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Title: Defining the Structure of a Protein–Spherical Nucleic Acid Conjugate and Its Counterionic Cloud

Abstract

Protein–spherical nucleic acid conjugates (Pro-SNAs) are an emerging class of bioconjugates that have properties defined by their protein cores and dense shell of oligonucleotides. They have been used as building blocks in DNA-driven crystal engineering strategies and show promise as agents that can cross cell membranes and affect both protein and DNA-mediated processes inside cells. However, ionic environments surrounding proteins can influence their activity and conformational stability, and functionalizing proteins with DNA substantively changes the surrounding ionic environment in a nonuniform manner. Techniques typically used to determine protein structure fail to capture such irregular ionic distributions. Here, we determine the counterion radial distribution profile surrounding Pro-SNAs dispersed in RbCl with 1 nm resolution through in situ anomalous small-angle X-ray scattering (ASAXS) and classical density functional theory (DFT). SAXS analysis also reveals the radial extension of the DNA and the linker used to covalently attach the DNA to the protein surface. At the experimental salt concentration of 50 mM RbCl, Rb+ cations compensate ~90% of the negative charge due to the DNA and linker. Above 75 mM, DFT calculations predict overcompensation of the DNA charge by Rb+. This study suggests a method for exploring Pro-SNA structure and function in different environmentsmore » through predictions of ionic cloud densities as a function of salt concentration, DNA grafting density, and length. Overall, our study demonstrates that solution X-ray scattering combined with DFT can discern counterionic distribution and submolecular features of highly charged, complex nanoparticle constructs such as Pro-SNAs and related nucleic acid conjugate materials.« less

Authors:
 [1];  [2];  [2];  [3];  [2]; ORCiD logo [4];  [5]; ORCiD logo [6]
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  1. Applied Physics Program, Northwestern University, Evanston, Illinois 60208, United States
  2. Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
  3. Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
  4. Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
  5. Applied Physics Program, Northwestern University, Evanston, Illinois 60208, United States, Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States, Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
  6. Applied Physics Program, Northwestern University, Evanston, Illinois 60208, United States, Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States, Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, United States
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Bio-Inspired Energy Science (CBES); Argonne National Laboratory (ANL), Argonne, IL (United States); Northwestern Univ., Evanston, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1425716
Alternate Identifier(s):
OSTI ID: 1435811; OSTI ID: 1498699
Grant/Contract Number:  
SC0000989; SC0018093; AC02-06CH11357
Resource Type:
Published Article
Journal Name:
ACS Central Science
Additional Journal Information:
Journal Name: ACS Central Science Journal Volume: 4 Journal Issue: 3; Journal ID: ISSN 2374-7943
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 36 MATERIALS SCIENCE

Citation Formats

Krishnamoorthy, Kurinji, Hoffmann, Kyle, Kewalramani, Sumit, Brodin, Jeffrey D., Moreau, Liane M., Mirkin, Chad A., Olvera de la Cruz, Monica, and Bedzyk, Michael J. Defining the Structure of a Protein–Spherical Nucleic Acid Conjugate and Its Counterionic Cloud. United States: N. p., 2018. Web. doi:10.1021/acscentsci.7b00577.
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Krishnamoorthy, Kurinji, Hoffmann, Kyle, Kewalramani, Sumit, Brodin, Jeffrey D., Moreau, Liane M., Mirkin, Chad A., Olvera de la Cruz, Monica, & Bedzyk, Michael J. Defining the Structure of a Protein–Spherical Nucleic Acid Conjugate and Its Counterionic Cloud. United States. https://doi.org/10.1021/acscentsci.7b00577
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Krishnamoorthy, Kurinji, Hoffmann, Kyle, Kewalramani, Sumit, Brodin, Jeffrey D., Moreau, Liane M., Mirkin, Chad A., Olvera de la Cruz, Monica, and Bedzyk, Michael J. Tue . "Defining the Structure of a Protein–Spherical Nucleic Acid Conjugate and Its Counterionic Cloud". United States. https://doi.org/10.1021/acscentsci.7b00577.
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@article{osti_1425716,
title = {Defining the Structure of a Protein–Spherical Nucleic Acid Conjugate and Its Counterionic Cloud},
author = {Krishnamoorthy, Kurinji and Hoffmann, Kyle and Kewalramani, Sumit and Brodin, Jeffrey D. and Moreau, Liane M. and Mirkin, Chad A. and Olvera de la Cruz, Monica and Bedzyk, Michael J.},
abstractNote = {Protein–spherical nucleic acid conjugates (Pro-SNAs) are an emerging class of bioconjugates that have properties defined by their protein cores and dense shell of oligonucleotides. They have been used as building blocks in DNA-driven crystal engineering strategies and show promise as agents that can cross cell membranes and affect both protein and DNA-mediated processes inside cells. However, ionic environments surrounding proteins can influence their activity and conformational stability, and functionalizing proteins with DNA substantively changes the surrounding ionic environment in a nonuniform manner. Techniques typically used to determine protein structure fail to capture such irregular ionic distributions. Here, we determine the counterion radial distribution profile surrounding Pro-SNAs dispersed in RbCl with 1 nm resolution through in situ anomalous small-angle X-ray scattering (ASAXS) and classical density functional theory (DFT). SAXS analysis also reveals the radial extension of the DNA and the linker used to covalently attach the DNA to the protein surface. At the experimental salt concentration of 50 mM RbCl, Rb+ cations compensate ~90% of the negative charge due to the DNA and linker. Above 75 mM, DFT calculations predict overcompensation of the DNA charge by Rb+. This study suggests a method for exploring Pro-SNA structure and function in different environments through predictions of ionic cloud densities as a function of salt concentration, DNA grafting density, and length. Overall, our study demonstrates that solution X-ray scattering combined with DFT can discern counterionic distribution and submolecular features of highly charged, complex nanoparticle constructs such as Pro-SNAs and related nucleic acid conjugate materials.},
doi = {10.1021/acscentsci.7b00577},
journal = {ACS Central Science},
number = 3,
volume = 4,
place = {United States},
year = {Tue Mar 13 00:00:00 EDT 2018},
month = {Tue Mar 13 00:00:00 EDT 2018}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acscentsci.7b00577
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Cited by: 23 works
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Figures / Tables:

Figure 1 Figure 1: Schematic illustration of Cg catalase functionalized with 18 base long ss-DNA strands. Each strand is composed of a linker region (L) composed of an NHS-PEG4-azide moiety and a DBCO dT group covalently anchoring the DNA to the protein surface (inset).
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