Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein

Chao Wu; Abraham J. Qavi; Austin B. Moyle; Nicole D. Wagner; Asmaa Hachim; Niloufar Kavian; Aidan R. Cole; Joyce Sweeney-Gibbons; Henry W. Rohrs; J. S.Malik Peiris; Christopher F. Basler; Michael L. Gross; Sophie A. Valkenburg; Christopher W. Farnsworth; Gaya K. Amarasinghe; Daisy W. Leung

doi:10.1016/j.xpro.2021.100906

Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein

Chao Wu, Abraham J. Qavi, Austin B. Moyle, Nicole D. Wagner, Asmaa Hachim, Niloufar Kavian, Aidan R. Cole, Joyce Sweeney-Gibbons, Henry W. Rohrs, J. S.Malik Peiris, Christopher F. Basler, Michael L. Gross, Sophie A. Valkenburg, Christopher W. Farnsworth, Gaya K. Amarasinghe, Daisy W. Leung

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Abstract

Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).

Original language	English
Article number	100906
Journal	STAR Protocols
Volume	2
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2021.100906
State	Published - Dec 17 2021

Keywords

Biophysics
Clinical Protocol
Health Sciences
Immunology
Mass Spectrometry
Microbiology
Microscopy
Molecular Biology
Protein Biochemistry
Protein expression and purification
Structural Biology

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10.1016/j.xpro.2021.100906

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Wu, C., Qavi, A. J., Moyle, A. B., Wagner, N. D., Hachim, A., Kavian, N., Cole, A. R., Sweeney-Gibbons, J., Rohrs, H. W., Peiris, J. S. M., Basler, C. F., Gross, M. L., Valkenburg, S. A., Farnsworth, C. W., Amarasinghe, G. K., & Leung, D. W. (2021). Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein. STAR Protocols, 2(4), Article 100906. https://doi.org/10.1016/j.xpro.2021.100906

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title = "Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein",

abstract = "Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).",

keywords = "Biophysics, Clinical Protocol, Health Sciences, Immunology, Mass Spectrometry, Microbiology, Microscopy, Molecular Biology, Protein Biochemistry, Protein expression and purification, Structural Biology",

author = "Chao Wu and Qavi, {Abraham J.} and Moyle, {Austin B.} and Wagner, {Nicole D.} and Asmaa Hachim and Niloufar Kavian and Cole, {Aidan R.} and Joyce Sweeney-Gibbons and Rohrs, {Henry W.} and Peiris, {J. S.Malik} and Basler, {Christopher F.} and Gross, {Michael L.} and Valkenburg, {Sophie A.} and Farnsworth, {Christopher W.} and Amarasinghe, {Gaya K.} and Leung, {Daisy W.}",

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year = "2021",

month = dec,

day = "17",

doi = "10.1016/j.xpro.2021.100906",

language = "English",

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Wu, C, Qavi, AJ, Moyle, AB, Wagner, ND, Hachim, A, Kavian, N, Cole, AR, Sweeney-Gibbons, J, Rohrs, HW, Peiris, JSM, Basler, CF, Gross, ML, Valkenburg, SA, Farnsworth, CW , Amarasinghe, GK & Leung, DW 2021, 'Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein', STAR Protocols, vol. 2, no. 4, 100906. https://doi.org/10.1016/j.xpro.2021.100906

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T1 - Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein

AU - Wu, Chao

AU - Qavi, Abraham J.

AU - Moyle, Austin B.

AU - Wagner, Nicole D.

AU - Hachim, Asmaa

AU - Kavian, Niloufar

AU - Cole, Aidan R.

AU - Sweeney-Gibbons, Joyce

AU - Rohrs, Henry W.

AU - Peiris, J. S.Malik

AU - Basler, Christopher F.

AU - Gross, Michael L.

AU - Valkenburg, Sophie A.

AU - Farnsworth, Christopher W.

AU - Amarasinghe, Gaya K.

AU - Leung, Daisy W.

PY - 2021/12/17

Y1 - 2021/12/17

N2 - Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).

AB - Nucleocapsid proteins are essential for SARS-CoV-2 life cycle. Here, we describe protocols to gather domain-specific insights about essential properties of nucleocapsids. These assays include dynamic light scattering to characterize oligomerization, fluorescence polarization to quantify RNA binding, hydrogen-deuterium exchange mass spectrometry to map RNA binding regions, negative-stain electron microscopy to visualize oligomeric species, interferon reporter assay to evaluate interferon signaling modulation, and a serology assay to reveal insights for improved sensitivity and specificity. These assays are broadly applicable to RNA-encapsidated nucleocapsids. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).

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KW - Clinical Protocol

KW - Health Sciences

KW - Immunology

KW - Mass Spectrometry

KW - Microbiology

KW - Microscopy

KW - Molecular Biology

KW - Protein Biochemistry

KW - Protein expression and purification

KW - Structural Biology

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VL - 2

JO - STAR Protocols

JF - STAR Protocols

IS - 4

M1 - 100906

ER -

Domain-specific biochemical and serological characterization of SARS-CoV-2 nucleocapsid protein

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