Multi-shell model of ion-induced nucleic acid condensation

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Baker, Nathan A.; Onufriev, Alexey V.

doi:10.1063/1.4945382

Title: Multi-shell model of ion-induced nucleic acid condensation

Journal Article · Thu Apr 21 00:00:00 EDT 2016 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4945382· OSTI ID:22660860

Tolokh, Igor S. ^[1]; Drozdetski, Aleksander V. ^[2]; Pollack, Lois ^[3]; Baker, Nathan A. ^[4]; Onufriev, Alexey V. ^[1]

Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States)
Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States)
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853-3501 (United States)
Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into “external” and “internal” ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the “external” shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the “internal” shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent “ion binding shells.”.

Cite

Export

Save

OSTI ID:: 22660860

Journal Information:: Journal of Chemical Physics, Vol. 144, Issue 15; Other Information: (c) 2016 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9606

Country of Publication:: United States

Language:: English

References (88)

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA Stigter, Dirk Biopolymers, Vol. 46, Issue 7 https://doi.org/10.1002/(sici)1097-0282(199812)46:7<503::aid-bip8>3.0.co;2-v	journal	December 1998
Interaction between parallel rodlike macroions Oosawa, Fumio Biopolymers, Vol. 6, Issue 11 https://doi.org/10.1002/bip.1968.360061108	journal	November 1968
Interactions of highly charged colloidal cylinders with applications to double-stranded DNA Stigter, Dirk Biopolymers, Vol. 16, Issue 7 https://doi.org/10.1002/bip.1977.360160705	journal	July 1977
The electrostatic potential of B-DNA Jayaram, B.; Sharp, Kim A.; Honig, Barry Biopolymers, Vol. 28, Issue 5 https://doi.org/10.1002/bip.360280506	journal	May 1989
Condensation of DNA by multivalent cations: Considerations on mechanism Bloomfield, Victor A. Biopolymers, Vol. 31, Issue 13 https://doi.org/10.1002/bip.360311305	journal	November 1991
Empirical force fields for biological macromolecules: Overview and issues Mackerell, Alexander D. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20082	journal	January 2004
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism 1 1Edited by I. Tinoco Matulis, Daumantas; Rouzina, Ioulia; Bloomfield, Victor A. Journal of Molecular Biology, Vol. 296, Issue 4 https://doi.org/10.1006/jmbi.1999.3470	journal	March 2000
DNA condensation with polyamines Gosule, Leonard C.; Schellman, John A. Journal of Molecular Biology, Vol. 121, Issue 3 https://doi.org/10.1016/0022-2836(78)90366-2	journal	May 1978
Cation-induced toroidal condensation of DNA Widom, Jonathan; Baldwin, Robert L. Journal of Molecular Biology, Vol. 144, Issue 4 https://doi.org/10.1016/0022-2836(80)90330-7	journal	December 1980
Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation Kornyshev, Alexei A.; Leikin, Sergey Biophysical Journal, Vol. 104, Issue 9 https://doi.org/10.1016/j.bpj.2013.03.033	journal	May 2013
Ion Competition in Condensed DNA Arrays in the Attractive Regime Qiu, Xiangyun; Giannini, John; Howell, Steven C. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.004	journal	August 2013
Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements Meisburger, Steve P.; Pabit, Suzette A.; Pollack, Lois Biophysical Journal, Vol. 108, Issue 12 https://doi.org/10.1016/j.bpj.2015.05.006	journal	June 2015
The Assembly Pathway of an Icosahedral Single-Stranded RNA Virus Depends on the Strength of Inter-Subunit Attractions Garmann, Rees F.; Comas-Garcia, Mauricio; Gopal, Ajaykumar Journal of Molecular Biology, Vol. 426, Issue 5 https://doi.org/10.1016/j.jmb.2013.10.017	journal	March 2014
