Recent advancement of light‐based single‐molecule approaches for studying biomolecules

Croop, Benjamin; Zhang, Chenyi; Lim, Youn Hee; Gelfand, Ryan M.; Han, Kyu Young

doi:10.1002/wsbm.1445

Cited by 4 publications

(4 citation statements)

References 135 publications

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“…These results indicate that the sensitivity of S2-78 IgG might be further evaluated when increasing the antigen concentration or adopting more sensitive platforms for detection, such as electrochemical platforms or single-molecule detection technologies. 31,32 In fact, we also performed S1-based ELISAs using a commercial kit with the same set of samples, and the overall performance of the S2-78 IgGbased ELISA was comparable to that of the commercial kits (data not shown).…”

Section: Discussionmentioning

confidence: 87%

Systematic evaluation of IgG responses to SARS-CoV-2 spike protein-derived peptides for monitoring COVID-19 patients

Lai

Lei

et al. 2021

Cell Mol Immunol

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Serological tests play an essential role in monitoring and combating the COVID-19 pandemic. Recombinant spike protein (S protein), especially the S1 protein, is one of the major reagents used for serological tests. However, the high cost of S protein production and possible cross-reactivity with other human coronaviruses pose unavoidable challenges. By taking advantage of a peptide microarray with full spike protein coverage, we analyzed 2,434 sera from 858 COVID-19 patients, 63 asymptomatic patients and 610 controls collected from multiple clinical centers. Based on the results, we identified several S protein-derived 12-mer peptides that have high diagnostic performance. In particular, for monitoring the IgG response, one peptide (aa 1148–1159 or S2–78) exhibited a sensitivity (95.5%, 95% CI 93.7–96.9%) and specificity (96.7%, 95% CI 94.8–98.0%) comparable to those of the S1 protein for the detection of both symptomatic and asymptomatic COVID-19 cases. Furthermore, the diagnostic performance of the S2–78 (aa 1148–1159) IgG was successfully validated by ELISA in an independent sample cohort. A panel of four peptides, S1–93 (aa 553–564), S1–97 (aa 577–588), S1–101 (aa 601–612) and S1–105 (aa 625–636), that likely will avoid potential cross-reactivity with sera from patients infected by other coronaviruses was constructed. The peptides identified in this study may be applied independently or in combination with the S1 protein for accurate, affordable, and accessible COVID-19 diagnosis.

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Section: Discussionmentioning

confidence: 87%

Systematic evaluation of IgG responses to SARS-CoV-2 spike protein-derived peptides for monitoring COVID-19 patients

Lai

Lei

et al. 2021

Cell Mol Immunol

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“…However, because it is hard to ensure extremely high purity when purifying recombinant proteins, the background of S1 IgG for control group is also higher than that of peptides. These results imply the sensitivity of S2-78 IgG might be further evaluated when raise the antigen concentration or adopt a more sensitive platform for detection, such as electrochemical platform or single-molecule detection technologies[28,29]. Indeed, we also performed S1 based ELISA assay by a commercial kit with the same set of samples, the overall performance of S2-78 IgG based ELISA is comparable to that of the commercial kits (data not shown).…”

Section: Discussionmentioning

confidence: 76%

Systematic evaluation of SARS-CoV-2 spike protein derived peptides for diagnosis of COVID-19 patients

Li¹,

Lai

Lei

et al. 2020

Preprint

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Serological test plays an essential role in monitoring and combating COVID-19 pandemic. Recombinant spike protein (S protein), especially S1 protein is one of the major reagents for serological tests. However, the high cost in production of S protein, and the possible cross-reactivity with other human coronaviruses poses unneglectable challenges. Taking advantage of a peptide microarray of full spike protein coverage, we analyzed 2,434 sera from 858 COVID-19 patients, sera from 63 asymptomatic patients and 610 controls collected from multiple clinical centers. Based on the results of the peptide microarray, we identified several S protein derived 12-mer peptides that have high diagnosis performance. Particularly, for monitoring IgG response, one peptide (aa 1148-1159 or S2-78) has a comparable sensitivity (95.5%, 95% CI 93.7-96.9%) and specificity (96.7%, 95% CI 94.8-98.0%) to that of S1 protein for detection of both COVID-19 patients and asymptomatic infections. Furthermore, the performance of S2-78 IgG for diagnosis was successfully validated by ELISA with an independent sample cohort. By combining S2-78/ S1 with other peptides, a two-step strategy was proposed to ensure both the sensitivity and specificity of S protein based serological assay. The peptide/s identified in this study could be applied independently or in combination with S1 protein for accurate, affordable, and accessible COVID-19 diagnosis.

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“…This level of detail is obscured in ensemble studies by dephasing processes. Over the past few decades, a large number of biological systems have been the subject of study with single-molecule techniques. − Due to technical limitations of these approaches, the majority of these studies have focused on individual, purified proteins in idealized chemical environments. Many early single-molecule assays used forced-based techniques, often tracking one DNA molecule at a time.…”

Section: Technological Advancesmentioning

confidence: 99%

Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines

Lewis,

van Oijen,

Spenkelink

2023

Chem. Rev.

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The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein–nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.

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Recent advancement of light‐based single‐molecule approaches for studying biomolecules

Cited by 4 publications

References 135 publications

Systematic evaluation of IgG responses to SARS-CoV-2 spike protein-derived peptides for monitoring COVID-19 patients

Systematic evaluation of IgG responses to SARS-CoV-2 spike protein-derived peptides for monitoring COVID-19 patients

Systematic evaluation of SARS-CoV-2 spike protein derived peptides for diagnosis of COVID-19 patients

Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines

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