A Sequential Multidimensional Analysis Algorithm for Aptamer Identification based on Structure Analysis and Machine Learning

Song, Jia; Zheng, Yuan F.; Huang, Mengjiao; Wu, Lingling; Wang, Wei; Zhu, Zhi; Song, Yanling; Yang, Chaoyong

doi:10.1021/acs.analchem.9b05203

Cited by 49 publications

(45 citation statements)

References 34 publications

(56 reference statements)

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“…SMART-Aptamer V2.0. SMART-Aptamer V2.0 was developed based on SMART-Aptamer V1.0 13 by redefining the MDA-score in the multidimensional evaluation process. After clustering the aptamer family based on the BLAST all-vs-all and MCL (Markov 227 Cluster) system, we characterized the variation of family size across the sequenced SELEX pools.…”

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confidence: 99%

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

Song¹,

Song²,

Wei³

et al. 2020

Preprint

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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 K<sub>d</sub> values of the optimized CoV2-RBD-1C and <a>CoV2-RBD-</a>4C aptamers against RBD were 5.8 nM and 19.9 nM, respectively. Simulated interaction modeling, along with competitive with 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.

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confidence: 99%

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

Song¹,

Song²,

Wei³

et al. 2020

Preprint

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“…[17a, 20d] Thus,i tc an also be expanded to more complex operations for more advanced cell-specific modulations. Moreover,S UDAsc ell-selectivity is realized by leveraging the switchable aptamer-based modulation of ligand-receptor interactions.A dvanced orthogonal designs can be created to control distinct cellular behaviors by replacing the DNA-lock module for designated ligands with scalability in future cellbased applications.I nt his study,t he potencyo ft he SUDA design has been demonstrated by the physiological levels for wound healing and programmed cell death by modulating HGF and TNFa,r espectively.R ecent machine learningassisted aptamer screening techniques are expected to increase the repertories of both aptamer-based TAGmodules and LOCK modules, [38] generating more tailored SUDAs for cell manipulations.T hus,a dvanced modular designing based on this approach could significantly improve the capacity and efficiency of the intelligent prototypes for bio-computational control over cellular behaviors.H owever,t he most critical challenges in the translation of the SUDAm ethod from in vitro to in vivo applications include serological stability against nuclease degradation and the in vivo dose-distribution profiles,w hich hinders the efficient delivery of the DNAbased modules to the target tissues.Chemical modification of the oligonucleotides might significantly increase the stability, providing apossible solution for future clinical translation. In addition, the SUDAsp erformance depends on the collaborative operation of multiple DNA-based modules in the DNA circuit.…”

Section: Resultsmentioning

confidence: 99%

Scan and Unlock: A Programmable DNA Molecular Automaton for Cell‐Selective Activation of Ligand‐Based Signaling

et al. 2021

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Selective modulation of ligand–receptor interaction is essential in targeted therapy. In this study, we design an intelligent “scan and unlock” DNA automaton (SUDA) system to equip a native protein‐ligand with cell‐identity recognition and receptor‐mediated signaling in a cell‐type‐specific manner. Using embedded DNA‐based chemical reaction networks (CRNs) on the cell surface, SUDA scans and evaluates molecular profiles of cell‐surface proteins via Boolean logic circuits. Therefore, it achieves cell‐specific signal modulation by quickly unlocking the protein‐ligand in proximity to the target cell‐surface to activate its cognate receptor. As a proof of concept, we non‐genetically engineered hepatic growth factor (HGF) with distinct logic SUDAs to elicit target cell‐specific HGF signaling and wound healing behaviors in multiple heterogeneous cell types. Furthermore, the versatility of the SUDA strategy was shown by engineering tumor necrotic factor‐α (TNFα) to induce programmed cell death of target cell subpopulations through cell‐specific modulation of TNFR1 signaling.

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“…For example, aptamers against specific biomarkers on bacteria/viruses, such as lipopolysaccharides (components of the membranes of Gram-negative bacteria) [21], hepatitis B surface antigen (HBsAg) [26], SARS-CoV spike protein [32], and proteins related with infection and assembly, such as hemagglutinin of the H9N2 avian influenza virus (adhering the sialic acid receptors on surfaces of host cells) [35] and HCV core protein (participating in virus assembly) [30], were obtained. In order to improve selection efficiency, an innovative selection technology based on microfluidic technology [36] and artificial intelligence [36,37] has been developed. Hong et al [38] proposed a microfluidic chip based on magnetic separation, which combined the cleaning process, operation of micromagnetic beads, and real-time evaluation of the screening effect.…”

Section: G4 Peroxidase Dnazyme Ps2m T a C Gmentioning

confidence: 99%

Selection and applications of functional nucleic acids for infectious disease detection and prevention

et al. 2021

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Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial-and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.

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A Sequential Multidimensional Analysis Algorithm for Aptamer Identification based on Structure Analysis and Machine Learning

Cited by 49 publications

References 34 publications

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

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

Scan and Unlock: A Programmable DNA Molecular Automaton for Cell‐Selective Activation of Ligand‐Based Signaling

Selection and applications of functional nucleic acids for infectious disease detection and prevention

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