Electrostatic interactions in strongly coupled soft matter Naji, Ali; Jungblut, Swetlana; Moreira, André G. Physica A: Statistical Mechanics and its Applications, Vol. 352, Issue 1 https://doi.org/10.1016/j.physa.2004.12.029	journal	July 2005
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy Swanson, Jessica M. J.; Henchman, Richard H.; McCammon, J. Andrew Biophysical Journal, Vol. 86, Issue 1 https://doi.org/10.1016/S0006-3495(04)74084-9	journal	January 2004
A Physical Method for Deriving the Electrostatic Interaction between Rod-Like Polyions at All Mutual Angles Brenner, Stephen L.; Parsegian, V. Adrian Biophysical Journal, Vol. 14, Issue 4 https://doi.org/10.1016/s0006-3495(74)85919-9	journal	April 1974
Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces Rau, D. C.; Parsegian, V. A. Biophysical Journal, Vol. 61, Issue 1 https://doi.org/10.1016/s0006-3495(92)81831-3	journal	January 1992
Precipitation of DNA by Polyamines: A Polyelectrolyte Behavior Raspaud, E.; Olvera de la Cruz, M.; Sikorav, J. -L. Biophysical Journal, Vol. 74, Issue 1 https://doi.org/10.1016/S0006-3495(98)77795-1	journal	January 1998
Competitive electrostatic binding of charged ligands to polyelectrolytes: practical approach using the non-linear Poisson-Boltzmann equation Rouzina, Ioulia; Bloomfield, Victor A. Biophysical Chemistry, Vol. 64, Issue 1-3 https://doi.org/10.1016/s0301-4622(96)02231-4	journal	February 1997
Competitive interactions of cobalt(3+)hexamine and sodium with helical B-DNA probed by cobalt-59 and sodium-23 NMR Braunlin, W. H.; Anderson, C. F.; Record, M. Thomas Biochemistry, Vol. 26, Issue 24 https://doi.org/10.1021/bi00398a028	journal	December 1987
Counterion-induced condensation of deoxyribonucleic acid. A light-scattering study Wilson, Robert Wilfred; Bloomfield, Victor A. Biochemistry, Vol. 18, Issue 11 https://doi.org/10.1021/bi00578a009	journal	May 1979
Design and Biophysical Characterization of Novel Polycationic ϵ-Peptides for DNA Compaction and Delivery Huang, Dandan; Korolev, Nikolay; Eom, Khee Dong Biomacromolecules, Vol. 9, Issue 1 https://doi.org/10.1021/bm700882g	journal	January 2008
Monte Carlo Simulation Study of Ion Distribution and Osmotic Pressure in Hexagonally Oriented DNA Lyubartsev, Alexander P.; Nordenskioeld, Lars The Journal of Physical Chemistry, Vol. 99, Issue 25 https://doi.org/10.1021/j100025a046	journal	June 1995
Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids Bai, Yu; Greenfeld, Max; Travers, Kevin J. Journal of the American Chemical Society, Vol. 129, Issue 48 https://doi.org/10.1021/ja075020g	journal	December 2007
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
DNA Attraction in Monovalent and Divalent Electrolytes Luan, Binquan; Aksimentiev, Aleksei Journal of the American Chemical Society, Vol. 130, Issue 47 https://doi.org/10.1021/ja804802u	journal	November 2008
Macroion Attraction Due to Electrostatic Correlation between Screening Counterions. 1. Mobile Surface-Adsorbed Ions and Diffuse Ion Cloud Rouzina, Ioulia; Bloomfield, Victor A. The Journal of Physical Chemistry, Vol. 100, Issue 23 https://doi.org/10.1021/jp960458g	journal	January 1996
Improved Parametrization of Li ⁺ , Na ⁺ , K ⁺ , and Mg ²⁺ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems Yoo, Jejoong; Aksimentiev, Aleksei The Journal of Physical Chemistry Letters, Vol. 3, Issue 1 https://doi.org/10.1021/jz201501a	journal	December 2011
An attractive force between two rodlike polyions mediated by the sharing of condensed counterions Ray, Jolly; Manning, Gerald S. Langmuir, Vol. 10, Issue 7 https://doi.org/10.1021/la00019a071	journal	July 1994
Attraction and Ionic Correlations between Charged Stiff Polyelectrolytes Deserno, Markus; Arnold, Axel; Holm, Christian Macromolecules, Vol. 36, Issue 1 https://doi.org/10.1021/ma020923+	journal	December 2002
