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

Krishnamoorthy, Kurinji; Hoffmann, Kyle; Kewalramani, Sumit; Brodin, Jeffrey D.; Moreau, Liane M.; Mirkin, Chad A.; Olvera de la Cruz, Monica; Bedzyk, Michael J.

doi:10.1021/acscentsci.7b00577

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

Journal Article · Tue Mar 13 00:00:00 EDT 2018 · ACS Central Science

DOI:https://doi.org/10.1021/acscentsci.7b00577· OSTI ID:1425716

Krishnamoorthy, Kurinji ^[1]; Hoffmann, Kyle ^[2]; Kewalramani, Sumit ^[2]; Brodin, Jeffrey D. ^[3]; Moreau, Liane M. ^[2];

^[4]; Olvera de la Cruz, Monica ^[5];

^[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 Chemistry, 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
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
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

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.

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Research Organization:: 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 Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0000989; SC0018093; AC02-06CH11357

OSTI ID:: 1425716

Alternate ID(s):: OSTI ID: 1435811; OSTI ID: 1498699

Journal Information:: ACS Central Science, Journal Name: ACS Central Science Vol. 4 Journal Issue: 3; ISSN 2374-7943

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 23 works

Citation information provided by
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References (39)

Counterion Distribution around DNA Probed by Solution X-Ray Scattering Das, R.; Mills, T. T.; Kwok, L. W. Physical Review Letters, Vol. 90, Issue 18 https://doi.org/10.1103/PhysRevLett.90.188103	journal	May 2003
CHOOCH : a program for deriving anomalous-scattering factors from X-ray fluorescence spectra Evans, Gwyndaf; Pettifer, Robert F. Journal of Applied Crystallography, Vol. 34, Issue 1 https://doi.org/10.1107/S0021889800014655	journal	February 2001
DNA-mediated nanoparticle crystallization into Wulff polyhedra Auyeung, Evelyn; Li, Ting I. N. G.; Senesi, Andrew J. Nature, Vol. 505, Issue 7481 https://doi.org/10.1038/nature12739	journal	November 2013
Collapse of flexible polyelectrolytes in multivalent salt solutions Solis, Francisco J.; de la Cruz, Monica Olvera The Journal of Chemical Physics, Vol. 112, Issue 4 https://doi.org/10.1063/1.480763	journal	January 2000
Spherical Nucleic Acid Nanoparticle Conjugates as an RNAi-Based Therapy for Glioblastoma Jensen, S. A.; Day, E. S.; Ko, C. H. Science Translational Medicine, Vol. 5, Issue 209 https://doi.org/10.1126/scitranslmed.3006839	journal	October 2013
Analysis of the correlation of counterions to rod-like macroions by anomalous small-angle X-ray scattering Patel, M.; Rosenfeldt, S.; Ballauff, M. Physical Chemistry Chemical Physics, Vol. 6, Issue 11 https://doi.org/10.1039/b402155j	journal	January 2004
Probing the extent of the Sr2+ ion condensation to anionic polyacrylate coils: A quantitative anomalous small-angle x-ray scattering study Goerigk, G.; Huber, K.; Schweins, R. The Journal of Chemical Physics, Vol. 127, Issue 15 https://doi.org/10.1063/1.2787008	journal	October 2007
Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion Wang, Mary X.; Brodin, Jeffrey D.; Millan, Jaime A. Nano Letters, Vol. 17, Issue 8 https://doi.org/10.1021/acs.nanolett.7b02502	journal	July 2017
