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1. Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition

   Zhou, L; Xiong, Y; Dwivedy, A; Zheng, M; Cooper, L; Shepherd, S; Song, TJ; Hong, W; Le, LTP; Chen, X; et al (November 2024, Science robotics)

   DNA has shown great biocompatibility, programmable mechanical properties, and precise structural addressabil- ity at the nanometer scale, rendering it a material for constructing versatile nanorobots for biomedical applica- tions. Here, we present the design principle, synthesis, and characterization of a DNA nanorobotic hand, called DNA NanoGripper, that contains a palm and four bendable fingers as inspired by naturally evolved human hands, bird claws, and bacteriophages. Each NanoGripper finger consists of three phalanges connected by three rotat- able joints that are bendable in response to the binding of other entities. NanoGripper functions are enabled and driven by the interactions between moieties attached to the fingers and their binding partners. We demonstrate that the NanoGripper can be engineered to effectively interact with and capture nanometer-scale objects, includ- ing gold nanoparticles, gold NanoUrchins, and SARS-CoV-2 virions. With multiple DNA aptamer nanoswitches programmed to generate a fluorescent signal that is enhanced on a photonic crystal platform, the NanoGripper functions as a highly sensitive biosensor that selectively detects intact SARS-CoV-2 virions in human saliva with a limit of detection of ~100 copies per milliliter, providing a sensitivity equal to that of reverse transcription quanti- tative polymerase chain reaction (RT-qPCR). Quantified by flow cytometry assays, we demonstrated that the NanoGripper-aptamer complex can effectively block viral entry into the host cells, suggesting its potential for in- hibiting virus infections. The design, synthesis, and characterization of a sophisticated nanomachine that can be tailored for specific applications highlight a promising pathway toward feasible and efficient solutions to the de- tection and potential inhibition of virus infections. 

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2. Direct detection of human adenovirus or SARS-CoV-2 with ability to inform infectivity using DNA aptamer-nanopore sensors

   https://doi.org/10.1126/sciadv.abh2848  

   Peinetti, Ana S.; Lake, Ryan J.; Cong, Wen; Cooper, Laura; Wu, Yuting; Ma, Yuan; Pawel, Gregory T.; Toimil-Molares, María Eugenia; Trautmann, Christina; Rong, Lijun; et al (September 2021, Science Advances)

   Viral infections are a major global health issue, but no current method allows rapid, direct, and ultrasensitive quantification of intact viruses with the ability to inform infectivity, causing misdiagnoses and spread of the viruses. Here, we report a method for direct detection and differentiation of infectious from noninfectious human adenovirus and SARS-CoV-2, as well as from other virus types, without any sample pretreatment. DNA aptamers are selected from a DNA library to bind intact infectious, but not noninfectious, virus and then incorporated into a solid-state nanopore, which allows strong confinement of the virus to enhance sensitivity down to 1 pfu/ml for human adenovirus and 1 × 10 4 copies/ml for SARS-CoV-2. Applications of the aptamer-nanopore sensors in different types of water samples, saliva, and serum are demonstrated for both enveloped and nonenveloped viruses, making the sensor generally applicable for detecting these and other emerging viruses of environmental and public health concern. 

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3. Rapid and specific detection of intact viral particles using functionalized microslit silicon membranes as a fouling-based sensor

   https://doi.org/10.1039/D1AN01504D  

   Klaczko, Michael E.; Lucas, Kilean; Salminen, Alec T.; McCloskey, Molly C.; Ozgurun, Baturay; Ward, Brian M.; Flax, Jonathan; McGrath, James L. (January 2022, The Analyst)