Fraction of Condensed Counterions around a Charged Rod: Comparison of Poisson−Boltzmann Theory and Computer Simulations Deserno, Markus; Holm, Christian; May, Sylvio Macromolecules, Vol. 33, Issue 1 https://doi.org/10.1021/ma990897o	journal	January 2000
Compact form of DNA induced by spermidine Gosule, Leonard C.; Schellman, John A. Nature, Vol. 259, Issue 5541 https://doi.org/10.1038/259333a0	journal	January 1976
Poly(dA)ṁpoly(dT) is a B-type double helix with a distinctively narrow minor groove Alexeev, D. G.; Lipanov, A. A.; Ya. Skuratovskii, I. Nature, Vol. 325, Issue 6107 https://doi.org/10.1038/325821a0	journal	February 1987
Crystal structure of the nucleosome core particle at 2.8 Å resolution Luger, Karolin; Mäder, Armin W.; Richmond, Robin K. Nature, Vol. 389, Issue 6648 https://doi.org/10.1038/38444	journal	September 1997
Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation Yoo, Jejoong; Kim, Hajin; Aksimentiev, Aleksei Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11045	journal	March 2016
Counterion-mediated electrostatic interactions between helical molecules Kanduč, M.; Dobnikar, J.; Podgornik, R. Soft Matter, Vol. 5, Issue 4 https://doi.org/10.1039/b811795k	journal	January 2009
Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties Manning, Gerald S. The Journal of Chemical Physics, Vol. 51, Issue 3 https://doi.org/10.1063/1.1672157	journal	August 1969
Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte Tan, Zhi-Jie; Chen, Shi-Jie The Journal of Chemical Physics, Vol. 122, Issue 4 https://doi.org/10.1063/1.1842059	journal	January 2005
Counterion-mediated weak and strong coupling electrostatic interaction between like-charged cylindrical dielectrics Kanduč, Matej; Naji, Ali; Podgornik, Rudolf The Journal of Chemical Physics, Vol. 132, Issue 22 https://doi.org/10.1063/1.3430744	journal	June 2010
Statistical mechanics of electrolytes and polyelectrolytes. III. The cylindrical Poisson–Boltzmann equation Ramanathan, G. V. The Journal of Chemical Physics, Vol. 78, Issue 6 https://doi.org/10.1063/1.445239	journal	March 1983
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
A Monte Carlo simulation study of electrostatic forces between hexagonally packed DNA double helices Guldbrand, Lars; Nilsson, Lars G.; Nordenskiöld, Lars The Journal of Chemical Physics, Vol. 85, Issue 11 https://doi.org/10.1063/1.451450	journal	December 1986
Theory of interaction between helical molecules Kornyshev, A. A.; Leikin, S. The Journal of Chemical Physics, Vol. 107, Issue 9 https://doi.org/10.1063/1.475320	journal	September 1997
Reentrant condensation of DNA induced by multivalent counterions Nguyen, T. T.; Rouzina, I.; Shklovskii, B. I. The Journal of Chemical Physics, Vol. 112, Issue 5 https://doi.org/10.1063/1.480819	journal	February 2000
Screening of a charged particle by multivalent counterions in salty water: Strong charge inversion Nguyen, T. T.; Grosberg, A. Yu.; Shklovskii, B. I. The Journal of Chemical Physics, Vol. 113, Issue 3 https://doi.org/10.1063/1.481890	journal	July 2000
Electrostatic origin of the genome packing in viruses Belyi, V. A.; Muthukumar, M. Proceedings of the National Academy of Sciences, Vol. 103, Issue 46 https://doi.org/10.1073/pnas.0608311103	journal	November 2006
DNA–DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting Marenduzzo, Davide; Orlandini, Enzo; Stasiak, Andrzej Proceedings of the National Academy of Sciences, Vol. 106, Issue 52 https://doi.org/10.1073/pnas.0907524106	journal	December 2009
Evidence that viral RNAs have evolved for efficient, two-stage packaging Borodavka, A.; Tuma, R.; Stockley, P. G. Proceedings of the National Academy of Sciences, Vol. 109, Issue 39 https://doi.org/10.1073/pnas.1204357109	journal	September 2012