DNA structure: cations in charge? McFail-Isom, Lori; Sines, Chad C.; Williams, Loren Dean Current Opinion in Structural Biology, Vol. 9, Issue 3 https://doi.org/10.1016/S0959-440X(99)80040-2	journal	June 1999
Salt effects on β-glucosidase: pH-profile narrowing Bowers, Erin M.; Ragland, Lindsey O.; Byers, Larry D. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1774, Issue 12 https://doi.org/10.1016/j.bbapap.2007.10.007	journal	December 2007
Nanoparticle Superlattice Engineering with DNA Macfarlane, R. J.; Lee, B.; Jones, M. R. Science, Vol. 334, Issue 6053, p. 204-208 https://doi.org/10.1126/science.1210493	journal	October 2011
CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates Svergun, D.; Barberato, C.; Koch, M. H. J. Journal of Applied Crystallography, Vol. 28, Issue 6 https://doi.org/10.1107/S0021889895007047	journal	December 1995
Ion condensation in salt‐free dilute polyelectrolyte solutions González‐Mozuelos, P.; de la Cruz, M. Olvera The Journal of Chemical Physics, Vol. 103, Issue 8 https://doi.org/10.1063/1.470248	journal	August 1995
Gene Regulation with Polyvalent siRNA−Nanoparticle Conjugates Giljohann, David A.; Seferos, Dwight S.; Prigodich, Andrew E. Journal of the American Chemical Society, Vol. 131, Issue 6 https://doi.org/10.1021/ja808719p	journal	February 2009
Salting the Charged Surface: pH and Salt Dependence of Protein G B1 Stability Lindman, Stina; Xue, Wei-Feng; Szczepankiewicz, Olga Biophysical Journal, Vol. 90, Issue 8 https://doi.org/10.1529/biophysj.105.071050	journal	April 2006
One-Pot Colorimetric Differentiation of Polynucleotides with Single Base Imperfections Using Gold Nanoparticle Probes Storhoff, James J.; Elghanian, Robert; Mucic, Robert C. Journal of the American Chemical Society, Vol. 120, Issue 9 https://doi.org/10.1021/ja972332i	journal	March 1998
IPC – Isoelectric Point Calculator Kozlowski, Lukasz P. Biology Direct, Vol. 11, Issue 1 https://doi.org/10.1186/s13062-016-0159-9	journal	October 2016
The Absolute Calibration of a Small-Angle Scattering Instrument with a Laboratory X-ray Source Fan, Lixin; Degen, Mike; Bendle, Scott Journal of Physics: Conference Series, Vol. 247 https://doi.org/10.1088/1742-6596/247/1/012005	journal	October 2010
DNA-Mediated Cellular Delivery of Functional Enzymes Brodin, Jeffrey D.; Sprangers, Anthony J.; McMillan, Janet R. Journal of the American Chemical Society, Vol. 137, Issue 47 https://doi.org/10.1021/jacs.5b09711	journal	November 2015
Brownian dynamics simulation of diffusion to irregular bodies Sharp, Kim.; Fine, Richard.; Schulten, Klaus. The Journal of Physical Chemistry, Vol. 91, Issue 13 https://doi.org/10.1021/j100297a032	journal	June 1987
Spermine-Induced Aggregation of DNA, Nucleosome, and Chromatin Raspaud, E.; Chaperon, I.; Leforestier, A. Biophysical Journal, Vol. 77, Issue 3 https://doi.org/10.1016/S0006-3495(99)77002-5	journal	September 1999
Local Ionic Environment around Polyvalent Nucleic Acid-Functionalized Nanoparticles Zwanikken, Jos W.; Guo, Peijun; Mirkin, Chad A. The Journal of Physical Chemistry C, Vol. 115, Issue 33 https://doi.org/10.1021/jp205583j	journal	August 2011
Scanometric DNA Array Detection with Nanoparticle Probes Taton, T. A. Science, Vol. 289, Issue 5485 https://doi.org/10.1126/science.289.5485.1757	journal	September 2000
DNA-programmable nanoparticle crystallization Park, Sung Yong; Lytton-Jean, Abigail K. R.; Lee, Byeongdu Nature, Vol. 451, Issue 7178, p. 553-556 https://doi.org/10.1038/nature06508	journal	January 2008
