1
|
He W, Kirmizialtin S. Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations. Biomacromolecules 2024; 25:4819-4830. [PMID: 39011747 PMCID: PMC11323003 DOI: 10.1021/acs.biomac.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, the mechanisms of DNA assembly in lipid bilayers remain insufficiently understood due to challenges in measuring and assessing each component's contribution in the lipid-DNA-cation system. This study uses all-atom molecular dynamics simulations to investigate DNA condensation in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between lipid and DNA drastically reduce charges, while mobile magnesium cations "ping-ponging" between double strands create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the spontaneous condensation of DNAs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.
Collapse
Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
2
|
Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
Collapse
Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| |
Collapse
|
3
|
Volpe Bossa G, Hobbie E, May S. Counterion Release from Macroion Assemblies of Planar Geometry. J Phys Chem B 2024; 128:6966-6974. [PMID: 38958595 DOI: 10.1021/acs.jpcb.4c03222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Macroions such as nanoparticles, polyelectrolytes, ionic gels, and amphiphiles can form condensed, often self-assembled, phases that are embedded in a solvent region. The condensed phase contains not only the partially or fully immobile charges of their macroions but also corresponding counterions that are mobile and thus free to migrate out of their confinement into the solvent region where they benefit from high translational entropy. Based on the nonlinear Poisson-Boltzmann model for monovalent ions, we quantify the corresponding fraction of released counterions for a planar slab geometry of the macroion phase. Slab thickness, extension of the solvent phase, fixed background charge density provided by the macroions, and dielectric constants inside slab and solvent combine into three dimensionless parameters that the fraction of released counterions depends on. We calculate that fraction and analyze the limits of a thin macroion phase, a large solvent phase, and linearized theory, where simple analytic results become available. Of particular interest is the presence of a single-planar interface that separates a bulk macroion phase from an extended solvent region. We calculate the apparent surface charge density that emerges due to the released counterions. Our model yields a comprehensive description of counterion partitioning between a planar macroion phase and a solvent region on the level of mean-field electrostatics in the absence of added salt ions.
Collapse
Affiliation(s)
- Guilherme Volpe Bossa
- Institute of Mathematical and Physical Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Erik Hobbie
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, United States
| | - Sylvio May
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, United States
| |
Collapse
|
4
|
Singh N, Singh A, Dhanka M, Bhatia D. DNA functionalized programmable hybrid biomaterials for targeted multiplexed applications. J Mater Chem B 2024. [PMID: 38973587 DOI: 10.1039/d4tb00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
With the advent of DNA nanotechnology, DNA-based biomaterials have emerged as a unique class of materials at the center of various biological advances. Owing to DNA's high modification capacity via programmable Watson-Crick base-pairing, DNA structures of desired design with increased complexity have been developed. However, the limited scalability, along with poor mechanical properties, high synthesis costs, and poor stability, reduced the adaptability of DNA-based materials to complex biological applications. DNA-based hybrid biomaterials were designed to overcome these limitations by conjugating DNA with functional materials. Today, DNA-based hybrid materials have attracted significant attention in biological engineering with broad application prospects in biomedicine, clinical diagnosis, and nanodevices. Here, we summarize the recent advances in DNA-based hybrid materials with an in-depth understanding of general molecular design principles, functionalities, and applications. Finally, the challenges and prospects associated with DNA-based hybrid materials are discussed at the end of this review.
Collapse
Affiliation(s)
- Nihal Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Ankur Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Mukesh Dhanka
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Dhiraj Bhatia
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| |
Collapse
|
5
|
Palma E, Santos JF, Fernandes C, Paulo A. DNA-Targeted Complexes of Tc and Re for Biomedical Applications. Chemistry 2024; 30:e202303591. [PMID: 38038361 DOI: 10.1002/chem.202303591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/02/2023]
Abstract
Due to their favorable chemical features, Re and Tc complexes have been widely used for the development of new therapeutic agents and imaging probes to solve problems of biomedical relevance. This review provides an update of the most relevant research efforts towards the development of novel cancer theranostic agents using Re and Tc-based compounds interacting with specific DNA structures. This includes a variety of homometallic complexes, namely those containing M(CO)3 (M=Re, Tc) moieties, that exhibit different modes of interaction with DNA, such as covalent binding, intercalation, groove binding or G-quadruplex DNA binding. Additionally, heterometallic complexes, designed to potentiate synergistic effects of different metal centers to improve DNA-targeting, cytotoxicity and fluorescence properties, are also reviewed. Particular attention is also given to 99m Tc- and 188 Re-labeled oligonucleotides that have been widely explored to develop imaging and therapeutic radiopharmaceuticals through the in vivo hybridization with a specific complementary DNA or RNA target sequence to provide useful molecular tools in precision medicine for cancer diagnosis and treatment. Finally, the need for further improvement of DNA-targeted Re and Tc-based compounds as potential therapeutic and diagnostic agents is highlighted, and future directions are discussed.
Collapse
Affiliation(s)
- Elisa Palma
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joana F Santos
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Célia Fernandes
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - António Paulo
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| |
Collapse
|
6
|
Koirala RP, Adhikari NP. Base flipping mechanism and binding strength of methyl-damaged DNA during the interaction with AGT. J Biol Phys 2024; 50:71-87. [PMID: 38150168 DOI: 10.1007/s10867-023-09649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Methyl damage to DNA bases is common in the cell nucleus. O6-alkylguanine-DNA alkyl transferase (AGT) may be a promising candidate for direct damage reversal in methylated DNA (mDNA) at the O6 point of the guanine. Indeed, atomic-level investigations in the contact region of AGT-DNA complex can provide an in-depth understanding of their binding mechanism, allowing to evaluate the silico-drug nature of AGT and its utility in removing methyl damage in DNA. In this study, molecular dynamics (MD) simulation was utilized to examine the flipping of methylated nucleotide, the binding mechanism between mDNA and AGT, and the comparison of binding strength prior and post methyl transfer to AGT. The study reveals that methylation at the O6 atom of guanine weakens the hydrogen bond (H-bond) between guanine and cytosine, permitting for the flipping of such nucleotide. The formation of a H-bond between the base pair of methylated nucleotide (i.e., cytosine) and the intercalated arginine of AGT also forces the nucleotide to rotate. Following that, electrostatics and van der Waals contacts as well as hydrogen bonding contribute to form the complex of DNA and protein. The stronger binding of AGT with DNA before methyl transfer creates the suitable condition to transfer methyl adduct from DNA to AGT.