Electrostatic interaction between helical macromolecules in dense aggregates: An impetus for DNA poly- and meso-morphism Kornyshev, A. A.; Leikin, S. Proceedings of the National Academy of Sciences, Vol. 95, Issue 23 https://doi.org/10.1073/pnas.95.23.13579	journal	November 1998
A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat Cheatham, Thomas E.; Cieplak, Piotr; Kollman, Peter A. Journal of Biomolecular Structure and Dynamics, Vol. 16, Issue 4 https://doi.org/10.1080/07391102.1999.10508297	journal	February 1999
Electrostatic correlations: from plasma to biology Levin, Yan Reports on Progress in Physics, Vol. 65, Issue 11 https://doi.org/10.1088/0034-4885/65/11/201	journal	September 2002
Non-mean-field screening by multivalent counterions Loth, M. S.; Shklovskii, B. I. Journal of Physics: Condensed Matter, Vol. 21, Issue 42 https://doi.org/10.1088/0953-8984/21/42/424104	journal	September 2009
Interplay of ion binding and attraction in DNA condensed by multivalent cations Todd, B. A.; Rau, D. C. Nucleic Acids Research, Vol. 36, Issue 2 https://doi.org/10.1093/nar/gkm1038	journal	November 2007
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA Pabit, Suzette A.; Qiu, Xiangyun; Lamb, Jessica S. Nucleic Acids Research, Vol. 37, Issue 12 https://doi.org/10.1093/nar/gkp257	journal	April 2009
Why double-stranded RNA resists condensation Tolokh, Igor S.; Pabit, Suzette A.; Katz, Andrea M. Nucleic Acids Research, Vol. 42, Issue 16 https://doi.org/10.1093/nar/gku756	journal	August 2014
Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA Wu, Yuan-Yan; Zhang, Zhong-Liang; Zhang, Jin-Si Nucleic Acids Research, Vol. 43, Issue 12 https://doi.org/10.1093/nar/gkv570	journal	May 2015
Structure in the electric potential emanating from DNA Edwards, Glenn; Hochberg, David; Kephart, Thomas W. Physical Review E, Vol. 50, Issue 2 https://doi.org/10.1103/physreve.50.r698	journal	August 1994
Screening of a macroion by multivalent ions: Correlation-induced inversion of charge Shklovskii, B. I. Physical Review E, Vol. 60, Issue 5 https://doi.org/10.1103/physreve.60.5802	journal	November 1999
Attraction between DNA molecules mediated by multivalent ions Allahyarov, E.; Gompper, G.; Löwen, H. Physical Review E, Vol. 69, Issue 4 https://doi.org/10.1103/physreve.69.041904	journal	April 2004
Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars Physical Review Letters, Vol. 100, Issue 11 https://doi.org/10.1103/physrevlett.100.118301	journal	March 2008
Abrupt Transition from a Free, Repulsive to a Condensed, Attractive DNA Phase, Induced by Multivalent Polyamine Cations Qiu, Xiangyun; Andresen, Kurt; Lamb, Jessica S. Physical Review Letters, Vol. 101, Issue 22 https://doi.org/10.1103/PhysRevLett.101.228101	journal	November 2008
Double-Stranded RNA Resists Condensation Li, Li; Pabit, Suzette A.; Meisburger, Steve P. Physical Review Letters, Vol. 106, Issue 10 https://doi.org/10.1103/physrevlett.106.108101	journal	March 2011
Wigner Crystal Model of Counterion Induced Bundle Formation of Rodlike Polyelectrolytes Shklovskii, B. I. Physical Review Letters, Vol. 82, Issue 16 https://doi.org/10.1103/physrevlett.82.3268	journal	April 1999
Electrostatic Zipper Motif for DNA Aggregation Kornyshev, A. A.; Leikin, S. Physical Review Letters, Vol. 82, Issue 20 https://doi.org/10.1103/physrevlett.82.4138	journal	May 1999
The Nature of Attraction between Like-Charged Rods Levin, Yan; Arenzon, Jeferson J.; Stilck, Jürgen F. Physical Review Letters, Vol. 83, Issue 13 https://doi.org/10.1103/physrevlett.83.2680	journal	September 1999
Manning-Oosawa Counterion Condensation O’Shaughnessy, Ben; Yang, Qingbo Physical Review Letters, Vol. 94, Issue 4 https://doi.org/10.1103/physrevlett.94.048302	journal	February 2005
Structure and interactions of biological helices Kornyshev, Alexei A.; Lee, Dominic J.; Leikin, Sergey Reviews of Modern Physics, Vol. 79, Issue 3 https://doi.org/10.1103/revmodphys.79.943	journal	August 2007