Spatial Distribution of Competing Ions around DNA in Solution Andresen, K.; Das, R.; Park, H. Y. Physical Review Letters, Vol. 93, Issue 24 https://doi.org/10.1103/PhysRevLett.93.248103	journal	December 2004
A structural and dynamic investigation of the inhibition of catalase by nitric oxide Candelaresi, Marco; Gumiero, Andrea; Adamczyk, Katrin Organic & Biomolecular Chemistry, Vol. 11, Issue 44 https://doi.org/10.1039/c3ob41977k	journal	January 2013
DNA‐Inspired Electrostatics Gelbart, William M.; Bruinsma, Robijn F.; Pincus, Philip A. Physics Today, Vol. 53, Issue 9 https://doi.org/10.1063/1.1325230	journal	September 2000
Counterion Distribution around a Spherical Polyelectrolyte Brush Probed by Anomalous Small-Angle X-ray Scattering Dingenouts, N.; Patel, M.; Rosenfeldt, S. Macromolecules, Vol. 37, Issue 21 https://doi.org/10.1021/ma048828j	journal	October 2004
Counterion Distribution Surrounding Spherical Nucleic Acid–Au Nanoparticle Conjugates Probed by Small-Angle X-ray Scattering Kewalramani, Sumit; Zwanikken, Jos W.; Macfarlane, Robert J. ACS Nano, Vol. 7, Issue 12 https://doi.org/10.1021/nn405109z	journal	November 2013
Modulating Nanoparticle Superlattice Structure Using Proteins with Tunable Bond Distributions McMillan, Janet R.; Brodin, Jeffrey D.; Millan, Jaime A. Journal of the American Chemical Society, Vol. 139, Issue 5 https://doi.org/10.1021/jacs.6b11893	journal	January 2017
Counting Ions around DNA with Anomalous Small-Angle X-ray Scattering Pabit, Suzette A.; Meisburger, Steve P.; Li, Li Journal of the American Chemical Society, Vol. 132, Issue 46 https://doi.org/10.1021/ja107259y	journal	November 2010
Reconstitution of Acid-denatured Catalase Samejima, Tatsuya; Yang, Jen Tsi Journal of Biological Chemistry, Vol. 238, Issue 10 https://doi.org/10.1016/S0021-9258(18)48655-3	journal	October 1963
Systematic Limitations in Concentration Analysis via Anomalous Small-Angle X-ray Scattering in the Small Structure Limit Goerigk, Guenter; Lages, Sebastian; Huber, Klaus Polymers, Vol. 8, Issue 3 https://doi.org/10.3390/polym8030085	journal	March 2016
A DNA-based method for rationally assembling nanoparticles into macroscopic materials Mirkin, Chad A.; Letsinger, Robert L.; Mucic, Robert C. Nature, Vol. 382, Issue 6592, p. 607-609 https://doi.org/10.1038/382607a0	journal	August 1996
DNA-mediated engineering of multicomponent enzyme crystals Brodin, Jeffrey D.; Auyeung, Evelyn; Mirkin, Chad A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 15 https://doi.org/10.1073/pnas.1503533112	journal	March 2015
Strong attractions and repulsions mediated by monovalent salts Li, Yaohua; Girard, Martin; Shen, Meng Proceedings of the National Academy of Sciences, Vol. 114, Issue 45 https://doi.org/10.1073/pnas.1713168114	journal	October 2017
Dominant forces in protein folding Dill, Ken A. Biochemistry, Vol. 29, Issue 31 https://doi.org/10.1021/bi00483a001	journal	August 1990
What Controls the Melting Properties of DNA-Linked Gold Nanoparticle Assemblies? Jin, Rongchao; Wu, Guosheng; Li, Zhi Journal of the American Chemical Society, Vol. 125, Issue 6 https://doi.org/10.1021/ja021096v	journal	February 2003
Polyvalent DNA Nanoparticle Conjugates Stabilize Nucleic Acids Seferos, Dwight S.; Prigodich, Andrew E.; Giljohann, David A. Nano Letters, Vol. 9, Issue 1 https://doi.org/10.1021/nl802958f	journal	January 2009