1
|
Xiong Q, Lee OS, Mirkin CA, Schatz G. Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State. J Am Chem Soc 2023; 145:706-716. [PMID: 36573457 DOI: 10.1021/jacs.2c11834] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation.
Collapse
Affiliation(s)
- Qinsi Xiong
- Department of Chemistry, Northwestern University, Evanston, Illinois60208-3113, United States
| | - One-Sun Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois60208-3113, United States
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, Evanston, Illinois60208-3113, United States.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois60208, United States.,International Institute for Nanotechnology, Northwestern University, Evanston, Illinois60208, United States
| | - George Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois60208-3113, United States
| |
Collapse
|
2
|
Ajamgard M, Sardroodi JJ, Ebrahimzadeh AR, Kamelabad MR. Molecular dynamics simulation study of gold nanosheet as drug delivery vehicles for anti-HIV-1 aptamers. Comput Biol Chem 2021; 95:107595. [PMID: 34739903 DOI: 10.1016/j.compbiolchem.2021.107595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/25/2021] [Accepted: 10/21/2021] [Indexed: 11/15/2022]
Abstract
The adsorption process of three aptamers with gold nanosheet (GNS) as a drug carrier has been investigated with the help of molecular dynamics simulations. The sequencing of the considered aptamers are as (CUUCAUUGUAACUUCUCAUAAUUUCCCGAGGCUUUUACUUUCGGGGUCCU) and (CCGGGUCGUCCCCUACGGGGACUAAAGACUGUGUCCAACCGCCCUCGCCU) for AP1 and AP2, respectively. AP3 is a muted version of AP1 in which nucleotide positions 4, 6, 18, 28 and 39 have C4A, U6G, A18G, G28A, and U39C mutations. At positions 24, and 40, a deletion mutation is seen to eliminate U24 and U40 bases. These aptamers are inhibitors for HIV-1 protease and can be candidates as potential pharmaceutics for treatment of AIDS in the future. The interactions between considered aptamers and GNS have been analyzed in detail with help of structural and energetic properties. These analyses showed that all three aptamers could well adsorb on GNS. Overall, the final results show that the adsorption of AP2 on the GNS is more favorable than other considered ones and consequently GNS can be considered as a device in order to immobilize these aptamers.
Collapse
Affiliation(s)
- Marzieh Ajamgard
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran.
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Physics, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Mahrokh Rezaei Kamelabad
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| |
Collapse
|
3
|
Lee OS, Madjet ME, Mahmoud KA. Antibacterial Mechanism of Multifunctional MXene Nanosheets: Domain Formation and Phase Transition in Lipid Bilayer. NANO LETTERS 2021; 21:8510-8517. [PMID: 34402623 DOI: 10.1021/acs.nanolett.1c01986] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
MXenes, two-dimensional metal carbides or nitrides with multifunctional surfaces, are one of the most promising antibacterial nanoscale materials. However, their putative bactericidal mechanism is elusive. To study their bactericidal mechanism, we investigated the interaction between a MXene nanosheet and a model bacterial membrane by molecular dynamics simulations and found that an adsorbed MXene on a membrane surface induced a local phase transition in a domain where the fluidity of the phospholipid in this domain at room temperature was comparable with that of the gel phase. The domain also showed a denser and thinner phospholipid membrane structure than the peripheral phospholipids. By comparing it with our previous experiments of the bactericidal activity of MXenes, we proposed the leakage of intercellular molecules at the phase boundary defects as a possible bactericidal mechanism of MXenes that leads to cell lysis. This study provides a useful model for tailoring new bactericidal nanomaterials.
Collapse
Affiliation(s)
- One-Sun Lee
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, PO Box 34110 Doha, Qatar
| | - Mohamed E Madjet
- Max-Planck-Institut für Physik, Komplexer Systeme, Nöthnitzer Straße 38, 01187 Dresden, Germany
| | - Khaled A Mahmoud
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, PO Box 34110 Doha, Qatar
| |
Collapse
|
4
|
Abstract
Gold nanorods assembled in a side-by-side chiral configuration have potential applications in sensing due to their strong chiroptical surface plasmon resonances. Recent experiments have shown that dimers of gold nanorods bridged by double-stranded DNA exhibit variable chiral configurations depending on the chemical and ionic properties of the solvent medium. Here, we uncover the underlying physics governing this intriguing chiral behavior of such DNA-bridged nanorods by theoretically evaluating their configurational free energy landscape. Our results reveal how chiral configurations emerge from an interplay between the twist-stretch coupling of the intervening DNA and the intermolecular interactions between the nanorods, with dimers exhibiting left-handed chirality when the interparticle interactions are dominated by attractive depletion or van der Waals forces and right-handed chirality when dominated by repulsive electrostatic or steric forces. We demonstrate how changes in the depletant or ion concentration of the solvent medium lead to different classes of configurational responses by the dimers, including chirality-switching behavior, in good agreement with experimental observations. Based on extensive analyses of how material properties like nanorod aspect ratio, DNA length, and graft height modulate the free energy landscape, we propose strategies for tuning the environmentally responsive reconfigurability of the nanorod dimers. Overall, this work should help control the chirality and related optical activity of nanoparticle dimers and higher-order assemblies for various applications.