RNA Interference: Biology, Mechanism, and Applications Agrawal, N.; Dasaradhi, P. V. N.; Mohmmed, A. Microbiology and Molecular Biology Reviews, Vol. 67, Issue 4 https://doi.org/10.1128/MMBR.67.4.657-685.2003	journal	December 2003
Attraction and unbinding of like-charged rods Naji, A.; Arnold, A.; Holm, C. Europhysics Letters (EPL), Vol. 67, Issue 1 https://doi.org/10.1209/epl/i2003-10275-y	journal	July 2004
Ion-Mediated Nucleic Acid Helix-Helix Interactions Tan, Zhi-Jie; Chen, Shi-Jie Biophysical Journal, Vol. 91, Issue 2 https://doi.org/10.1529/biophysj.106.084285	journal	July 2006
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Pérez, Alberto; Marchán, Iván; Svozil, Daniel Biophysical Journal, Vol. 92, Issue 11 https://doi.org/10.1529/biophysj.106.097782	journal	June 2007
Mono- and Trivalent Ions around DNA: A Small-Angle Scattering Study of Competition and Interactions Andresen, Kurt; Qiu, Xiangyun; Pabit, Suzette A. Biophysical Journal, Vol. 95, Issue 1 https://doi.org/10.1529/biophysj.107.123174	journal	July 2008
RNA Interference and its Role in Cancer Therapy Mansoori, Behzad; Sandoghchian Shotorbani, Siamak; Baradaran, Behzad Tabriz University of Medical Sciences https://doi.org/10.5681/apb.2014.046	text	January 2014
Statistical mechanics Klein, Martin J. Information and Control, Vol. 3, Issue 4 https://doi.org/10.1016/s0019-9958(60)90981-5	journal	December 1960
Non-mean-field screening by multivalent counterions Loth, M. S.; Shklovskii, B. I. arXiv https://doi.org/10.48550/arxiv.0902.3009	text	January 2009
Counterion-Mediated Weak and Strong Coupling Electrostatic Interaction between Like-Charged Cylindrical Dielectrics Kanduc, Matej; Naji, Ali; Podgornik, Rudolf arXiv https://doi.org/10.48550/arxiv.1003.1726	text	January 2010
Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA Wu, Yuan-Yan; Zhang, Zhong-Liang; Zhang, Jin-Si arXiv https://doi.org/10.48550/arxiv.1507.02774	text	January 2015
Screening of a charged particle by multivalent counterions in salty water: Giant charge inversion Nguyen, T. T.; Grosberg, A. Yu.; Shklovskii, B. I. arXiv https://doi.org/10.48550/arxiv.cond-mat/0002305	text	January 2000
Attraction and ionic correlations between charged stiff polyelectrolytes Deserno, Markus; Arnold, Axel; Holm, Christian arXiv https://doi.org/10.48550/arxiv.cond-mat/0206126	text	January 2002
Electrostatic correlations: from Plasma to Biology Levin, Yan arXiv https://doi.org/10.48550/arxiv.cond-mat/0207086	text	January 2002
Attraction between DNA molecules mediated by multivalent ions Allahyarov, E.; Gompper, G.; Löwen, H. arXiv https://doi.org/10.48550/arxiv.cond-mat/0311324	text	January 2003
Attraction and unbinding of like-charged rods Naji, Ali; Arnold, Axel; Holm, Christian arXiv https://doi.org/10.48550/arxiv.cond-mat/0504393	text	January 2005
The fraction of condensed counterions around a charged rod: Comparison of Poisson-Boltzmann theory and computer simulations Deserno, Markus; Holm, Christian; May, Sylvio arXiv https://doi.org/10.48550/arxiv.cond-mat/9906277	text	January 1999
Screening of a macroion by multivalent ions: Correlation induced inversion of charge Shklovskii, B. I. arXiv https://doi.org/10.48550/arxiv.cond-mat/9907351	text	January 1999
Evaluation of the counterion condensation theory of polyelectrolytes Stigter, D. Biophysical Journal, Vol. 69, Issue 2 https://doi.org/10.1016/s0006-3495(95)79910-6	journal	August 1995
Counterion-mediated Electrostatic Interactions between Helical Molecules Kanduc, M.; Dobnikar, J.; Podgornik, R. arXiv https://doi.org/10.48550/arxiv.0807.1586	text	January 2008
The nature of attraction between like charged rods Levin, Yan; Arenzon, Jeferson J.; Stilck, Jurgen F. arXiv https://doi.org/10.48550/arxiv.cond-mat/9907428	text	January 1999