Collapse
|
7
|
Kim T, Lee C, Lee JY, Kim DN. Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures. ACS NANO 2024; 18:3414-3423. [PMID: 38236130 DOI: 10.1021/acsnano.3c10386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.
Collapse
Affiliation(s)
- Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| |
Collapse
|
8
|
Ruixuan H, Majee A, Dobnikar J, Podgornik R. Electrostatic interactions between charge regulated spherical macroions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:115. [PMID: 38019363 DOI: 10.1140/epje/s10189-023-00373-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023]
Abstract
We study the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups immersed in a monovalent electrolyte solution. The charge dissociation is modelled via the Frumkin-Fowler-Guggenheim isotherm, which allows for multiple adsorption equilibrium states. The interactions are derived from the solutions of the mean-field Poisson-Boltzmann type theory with charge regulation boundary conditions. For a range of conditions we find symmetry breaking transitions from symmetric to asymmetric charge distribution exhibiting annealed charge patchiness, which results in like-charge attraction even in a univalent electrolyte-thus fundamentally modifying the nature of electrostatic interactions in charge-stabilized colloidal suspensions.
Collapse
Affiliation(s)
- Hu Ruixuan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arghya Majee
- Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany
| | - Jure Dobnikar
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- Songshan Lake Materials Laboratory, Guangdong, 523808, Dongguan, China
| | - Rudolf Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000, Ljubljana, Slovenia.
| |
Collapse
|
9
|
Yang ZY, Jiang WY, Ran SY. Reductant-dependent DNA-templated silver nanoparticle formation kinetics. Phys Chem Chem Phys 2023; 25:23197-23206. [PMID: 37605826 DOI: 10.1039/d3cp02623j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.
Collapse
Affiliation(s)
- Zi-Yang Yang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Wen-Yan Jiang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
10
|
Sun H, Yao Z. Conformal order and Poincaré-Klein mapping underlying electrostatics-driven inhomogeneity in tethered membranes. Phys Rev E 2023; 108:025001. [PMID: 37723772 DOI: 10.1103/physreve.108.025001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/17/2023] [Indexed: 09/20/2023]
Abstract
Understanding the organization of matter under the long-range electrostatic force is a fundamental problem in multiple fields. In this work, based on the electrically charged tethered membrane model, we reveal regular structures underlying the lowest-energy states of inhomogeneously stretched planar lattices by a combination of numerical simulation and analytical geometric analysis. Specifically we show the conformal order characterized by the preserved bond angle in the lattice deformation and reveal the Poincaré-Klein mapping underlying the electrostatics-driven inhomogeneity. The discovery of the Poincaré-Klein mapping, which connects the Poincaré disk and the Klein disk for the hyperbolic plane, implies the connection of long-range electrostatic force and hyperbolic geometry. We also discuss lattices with patterned charges of opposite signs for modulating in-plane inhomogeneity and even creating 3D shapes, which may have a connection to metamaterials design. This work suggests the geometric analysis as a promising approach for elucidating the organization of matter under the long-range force.
Collapse
Affiliation(s)
- Honghui Sun
- School of Physics and Astronomy, and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenwei Yao
- School of Physics and Astronomy, and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
11
|
Xu Y, Qian C, Yu Y, Yang S, Shi F, Xu L, Gao X, Liu Y, Huang H, Stewart C, Li F, Han J. Machine Learning-Assisted Nanoenzyme/Bioenzyme Dual-Coupled Array for Rapid Detection of Amyloids. Anal Chem 2023; 95:4605-4611. [PMID: 36859794 DOI: 10.1021/acs.analchem.2c04244] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Array-based sensing methods offer significant advantages in the simultaneous detection of multiple amyloid biomarkers and thus have great potential for diagnosing early-stage Alzheimer's disease. Yet, detecting low concentrations of amyloids remains exceptionally challenging. Here, we have developed a fluorescent sensor array based on the dual coupling of a nanoenzyme (AuNPs) and bioenzyme (horseradish peroxidase) to detect amyloids. Various ss-DNAs were bound to the nanoenzyme for regulating enzymatic activity and recognizing amyloids. A simplified sensor array was generated from a screening model via machine learning algorithms and achieved signal amplification through a two-step enzymatic reaction. As a result, our sensing system could discriminate the aggregation species and aggregation kinetics at 200 nM with 100% accuracy. Moreover, AD model mice and healthy mice were distinguished with 100% accuracy through the sensor array, providing a powerful sensing platform for diagnosing AD.