Collapse
Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
5
|
Khavani M, Izadyar M, Housaindokht MR. RNA aptasensor based on gold nanoparticles for selective detection of neomycin B, molecular approach. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01708-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
6
|
Lee S, Johnson SN, Ellington TL, Mirsaleh-Kohan N, Tschumper GS. Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions. ACS OMEGA 2018; 3:12936-12943. [PMID: 31458017 PMCID: PMC6645001 DOI: 10.1021/acsomega.8b01895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 06/10/2023]
Abstract
This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.
Collapse
Affiliation(s)
- Suhwan
Paul Lee
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Sarah N. Johnson
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Thomas L. Ellington
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Nasrin Mirsaleh-Kohan
- Department
of Chemistry and Biochemistry, Texas Woman’s
University, Denton, Texas 76204, United States
| | - Gregory S. Tschumper
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| |
Collapse
|
7
|
Gabrys PA, Seo SE, Wang MX, Oh E, Macfarlane RJ, Mirkin CA. Lattice Mismatch in Crystalline Nanoparticle Thin Films. NANO LETTERS 2018; 18:579-585. [PMID: 29271207 DOI: 10.1021/acs.nanolett.7b04737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
For atomic thin films, lattice mismatch during heteroepitaxy leads to an accumulation of strain energy, generally causing the films to irreversibly deform and generate defects. In contrast, more elastically malleable building blocks should be better able to accommodate this mismatch and the resulting strain. Herein, that hypothesis is tested by utilizing DNA-modified nanoparticles as "soft," programmable atom equivalents to grow a heteroepitaxial colloidal thin film. Calculations of interaction potentials, small-angle X-ray scattering data, and electron microscopy images show that the oligomer corona surrounding a particle core can deform and rearrange to store elastic strain up to ±7.7% lattice mismatch, substantially exceeding the ±1% mismatch tolerated by atomic thin films. Importantly, these DNA-coated particles dissipate strain both elastically through a gradual and coherent relaxation/broadening of the mismatched lattice parameter and plastically (irreversibly) through the formation of dislocations or vacancies. These data also suggest that the DNA cannot be extended as readily as compressed, and thus the thin films exhibit distinctly different relaxation behavior in the positive and negative lattice mismatch regimes. These observations provide a more general understanding of how utilizing rigid building blocks coated with soft compressible polymeric materials can be used to control nano- and microstructure.
Collapse
Affiliation(s)
- Paul A Gabrys
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | | | | | | | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT) , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | | |
Collapse
|
8
|
Sun M, Xu L, Bahng JH, Kuang H, Alben S, Kotov NA, Xu C. Intracellular localization of nanoparticle dimers by chirality reversal. Nat Commun 2017; 8:1847. [PMID: 29185441 PMCID: PMC5707389 DOI: 10.1038/s41467-017-01337-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/11/2017] [Indexed: 01/01/2023] Open
Abstract
The intra- and extracellular positioning of plasmonic nanoparticles (NPs) can dramatically alter their curative/diagnostic abilities and medical outcomes. However, the inability of common spectroscopic identifiers to register the events of transmembrane transport denies their intracellular vs. extracellular localization even for cell cultures. Here we show that the chiroptical activity of DNA-bridged NP dimers allows one to follow the process of internalization of the particles by the mammalian cells and to distinguish their extra- vs intra-cellular localizations by real-time spectroscopy in ensemble. Circular dichroism peaks in the visible range change from negative to positive during transmembrane transport. The chirality reversal is associated with a spontaneous twisting motion around the DNA bridge caused by the large change in electrostatic repulsion between NPs when the dimers move from interstitial fluid to cytosol. This finding opens the door for spectroscopic targeting of plasmonic nanodrugs and quantitative assessment of nanoscale interactions. The efficacy of dichroic targeting of chiral nanostructures for biomedical applications is exemplified here as photodynamic therapy of malignancies. The efficacy of cervical cancer cell elimination was drastically increased when circular polarization of incident photons matched to the preferential absorption of dimers localized inside the cancer cells, which is associated with the increased generation of reactive oxygen species and their preferential intracellular localization. The ability to spectroscopically pinpoint whether nanoparticles are located inside or outside of cells represents an overarching need in biology and medicine. Here, the authors show that the chirality of DNA-bridged particle dimers reverses when they cross the cell membrane, providing a real-time chiroptical signature of their intra- or extracellular location.