   The COVID-19 pandemic demonstrated the public health benefits of reliable and accessible point-of-care (POC) diagnostic tests for viral infections. Despite the rapid development of gold-standard reverse transcription polymerase chain reaction (RT-PCR) assays for SARS-CoV-2 only weeks into the pandemic, global demand created logistical challenges that delayed access to testing for months and helped fuel the spread of COVID-19. Additionally, the extreme sensitivity of RT-PCR had a costly downside as the tests could not differentiate between patients with active infection and those who were no longer infectious but still shedding viral genomes. To address these issues for the future, we propose a novel membrane-based sensor that only detects intact virions. The sensor combines affinity and size based detection on a membrane-based sensor and does not require external power to operate or read. Specifically, the presence of intact virions, but not viral debris, fouls the membrane and triggers a macroscopically visible hydraulic switch after injection of a 40 μL sample with a pipette. The device, which we call the μSiM-DX (microfluidic device featuring a silicon membrane for diagnostics), features a biotin-coated microslit membrane with pores ∼2–3× larger than the intact virus. Streptavidin-conjugated antibody recognizing viral surface proteins are incubated with the sample for ∼1 hour prior to injection into the device, and positive/negative results are obtained within ten seconds of sample injection. Proof-of-principle tests have been performed using preparations of vaccinia virus. After optimizing slit pore sizes and porous membrane area, the fouling-based sensor exhibits 100% specificity and 97% sensitivity for vaccinia virus ( n = 62). Moreover, the dynamic range of the sensor extends at least from 10 5.9 virions per mL to 10 10.4 virions per mL covering the range of mean viral loads in symptomatic COVID-19 patients (10 5.6 –10 7 RNA copies per mL). Forthcoming work will test the ability of our sensor to perform similarly in biological fluids and with SARS-CoV-2, to fully test the potential of a membrane fouling-based sensor to serve as a PCR-free alternative for POC containment efforts in the spread of infectious disease. 

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4. Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

   https://doi.org/10.1142/9789811232701_0015  

   Kshirsagar, Meghana; Tasnina, Nure; Ward, Michael D.; Law, Jeffrey N.; Murali, T. M.; Lavista Ferres, Juan M.; Bowman, Gregory R.; Klein-Seetharaman, Judith (November 2020, Pacific Symposium of Biocomputing)

   null (Ed.)

   Viruses such as the novel coronavirus, SARS-CoV-2, that is wreaking havoc on the world, depend on interactions of its own proteins with those of the human host cells. Relatively small changes in sequence such as between SARS-CoV and SARS-CoV-2 can dramatically change clinical phenotypes of the virus, including transmission rates and severity of the disease. On the other hand, highly dissimilar virus families such as Coronaviridae, Ebola, and HIV have overlap in functions. In this work we aim to analyze the role of protein sequence in the binding of SARS-CoV-2 virus proteins towards human proteins and compare it to that of the above other viruses. We build supervised machine learning models, using Generalized Additive Models to predict interactions based on sequence features and find that our models perform well with an AUC-PR of 0.65 in a class-skew of 1:10. Analysis of the novel predictions using an independent dataset showed statistically significant enrichment. We further map the importance of specific amino-acid sequence features in predicting binding and summarize what combinations of sequences from the virus and the host is correlated with an interaction. By analyzing the sequence-based embeddings of the interactomes from different viruses and clustering them together we find some functionally similar proteins from different viruses. For example, vif protein from HIV-1, vp24 from Ebola and orf3b from SARS-CoV all function as interferon antagonists. Furthermore, we can differentiate the functions of similar viruses, for example orf3a’s interactions are more diverged than orf7b interactions when comparing SARS-CoV and SARS-CoV-2. 

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5. Organic Electrochemical Transistors functionalized with Protein Minibinders for Sensitive and Specific Detection of SARS‐CoV‐2

   https://doi.org/10.1002/admi.202202409  

   Huang, Po‐Chun; Zhou, Ying; Porter, Erin B.; Saxena, Ravindra G.; Gomez, Andrea; Ykema, Matthew; Senehi, Naomi L.; Lee, Dongjoo; Tseng, Chia‐Ping; Alvarez, Pedro J.; et al (May 2023, Advanced materials interfaces)

   There is a need for rapid, sensitive, specific, and low-cost virus sensors. Recent work has demonstrated that organic electrochemical transistors (OECTs) can detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Here, a simple and low-cost approach to the fabrication of OECT devices with excellent stability and unprecedented sensitivity and specificity for the detection of SARS-CoV-2 virus is demonstrated. The devices rely on the engineered protein minibinder LCB1, which binds strongly to SARS-CoV-2. The resulting devices exhibit excellent sensitivity for the detection of SARS-CoV-2 virus and SARS-CoV-2 spike protein receptor binding domain (RBD). These results demonstrate a simple, effective, and low-cost biomolecular sensor applicable to the real-time detection of SARS-CoV-2 virus and a general strategy for OECT device design that can be applied for the detection of other pathogenic viruses. 

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