Collapse
Affiliation(s)
- Yu Xu
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Qian
- Department of Pathology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Yang Yu
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Shijie Yang
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Fangfang Shi
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Lian Xu
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Xu Gao
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Yuhang Liu
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Huang
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Callum Stewart
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Stockholm 17177, Sweden
| | - Fei Li
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Jinsong Han
- State Key Laboratory of Natural Medicines, National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
12
|
Quiñones AO, Bhuiyan LB, Abbas Z, Outhwaite CW. Influence of concentration and temperature dependent dielectric constants on the thermodynamics of electrolytes. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
13
|
Petretto E, Ong QK, Olgiati F, Mao T, Campomanes P, Stellacci F, Vanni S. Monovalent ion-mediated charge-charge interactions drive aggregation of surface-functionalized gold nanoparticles. NANOSCALE 2022; 14:15181-15192. [PMID: 36214308 PMCID: PMC9585526 DOI: 10.1039/d2nr02824g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Monolayer-protected metal nanoparticles (NPs) are not only promising materials with a wide range of potential industrial and biological applications, but they are also a powerful tool to investigate the behaviour of matter at nanoscopic scales, including the stability of dispersions and colloidal systems. This stability is dependent on a delicate balance between attractive and repulsive interactions that occur in the solution, and it is described in quantitative terms by the classic Derjaguin-Landau-Vewey-Overbeek (DLVO) theory, that posits that aggregation between NPs is driven by van der Waals interactions and opposed by electrostatic interactions. To investigate the limits of this theory at the nanoscale, where the continuum assumptions required by the DLVO theory break down, here we investigate NP dimerization by computing the Potential of Mean Force (PMF) of this process using fully atomistic MD simulations. Serendipitously, we find that electrostatic interactions can lead to the formation of metastable NP dimers at physiological ion concentrations. These dimers are stabilized by complexes formed by negatively charged ligands belonging to distinct NPs that are bridged by positively charged monovalent ions present in solution. We validate our findings by collecting tomographic EM images of NPs in solution and by quantifying their radial distribution function, that shows a marked peak at interparticle distance comparable with that of MD simulations. Taken together, our results suggest that not only van der Waals interactions, but also electrostatic interactions mediated by monovalent ions at physiological concentrations, contribute to attraction between nano-sized charged objects at very short length scales.
Collapse
Affiliation(s)
- Emanuele Petretto
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Quy K Ong
- Institute of Materials, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Francesca Olgiati
- Institute of Materials, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Ting Mao
- Institute of Materials, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Francesco Stellacci
- Institute of Materials, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| |
Collapse
|
14
|
Bodapati ATS, Sahoo BK, Reddy RS, Lavanya K, Madku SR. Deciphering the nature of binding of dexlansoprazole with DNA: Biophysical and docking approaches. Int J Biol Macromol 2022; 217:1027-1036. [PMID: 35907469 DOI: 10.1016/j.ijbiomac.2022.07.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
Abstract
Drugs, in general, exhibit their pharmacological activity in binding with intracellular targets. Numerous anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Dexlansoprazole (DLP) is a heterocyclic compound containing benzimidazole moiety and a proton pump inhibitor used to treat gastroesophageal reflux disease. The interaction of dexlansoprazole with calf thymus DNA (ct-DNA) has been studied using biophysical methods. The UV-Visible studies revealed a binding constant of 2.15 ± 0.3 × 104 M-1 which is close to the value of 2.44 ± 0.3 × 104 M-1 obtained from the fluorescence studies. Competitive displacement studies using the fluorescence spectroscopic method with ethidium bromide and Hoechst as DNA markers suggested the groove binding mode of DLP in ct-DNA. The groove binding mode of DLP in ct-DNA was complemented by the results of viscosity and DNA melting studies. Further studies on the effect of ionic strength and potassium iodide on DLP binding with ct-DNA supported the observed binding mode. Circular dichroism studies reflected no significant conformational variation in ct-DNA after the interaction. The binding mode obtained from the experimental studies was corroborated by the molecular docking studies that showed the position of DLP in the minor groove of ct-DNA along with the receptor interface restudies involved in the interaction.
Collapse
Affiliation(s)
- Anna Tanuja Safala Bodapati
- Chemistry Division, BS&H Department, BVRIT Hyderabad, College of Engineering for Women, Hyderabad 500090, India; Department of Chemistry, GITAM Deemed to be University, Hyderabad Campus 502329, India
| | - Bijaya Ketan Sahoo
- Department of Chemistry, GITAM Deemed to be University, Hyderabad Campus 502329, India.
| | - Ragaiahgari Srinivas Reddy
- Department of Chemistry, GITAM Deemed to be University, Hyderabad Campus 502329, India; Department of Chemistry, B V Raju Institute of Technology (BVRIT), Narsapur 502313, India
| | - Kandikonda Lavanya
- Department of Chemistry, GITAM Deemed to be University, Hyderabad Campus 502329, India; Department of Chemistry, Gokaraju Rangaraju Institute of Engineering and Technology, Hyderabad 500090, India
| | - Shravya Rao Madku
- Department of Chemistry, GITAM Deemed to be University, Hyderabad Campus 502329, India; Department of Chemistry, St. Francis College for Women, Hyderabad 500016, India
| |
Collapse
|
15
|
Tsai E, Gallage Dona HK, Tong X, Du P, Novak B, David R, Rick SW, Zhang D, Kumar R. Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations. Macromolecules 2022; 55:5197-5212. [PMID: 35784657 PMCID: PMC9245439 DOI: 10.1021/acs.macromol.2c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/26/2022] [Indexed: 11/28/2022]
Abstract
![]()
Electrostatic interactions
play a significant role in regulating
biological systems and have received increasing attention due to their
usefulness in designing advanced stimulus-responsive materials. Polypeptoids
are highly tunable N-substituted peptidomimetic polymers that lack
backbone hydrogen bonding and chirality. Therefore, polypeptoids are
suitable systems to study the effect of noncovalent interactions of
substituents without complications of backbone intramolecular and
intermolecular hydrogen bonding. In this study, all-atom molecular
dynamics (MD) simulations were performed on micelles formed by a series
of sequence-defined ionic polypeptoid block copolymers consisting
of a hydrophobic segment and a hydrophilic segment in an aqueous solution.
