In Silico discovery of aptamers with an enhanced library design strategy

Chen, Long; Zhang, Bibi; Wu, Zengrui; Liu, Guixia; Li, Weihua; Tang, Yun

doi:10.1016/j.csbj.2023.01.002

Cited by 11 publications

(6 citation statements)

References 47 publications

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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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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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“…The SELEX process offers considerable potential for the utilisation of in silico methods [54], which are based on the knowledge that the specific structure of the aptamer will bind the given target ligand. In order to achieve this, it is necessary to sequence a wide range of structures that are able to bind ligands and to reveal the principles of relationships between the structure of aptamers and their binding capabilities.…”

Section: Separation Of Amplified Aptamersmentioning

confidence: 99%

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Domsicova,

Korcekova,

Poturnayova

et al. 2024

IJMS

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Aptamers are short oligonucleotides with single-stranded regions or peptides that recently started to transform the field of diagnostics. Their unique ability to bind to specific target molecules with high affinity and specificity is at least comparable to many traditional biorecognition elements. Aptamers are synthetically produced, with a compact size that facilitates deeper tissue penetration and improved cellular targeting. Furthermore, they can be easily modified with various labels or functional groups, tailoring them for diverse applications. Even more uniquely, aptamers can be regenerated after use, making aptasensors a cost-effective and sustainable alternative compared to disposable biosensors. This review delves into the inherent properties of aptamers that make them advantageous in established diagnostic methods. Furthermore, we will examine some of the limitations of aptamers, such as the need to engage in bioinformatics procedures in order to understand the relationship between the structure of the aptamer and its binding abilities. The objective is to develop a targeted design for specific targets. We analyse the process of aptamer selection and design by exploring the current landscape of aptamer utilisation across various industries. Here, we illuminate the potential advantages and applications of aptamers in a range of diagnostic techniques, with a specific focus on quartz crystal microbalance (QCM) aptasensors and their integration into the well-established ELISA method. This review serves as a comprehensive resource, summarising the latest knowledge and applications of aptamers, particularly highlighting their potential to revolutionise diagnostic approaches.

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“…A Study to Establish the Safety and Tolerability of Zimura ® in Catuogno and Esposito, 2017;Kohlberger and Gadermaier, 2022;Chen et al, 2023). The first aptamer for therapeutic use in humans, pegaptanib, was approved in 2004 by the FDA for use in wet agerelated macular degeneration (Takeda et al, 2007).…”

Section: Study Title Patient Population Intervention Metric Outcome S...mentioning

confidence: 99%

“…The methodology known as Systematic Evolution of Ligands by Exponential enrichment (SELEX), invented around 1990, is a technique used to identify specific oligonucleotides with high affinity and selectivity for their target ( Ellington and Szostak, 1990 ; Tuerk and Gold, 1990 ). The advances of SELEX technology has led to more efficient and cost-effective development of specific and stable aptamers ( Darmostuk et al, 2015 ; Guo et al, 2008 ; Catuogno and Esposito, 2017 ; Kohlberger and Gadermaier, 2022 ; Chen et al, 2023 ). The first aptamer for therapeutic use in humans, pegaptanib, was approved in 2004 by the FDA for use in wet age-related macular degeneration ( Takeda et al, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

“…Unmodified aptamers are highly susceptible to degradation in serum but conjugated (polyethylene glycol or cholesterol) aptamers rather have increased the circulating half-life and nuclease resistance ( Kang et al, 2007 ). Aptamer technologies have been optimized for activity and persistence under physiological conditions during selection ( Guo et al, 2008 ; Catuogno and Esposito, 2017 ; Kohlberger and Gadermaier, 2022 ; Chen et al, 2023 ). Advancements in aptamer research have allowed sensitive pH responses to enhance control over molecular devices, and improve their diagnostic and therapeutic efficacy ( Wilson et al, 2019 ; Thompson et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Anti-nucleolin aptamer AS1411: an advancing therapeutic

Van den Avont,

Sharma-Walia

2023

Front. Mol. Biosci.

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Targeted therapy is highly desirable, as it allows for selective cytotoxicity on diseased cells without off-target side effects. Nucleolin is a remarkable target for cancer therapy given its high abundance, selective presence on the plasma membrane, and multifaceted influence on the initiation and progression of cancer. Nucleolin is a protein overexpressed on the cell membrane in many tumors and serves as a binding protein for several ligands implicated in angiogenesis and tumorigenesis. Nucleolin is present in the cytoplasm, nucleoplasm, and nucleolus and is used by selected pathogens for cell entry. AS1411 is a guanosine-rich oligonucleotide aptamer that binds nucleolin and is internalized in the tumor cells. AS1411 is well tolerated at therapeutic doses and localizes to tumor cells overexpressing nucleolin. AS1411 has a good safety profile with efficacy in relapsed acute myeloid leukemia and renal cell carcinoma producing mild or moderate side effects. The promising potential of AS1411 is its ability to be conjugated to drugs and nanoparticles. When a drug is bound to AS1411, the drug will localize to tumor cells leading to targeted therapy with fewer systemic side effects than traditional practices. AS1411 can also be bound to nanoparticles capable of detecting nucleolin at concentrations far lower than lab techniques used today for cancer diagnosis. AS1411 has a promising potential to change cancer diagnoses and treatment.

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In Silico discovery of aptamers with an enhanced library design strategy

Cited by 11 publications

References 47 publications

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

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

New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers

Anti-nucleolin aptamer AS1411: an advancing therapeutic

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