Cited By (2)

Explicit ions/implicit water generalized Born model for nucleic acids Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V. The Journal of Chemical Physics, Vol. 148, Issue 19 https://doi.org/10.1063/1.5027260	journal	May 2018
Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation Roodhuizen, Job A. L.; Hendrikx, Philip J. T. M.; Hilbers, Peter A. J. ACS Nano, Vol. 13, Issue 9 https://doi.org/10.1021/acsnano.9b05650	journal	September 2019

Similar Records

Multi-shell model of ion-induced nucleic acid condensation

Journal Article · Thu Apr 21 00:00:00 EDT 2016 · Journal of Chemical Physics · OSTI ID:22660860

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; +2 more

Why double-stranded RNA resists condensation

Journal Article · Mon Sep 15 00:00:00 EDT 2014 · Nucleic Acids Research, 42(16):10823-10831 · OSTI ID:22660860

Tolokh, Igor S.; Pabit, Suzette; Katz, Andrea M.; +5 more

Explicit ions/implicit water generalized Born model for nucleic acids

Journal Article · Fri May 18 00:00:00 EDT 2018 · Journal of Chemical Physics · OSTI ID:22660860

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Related Subjects

37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY
AGGLOMERATION
FREE ENERGY
IONS
MOLECULAR DYNAMICS METHOD
POISSON EQUATION
RNA
SIMULATION

Title: Multi-shell model of ion-induced nucleic acid condensation

Citation Formats

References (88)

Cited By (2)

Similar Records

Related Subjects