By combining the results from MD simulations and experimental small-angle
neutron scattering data, further insights were gained into the internal
structure of the formed polypeptoid micelles, which is not always
directly accessible from experiments. In addition, information was
gained into the physics of the noncovalent interactions responsible
for the self-assembly of weakly charged polypeptoids in an aqueous
solution. While the aggregation number is governed by electrostatic
repulsion of the negatively charged carboxylate (COO–) substituents on the polypeptoid chain within the micelle, MD simulations
indicate that the position of the charge on singly charged chains
mediates the shape of the micelle through the charge–dipole
interactions between the COO– substituent and the
surrounding water. Therefore, the polypeptoid micelles formed from
the single-charged series offer the possibility for tailorable micelle
shapes. In contrast, the polypeptoid micelles formed from the triple-charged
series are characterized by more pronounced electrostatic repulsion
that competes with more significant charge–sodium interactions,
making it difficult to predict the shape of the micelles. This work
has helped further develop design principles for the shape and structure
of self-assembled micelles by controlling the position of charged
moieties on the backbone of polypeptoid block copolymers.
Collapse
Affiliation(s)
- Erin Tsai
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Xinjie Tong
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pu Du
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Brian Novak
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Rolf David
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Donghui Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
16
|
Sun T, Minhas V, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions. J Chem Theory Comput 2022; 18:3948-3960. [PMID: 35580041 PMCID: PMC9202350 DOI: 10.1021/acs.jctc.2c00083] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.
Collapse
Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| |
Collapse
|
17
|
Ru XM, Yang ZY, Ran SY. Lanthanide ions induce DNA compaction with ionic specificity. Int J Biol Macromol 2022; 210:292-299. [DOI: 10.1016/j.ijbiomac.2022.04.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022]
|
18
|
Gökoğlu E, Kıpçak F, Taskin-Tok T, Duyar H, Seferoğlu Z. Structural analysis and calf thymus DNA/HSA binding properties of new carbazole derivative containing piperazine. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
19
|
Si DQ, Liu XY, Wu JB, Hu GH. Modulation of DNA conformation in electrolytic nanodroplets. Phys Chem Chem Phys 2022; 24:6002-6010. [PMID: 35199810 DOI: 10.1039/d1cp05329a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.
Collapse
Affiliation(s)
- Dong-Qing Si
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Xin-Yue Liu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Jin-Bo Wu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Guo-Hui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| |
Collapse
|
20
|
Hu SQ, Ran SY. Single Molecular Chelation Dynamics Reveals That DNA Has a Stronger Affinity toward Lead(II) than Cadmium(II). J Phys Chem B 2022; 126:1876-1884. [PMID: 35196016 DOI: 10.1021/acs.jpcb.1c10487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lead ions can bind to DNA via nonelectrostatic interactions and hence alter its structure, which may be related to their adverse effects. The dynamics of Pb2+-DNA interaction has not been well understood. In this study, we report the monomolecular dynamics of the Pb2+-DNA interaction using a magnetic tweezers (MT) setup. We found that lead cations could induce DNA compaction at ionic strengths above 1 μM, which was also confirmed by morphology characterization. The chelation behavior of the Pb2+-DNA and the Cd2+-DNA complex solutions after adding EDTA were compared. The results showed that EDTA chelated with the bound metal ions on DNA and consequently led to restoring the DNA to its original length but with different restoration speeds for the two solutions. The fast binding dynamics and the slower chelation dynamics of the Pb2+ scenario compared to that of Cd2+ suggested that Pb2+ was more capable to induce DNA conformational change and that the Pb2+-DNA complex was more stable than the Cd2+-DNA complex. The stronger affinities for DNA bases and the inner binding of lead cations were two possible causes of the dynamics differences. Three agents, including EDTA, sodium gluconate, and SDBS, were used to remove the bound lead ions on DNA. It was shown that EDTA was the most efficient, and sodium gluconate could not fully restore DNA from its compact state. We concluded that both EDTA and SDBS were good candidates to restore the Pb2+-bound DNA to its original state.
Collapse
Affiliation(s)
- Shu-Qian Hu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| |
Collapse
|
21
|
Jambrec D, Gebala M. DNA Electrostatics: From Theory to Application. ChemElectroChem 2022. [DOI: 10.1002/celc.202101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytische Chemie – Elektroanalytik & Sensorik Ruhr-Universität Bochum Universitätsstr. 150 D-44780 Bochum Germany
| | - Magdalena Gebala
- Department of Biochemistry Stanford University Stanford 94305, CA USA
| |
Collapse
|
22
|
Murade CU, Shubeita GT. A fluorescent reporter on electrostatic DNA-ligand interactions. BIOMEDICAL OPTICS EXPRESS 2022; 13:159-167. [PMID: 35154861 PMCID: PMC8803044 DOI: 10.1364/boe.439791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Among the various types of interactions between biomolecules, electrostatic interactions dominate as these are long-range interactions and are often a generic first step in the recruitment of specific ligands. DNA, being a highly charged molecule, attracts a plethora of molecules. Interactions between DNA and proteins or small molecules shape the overall function of the cell. Various processes such as DNA replication, DNA repair, synthesis of mRNA, and packaging of DNA are mediated by interactions between protein molecules and DNA that are predominantly electrostatic. Here, we present a fluorescence resonance energy transfer (FRET)-based probe which can report on the electrostatic interactions between the negatively-charged DNA and positively-charged metal ions, oligopeptides, as well as DNA groove-binding drug molecules. The simplicity, sensitivity, and versatility of the DNA-based probe makes it suited for applications where specific protein-DNA interactions can be probed, and DNA-binding drugs can be discovered in high-throughput screens of compound libraries. This is particularly relevant given that some of the most potent antitumor and antimicrobial drugs associate with DNA electrostatically.
Collapse
|
23
|
Kravets K, Kravets M, Butkiewicz H, Kosiorek S, Sashuk V, Danylyuk O. Electrostatic co-assembly of pillar[n]pyridiniums and calix[4]arene in aqueous media. CrystEngComm 2022. [DOI: 10.1039/d2ce00232a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cationic pillar[n]pyridiniums and anionic p-sulfonatocalix[4]arene co-assemble into all-organic supersalts through encaging of the supercation units within/between the capsules emerged from superanion pairs. The encapsulation occures both in the solid...
