenes are introduced from their definition and synthesis process to their characterization followed by their use in NA-mediated biosensor fabrication. The emphasis is placed on the detection of various targets relevant to agricultural and food systems, including microbial pathogens, chemical toxicants, heavy metals, organic pollutants, etc. Finally, current challenges and future perspectives are presented with an eye toward the development of advanced biosensors with improved detection performance.

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CRISPR-Mediated Isogenic Cell-SELEX Approach for Generating Highly Specific Aptamers Against Native Membrane Proteins

Cited by 16 publications

References 35 publications

Albumin-binding Aptamer Chimeras for Improved siRNA Bioavailability

Albumin-binding Aptamer Chimeras for Improved siRNA Bioavailability

RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics

MXene-Based Nucleic Acid Biosensors for Agricultural and Food Systems

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