Collapse
|
24
|
Whitfield C, Zhang M, Winterwerber P, Wu Y, Ng DYW, Weil T. Functional DNA-Polymer Conjugates. Chem Rev 2021; 121:11030-11084. [PMID: 33739829 PMCID: PMC8461608 DOI: 10.1021/acs.chemrev.0c01074] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 02/07/2023]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of solid phase synthesis and the discovery of DNA nanostructures. Solid phase synthesis has facilitated the availability of short DNA sequences and the expansion of the DNA toolbox to increase the chemical functionalities afforded on DNA, which in turn enabled the conception and synthesis of sophisticated and complex 2D and 3D nanostructures. In parallel, polymer science has developed several polymerization approaches to build di- and triblock copolymers bearing hydrophilic, hydrophobic, and amphiphilic properties. By bringing together these two emerging technologies, complementary properties of both materials have been explored; for example, the synthesis of amphiphilic DNA-polymer conjugates has enabled the production of several nanostructures, such as spherical and rod-like micelles. Through both the DNA and polymer parts, stimuli-responsiveness can be instilled. Nanostructures have consequently been developed with responsive structural changes to physical properties, such as pH and temperature, as well as short DNA through competitive complementary binding. These responsive changes have enabled the application of DNA-polymer conjugates in biomedical applications including drug delivery. This review discusses the progress of DNA-polymer conjugates, exploring the synthetic routes and state-of-the-art applications afforded through the combination of nucleic acids and synthetic polymers.
Collapse
Affiliation(s)
- Colette
J. Whitfield
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Meizhou Zhang
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - Pia Winterwerber
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuzhou Wu
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
25
|
Händler T, Tutmarc C, Glaser M, Freitag JS, Smith DM, Schnauß J. Measuring structural parameters of crosslinked and entangled semiflexible polymer networks with single-filament tracing. Phys Rev E 2021; 103:062501. [PMID: 34271634 DOI: 10.1103/physreve.103.062501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/17/2021] [Indexed: 12/15/2022]
Abstract
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular interactions with the surrounding network impacts the measurement of these parameters has not been possible with the established experimental systems. Here we use mechanically programmable DNA nanotubes embedded in crosslinked and entangled F-actin networks, as well as in synthetic DNA networks, in order to measure fundamental, structural network properties like tube width and mesh size with respect to the stiffness of the tracers. While we confirm some predictions derived from models based purely on steric interactions, our results indicate that these models should be expanded to account for additional interfilament interactions, thereby describing the behavior of real polymer networks.
Collapse
Affiliation(s)
- Tina Händler
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Cary Tutmarc
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Martin Glaser
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany
| | - David M Smith
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany.,Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India
| | - Jörg Schnauß
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany.,Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
| |
Collapse
|
26
|
Prokhorov VV, Barinov NA, Prusakov KA, Dubrovin EV, Frank-Kamenetskii MD, Klinov DV. Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations. NANO-MICRO LETTERS 2021; 13:130. [PMID: 34138333 PMCID: PMC8141082 DOI: 10.1007/s40820-021-00626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.
Collapse
Affiliation(s)
- Valery V Prokhorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Leninsky prospect 31, Moscow, 199071, Russian Federation.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
| | - Kirill A Prusakov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation
- Lomonosov Moscow State University, Leninskie gory, 1-2, Moscow, 119991, Russian Federation
| | | | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya, 1a, Moscow, 119435, Russian Federation.
- Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, 141700, Moscow, Russian Federation.
| |
Collapse
|
27
|
Lamperski S, Bhuiyan LB. Entropy formation of an electrical double layer with divalent off-centre charge cations: Monte Carlo studies. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1918774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Stanisław Lamperski
- Department of Physical Chemistry, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Lutful Bari Bhuiyan
- Department of Physics, Laboratory of Theoretical Physics, University of Puerto Rico, San Juan, PR, USA
| |
Collapse
|
28
|
Bovone G, Dudaryeva OY, Marco-Dufort B, Tibbitt MW. Engineering Hydrogel Adhesion for Biomedical Applications via Chemical Design of the Junction. ACS Biomater Sci Eng 2021; 7:4048-4076. [PMID: 33792286 DOI: 10.1021/acsbiomaterials.0c01677] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrogel adhesion inherently relies on engineering the contact surface at soft and hydrated interfaces. Upon contact, adhesion normally occurs through the formation of chemical or physical interactions between the disparate surfaces. The ability to form these adhesion junctions is challenging for hydrogels as the interfaces are wet and deformable and often contain low densities of functional groups. In this Review, we link the design of the binding chemistries or adhesion junctions, whether covalent, dynamic covalent, supramolecular, or physical, to the emergent adhesive properties of soft and hydrated interfaces. Wet adhesion is useful for bonding to or between tissues and implants for a range of biomedical applications. We highlight several recent and emerging adhesive hydrogels for use in biomedicine in the context of efficient junction design. The main focus is on engineering hydrogel adhesion through molecular design of the junctions to tailor the adhesion strength, reversibility, stability, and response to environmental stimuli.
Collapse
Affiliation(s)
- Giovanni Bovone
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Oksana Y Dudaryeva
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Marco-Dufort
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Mark W Tibbitt
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| |
Collapse
|
29
|
Emanuel MD, Cherstvy AG, Metzler R, Gompper G. Buckling transitions and soft-phase invasion of two-component icosahedral shells. Phys Rev E 2021; 102:062104. [PMID: 33465945 DOI: 10.1103/physreve.102.062104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/11/2020] [Indexed: 12/18/2022]
Abstract
What is the optimal distribution of two types of crystalline phases on the surface of icosahedral shells, such as of many viral capsids? We here investigate the distribution of a thin layer of soft material on a crystalline convex icosahedral shell. We demonstrate how the shapes of spherical viruses can be understood from the perspective of elasticity theory of thin two-component shells. We develop a theory of shape transformations of an icosahedral shell upon addition of a softer, but still crystalline, material onto its surface. We show how the soft component "invades" the regions with the highest elastic energy and stress imposed by the 12 topological defects on the surface. We explore the phase diagram as a function of the surface fraction of the soft material, the shell size, and the incommensurability of the elastic moduli of the rigid and soft phases. We find that, as expected, progressive filling of the rigid shell by the soft phase starts from the most deformed regions of the icosahedron. With a progressively increasing soft-phase coverage, the spherical segments of domes are filled first (12 vertices of the shell), then the cylindrical segments connecting the domes (30 edges) are invaded, and, ultimately, the 20 flat faces of the icosahedral shell tend to be occupied by the soft material. We present a detailed theoretical investigation of the first two stages of this invasion process and develop a model of morphological changes of the cone structure that permits noncircular cross sections. In conclusion, we discuss the biological relevance of some structures predicted from our calculations, in particular for the shape of viral capsids.
Collapse
Affiliation(s)
- Marc D Emanuel
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Kavli Institute for Nanoscience, Technical University Delft, 2628 CJ Delft, Netherlands
| | - Andrey G Cherstvy
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
30
|
Xie X, Zheng T, Li W. Recent Progress in Ionic Coassembly of Cationic Peptides and Anionic Species. Macromol Rapid Commun 2020; 41:e2000534. [PMID: 33225490 DOI: 10.1002/marc.202000534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Peptide assembly has been extensively exploited as a promising platform for the creation of hierarchical nanostructures and tailor-made bioactive materials. Ionic coassembly of cationic peptides and anionic species is paving the way to provide particularly important contribution to this topic. In this review, the recent progress of ionic coassembly soft materials derived from the electrostatic coupling between cationic peptides and anionic species in aqueous solution is systematically summarized. The presentation of this review starts from a brief background on the general importance and advantages of peptide-based ionic coassembly. After that, diverse combinations of cationic peptides with small anions, macro- and/or oligo-anions, anionic polymers, and inorganic polyoxometalates are described. Emphasis is placed on the hierarchical structures, value-added properties, and applications. The molecular design of cationic peptides and the general principles behind the ionic coassembled structures are discussed. It is summarized that the combination of interesting and unique characteristics that arise both from the chemical diversity of peptides and the wide range of anionic species may contribute in a variety of output, including drug delivery, tissue engineering, gene transfection, and antibacterial activity. The emergent new phenomena and findings are illustrated. Finally, the outlook for the peptide-based ionic coassembly systems is also presented.
Collapse
Affiliation(s)
- Xiaoming Xie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjing Avenue 2699, Changchun, 130012, China.,Department of Chemistry, Xinzhou Teachers' University, Xinzhou, Shanxi, 034000, China
| | - Tingting Zheng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjing Avenue 2699, Changchun, 130012, China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjing Avenue 2699, Changchun, 130012, China
| |
Collapse
|
31
|
Liu YF, Ran SY. Divalent metal ions and intermolecular interactions facilitate DNA network formation. Colloids Surf B Biointerfaces 2020; 194:111117. [PMID: 32512310 DOI: 10.1016/j.colsurfb.2020.111117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn2+, Zn2+, Co2+, Ni2+, and Cd2+), except Mg2+ and Ca2+, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.
Collapse
Affiliation(s)
- Yin-Feng Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
32
|
Munawar KS, Ali S, Tahir MN, Khalid N, Abbas Q, Qureshi IZ, Hussain S, Ashfaq M. Synthesis, spectroscopic characterization, X-ray crystal structure, antimicrobial, DNA-binding, alkaline phosphatase and insulin-mimetic studies of oxidovanadium(IV) complexes of azomethine precursors. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1813282] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Khurram Shahzad Munawar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
- Department of Chemistry, University of Mianwali, Mianwali, Pakistan
| | - Saqib Ali
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Nasir Khalid
- Chemistry Division, Pakistan Institute of Nuclear Science & Technology, Islamabad, Pakistan
| | - Qamar Abbas
- Department of Physiology, University of Sindh, Jamshroo, Pakistan
| | - Irfan Zia Qureshi
- Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shabbir Hussain
- Department of Chemistry, Lahore Garrison University, Lahore, Pakistan
| | - Muhammad Ashfaq
- Department of Physics, University of Sargodha, Sargodha, Pakistan
| |
Collapse
|
33
|
Caetano DLZ, de Carvalho SJ, Metzler R, Cherstvy AG. Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption-desorption transition boundary. J R Soc Interface 2020; 17:20200199. [PMID: 32574545 PMCID: PMC7328387 DOI: 10.1098/rsif.2020.0199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption-the phase-separation curve between the adsorbed and desorbed states of the PEs-as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE-SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption-desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.
Collapse
Affiliation(s)
- Daniel L. Z. Caetano
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, Campus São José do Rio Preto, 15054-000 Brazil
- Institute of Chemistry, State University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
- Center for Computational Engineering and Sciences, State University of Campinas (UNICAMP), 13083-970 Campinas, Brazil
| | - Sidney J. de Carvalho
- São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, Campus São José do Rio Preto, 15054-000 Brazil
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G. Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| |
Collapse
|
34
|
Sachdev S, Feijoo Moreira S, Keehnen Y, Rems L, Kreutzer MT, Boukany PE. DNA-membrane complex formation during electroporation is DNA size-dependent. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183089. [DOI: 10.1016/j.bbamem.2019.183089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 09/11/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023]
|
35
|
Chen X, Chen EQ, Yang S. Multivalent counterions induced attraction between DNA polyelectrolytes. RSC Adv 2020; 10:1890-1900. [PMID: 35494593 PMCID: PMC9048762 DOI: 10.1039/c9ra09694a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/30/2019] [Indexed: 12/26/2022] Open
Abstract
In this paper we study the electrostatic attraction between two parallel rodlike DNA polyelectrolytes induced by neutralizing multivalent counterions at the zero temperature limit. The counterions crystallize on the charged surfaces of DNA so that we can handle the system by using the Wigner crystal lattice model. We derived the 3D ground state configuration of counterions with minimized energy by use of the gradient descent method, and calculated the interaction between two DNA cylinders with divalent or trivalent counterions when they approach. The results show that the complex ground state configuration of counterions plays a key role in determining the caused attraction. The counterions form three-dimensional Wigner crystals on each cylinder at large separation. When the cylinders are brought together, some counterion lines will move towards the inner region and lead to strong attraction. The calculated interaction from our model is in good agreement with the simulation result, however, the single particle approximation considerably overestimates the attraction. Counterions in the ground state partially condense in the intervening region of two approaching DNA cylinders and result in attraction.![]()
Collapse
Affiliation(s)
- Xu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Mater Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Er-Qiang Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Mater Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Mater Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
| |
Collapse
|
36
|
Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci 2019; 10:9315-9325. [PMID: 32110294 PMCID: PMC7006624 DOI: 10.1039/c9sc02990g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA-protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA-protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules.
Collapse
Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Eiji Nakata
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Zhengxiao Zhang
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Masayuki Saimura
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Huyen Dinh
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Takashi Morii
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| |
Collapse
|
37
|
Lamperski S, Henderson D, Bhuiyan LB. Off-centre charge model of the planar electric double layer for asymmetric 2:1/1:2 valencies. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1642527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Stanisław Lamperski
- Department of Physical Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, Poznań, Poland
| | - Douglas Henderson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Lutful Bari Bhuiyan
- Laboratory of Theoretical Physics, Department of Physics, University of Puerto Rico, San Juan, PR, USA
| |
Collapse
|
38
|
Liu KT, Ran SY. Multistage dynamics of Hg 2+-DNA interactions: a single-molecule study. Phys Chem Chem Phys 2019; 21:2919-2928. [PMID: 30675618 DOI: 10.1039/c8cp07399f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The metal ion-DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T-Hg2+-T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanism has not been fully understood. In the present study, we used magnetic tweezers to explore the interactions between λ-DNA and two metal ions, Hg2+ and Cd2+, at the single-molecule level. Both metal ions caused considerable DNA conformational changes. The resulting DNA compaction dynamics were related to the ion concentration and the exerted force. The increase in the ion concentration promoted DNA compaction, whereas exerting greater forces inhibited this process. Application of a high force generated two-stage dynamics of the Hg2+-DNA interaction. However, at a sufficiently high Hg2+ concentration, a lower force led to a three-stage process. In contrast, the curves of the binding of Cd2+ ions to DNA had a stepwise pattern. Both the AFM scanning results and the single-molecule measurements confirmed that Hg2+ influences the DNA conformation in a more pronounced manner than Cd2+. The multistage Hg2+-DNA interaction was considered to be a result of the different binding mechanisms, including the mismatched base-pair formation. A model was then proposed to explain the peculiar dynamics.
Collapse
Affiliation(s)
- Kang-Tao Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | | |
Collapse
|
39
|
González-Tovar E, Lozada-Cassou M, Bhuiyan LB, Outhwaite CW. Comparison of zeta potentials and structure for statistical mechanical theories of a model cylindrical double layer. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
40
|
Lamperski S, Bhuiyan LB, Henderson D. Off-center charge model revisited: Electrical double layer with multivalent cations. J Chem Phys 2018; 149:084706. [PMID: 30193502 DOI: 10.1063/1.5048309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The off-center charge model of ions is a relatively simple model for introducing asymmetry in Coulomb interaction while retaining the simplicity and convenience of the spherical hard core geometry. A Monte Carlo simulation analysis of the planar electric double layer formed by this ionic model for 1+:1- valence systems [S. Lamperski et al., Langmuir 33, 11554-11560 (2017)] is extended to include solutions of multivalent (2+, 3+) hard spherical cations and single valence (1-) hard spherical anions near a uniformly charged, planar electrode. The solvent is modelled as a uniform dielectric continuum with a dielectric constant equal to that of the pure solvent, viz., the primitive model. Results are reported for the ion density, the cation charge profile, and the electrostatic potential profile at 1 mol/dm3 salt concentration. Additionally, the double layer potential drop, that is, the electrode potential, and the integral and the differential capacitances are computed as functions of the electrode surface charge density. The latter two quantities show an expected asymmetry as long as the cation valence is not too great and the charge of the off-center ion cannot approach too close to the electrode surface. It is unusual that the integral and differential capacitances are negative for high valence cations and a negatively charged electrode when the off-center charge is large and can be very near the surface of the electrode. The corresponding electrode potential versus surface charge density curve becomes non-monotonic and shows a change of slope, and thus the resultant integral and differential capacitances can become negative. This nonphysical result is the result of an incipient singularity when a large positive charge is too near a negatively charged electrode. Overall, the off-center charge model suggests a useful recipe to model electrical asymmetry within the broader context of the primitive model provided that the off-center charge is not too near the surface of the electrode.
Collapse
Affiliation(s)
- Stanisław Lamperski
- Department of Physical Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań, Poland
| | - Lutful Bari Bhuiyan
- Laboratory of Theoretical Physics, Department of Physics, University of Puerto Rico, San Juan, Puerto Rico 00931-3343, USA
| | - Douglas Henderson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602-5700, USA
| |
Collapse
|
41
|
Zavadlav J, Sablić J, Podgornik R, Praprotnik M. Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution. Biophys J 2018; 114:2352-2362. [PMID: 29650370 PMCID: PMC6129463 DOI: 10.1016/j.bpj.2018.02.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/24/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.
Collapse
Affiliation(s)
- Julija Zavadlav
- Computational Science & Engineering Laboratory, ETH Zurich, Zurich, Switzerland
| | - Jurij Sablić
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Rudolf Podgornik
- Theoretical Physics Department, J. Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.
| |
Collapse
|
42
|
Wang Y, Wang R, Gao T, Yang G. The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength. Polymers (Basel) 2018; 10:E244. [PMID: 30966279 PMCID: PMC6415083 DOI: 10.3390/polym10030244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 12/18/2022] Open
Abstract
DNA compaction and charge neutralization in a mixing counterion solution involves competitive and cooperative electrostatic binding, and sometimes counterion complexation. At normal ionic strength, it has been found that the charge neutralization of DNA by the multivalent counterion is suppressed when being added extra mono- and di-valent counterions. Here, we explore the effect mixing counterion on DNA compaction and charge neutralization under the condition of low ionic strength. Being quite different from normal ionic strength, the electrophoretic mobility of DNA in multivalent counterion solution (octalysine, spermine) increases the presence of mono- and di-valent cations, such as sodium and magnesium ions. It means that the charge neutralization of DNA by the multivalent counterion is promoted rather than suppressed when introducing extra mono- and di-valent counterions into solution. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates under the same condition by single molecular magnetic tweezers. This mixing effect can be attributed to the cooperative electrostatic binding of counterions to DNA when the concentration of counterions in solution is below a critical concentration.
Collapse
Affiliation(s)
- Yanwei Wang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Ruxia Wang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- College of Mathematical, Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
43
|
Korolev N, Lyubartsev AP, Nordenskiöld L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep 2018; 8:1543. [PMID: 29367745 PMCID: PMC5784010 DOI: 10.1038/s41598-018-19875-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
Collapse
Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
44
|
|
45
|
Leung KK, Gaxiola AD, Yu HZ, Bizzotto D. Tailoring the DNA SAM surface density on different surface crystallographic features using potential assisted thiol exchange. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2017.12.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
46
|
Kar P, Cherstvy AG, Metzler R. Acceleration of bursty multiprotein target search kinetics on DNA by colocalisation. Phys Chem Chem Phys 2018; 20:7931-7946. [DOI: 10.1039/c7cp06922g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proteins are capable of locating specific targets on DNA by employing a facilitated diffusion process with intermittent 1D and 3D search steps. We here uncover the implications of colocalisation of protein production and DNA binding sites via computer simulations.
Collapse
Affiliation(s)
- Prathitha Kar
- Dept of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bengaluru
- India
- Institute for Physics & Astronomy
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| |
Collapse
|
47
|
Zhitnikova M, Shestopalova A. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations. J Biomol Struct Dyn 2017; 35:3384-3397. [DOI: 10.1080/07391102.2016.1255259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M.Y. Zhitnikova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
| | - A.V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
| |
Collapse
|
48
|
Zhang JS, Zhang X, Zhang ZL, Tan ZJ. Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson-Boltzmann theory and Monte Carlo simulations. Sci Rep 2017; 7:14145. [PMID: 29074886 PMCID: PMC5658377 DOI: 10.1038/s41598-017-14636-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/12/2017] [Indexed: 01/31/2023] Open
Abstract
Ion-mediated interactions between like-charged polyelectrolytes have been paid much attention, and the Poisson-Boltzmann (PB) theory has been shown to fail in qualitatively predicting multivalent ion-mediated like-charge attraction. However, inadequate attention has been paid to the ion-mediated interactions between oppositely charged polyelectrolytes. In this work, the potentials of mean force (PMF) between oppositely charged nanoparticles in 1:1 and 2:2 salt solutions were investigated by Monte Carlo simulations and the PB theory. Our calculations show that the PMFs between oppositely charged nanoparticles are generally attractive in 1:1 and 2:2 salt solutions and that such attractive PMFs become weaker at higher 1:1 or 2:2 salt concentrations. The comprehensive comparisons show that the PB theory can quantitatively predict the PMFs between oppositely charged nanoparticles in 1:1 salt solutions, except for the slight deviation at very high 1:1 salt concentration. However, for 2:2 salt solutions, the PB theory generally overestimates the attractive PMF between oppositely charged nanoparticles, and this overestimation becomes more pronounced for nanoparticles with higher charge density and for higher 2:2 salt concentration. Our microscopic analyses suggest that the overestimation of the PB theory on the attractive PMFs for 2:2 salt solutions is attributed to the underestimation of divalent ions bound to nanoparticles.
Collapse
Affiliation(s)
- Jin-Si Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
49
|
Zhang ZL, Wu YY, Xi K, Sang JP, Tan ZJ. Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex. Biophys J 2017; 113:517-528. [PMID: 28793207 DOI: 10.1016/j.bpj.2017.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.
Collapse
Affiliation(s)
- Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Jian-Ping Sang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| |
Collapse
|
50
|
Zavadlav J, Podgornik R, Praprotnik M. Order and interactions in DNA arrays: Multiscale molecular dynamics simulation. Sci Rep 2017; 7:4775. [PMID: 28684875 PMCID: PMC5500594 DOI: 10.1038/s41598-017-05109-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/06/2017] [Indexed: 11/21/2022] Open
Abstract
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
Collapse
Affiliation(s)
- Julija Zavadlav
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.,Chair of Computational Science, ETH Zurich, Clausiusstrasse 33, CH-8092, Zurich, Switzerland
| | - Rudolf Podgornik
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia. .,Theoretical Physics Department, J. Stefan Institute, Jamova c. 39, SI-1000, Ljubljana, Slovenia.
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia. .,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.
| |
Collapse
|