Collapse
Affiliation(s)
- Maozhong Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, 214122, China
| | - Liguang Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, 214122, China
| | - Joong Hwan Bahng
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hua Kuang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, 214122, China.
| | - Silas Alben
- Department of Mathematics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicholas A Kotov
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Material Sciences and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, 48109, USA. .,Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Chuanlai Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
9
|
Seo SE, Li T, Senesi AJ, Mirkin CA, Lee B. The Role of Repulsion in Colloidal Crystal Engineering with DNA. J Am Chem Soc 2017; 139:16528-16535. [DOI: 10.1021/jacs.7b06734] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Soyoung E. Seo
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Tao Li
- X-ray
Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, Illinois 60439, United States
| | - Andrew J. Senesi
- X-ray
Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, Illinois 60439, United States
| | - Chad A. Mirkin
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Byeongdu Lee
- X-ray
Science Division, Argonne National Laboratory, 9700 Cass Avenue, Lemont, Illinois 60439, United States
| |
Collapse
|
10
|
Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
Collapse
Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| |
Collapse
|
11
|
Ruan M, Seydou M, Noel V, Piro B, Maurel F, Barbault F. Molecular Dynamics Simulation of a RNA Aptasensor. J Phys Chem B 2017; 121:4071-4080. [PMID: 28363022 DOI: 10.1021/acs.jpcb.6b12544] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
Collapse
Affiliation(s)
- Min Ruan
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France.,School of Materials and Metallurgy, Hubei Polytechnic University , Huangshi, Hubei, China
| | - Mahamadou Seydou
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Vincent Noel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Benoit Piro
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - François Maurel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Florent Barbault
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| |
Collapse
|
12
|
Mason JA, Laramy CR, Lai CT, O'Brien MN, Lin QY, Dravid VP, Schatz GC, Mirkin CA. Contraction and Expansion of Stimuli-Responsive DNA Bonds in Flexible Colloidal Crystals. J Am Chem Soc 2016; 138:8722-5. [PMID: 27402303 DOI: 10.1021/jacs.6b05430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA surface ligands can be used as programmable "bonds" to control the arrangement of nanoparticles into crystalline superlattices. Here, we study the intrinsic responsiveness of these DNA bonds to changes in local dielectric constant (εr) as a new approach to dynamically modulate superlattice structure. Remarkably, ethanol (EtOH) addition can be used to controllably tune DNA bond length from 16 to 3 nm and to increase bond stability by >40 °C, while retaining long-range order and crystal habit. Interestingly, we find that these structural changes, which involve the expansion and contraction of crystals by up to 75% in volume, occur in a cooperative fashion once a critical percentage of EtOH is reached. These results provide a facile and robust approach to create stimuli-responsive lattices, to access high volume fractions, and to improve thermal stability.
Collapse
Affiliation(s)
- Jarad A Mason
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Christine R Laramy
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Cheng-Tsung Lai
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Matthew N O'Brien
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Qing-Yuan Lin
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - George C Schatz
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Chemical and Biological Engineering, and ∥Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| |
Collapse
|
13
|
Charchar P, Christofferson AJ, Todorova N, Yarovsky I. Understanding and Designing the Gold-Bio Interface: Insights from Simulations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2395-418. [PMID: 27007031 DOI: 10.1002/smll.201503585] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/01/2016] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.
Collapse
Affiliation(s)
- Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | | | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| |
Collapse
|
14
|
Chandra GK, Eklouh-Molinier C, Fere M, Angiboust JF, Gobinet C, Van-Gulick L, Jeannesson P, Piot O. Probing in Vitro Ribose Induced DNA-Glycation Using Raman Microspectroscopy. Anal Chem 2015; 87:2655-64. [DOI: 10.1021/acs.analchem.5b00182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Goutam Kumar Chandra
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Christophe Eklouh-Molinier
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Michael Fere
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Jean-François Angiboust
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Cyril Gobinet
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Laurence Van-Gulick
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Pierre Jeannesson
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Olivier Piot
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| |
Collapse
|
15
|
Radha B, Senesi AJ, O'Brien MN, Wang MX, Auyeung E, Lee B, Mirkin CA. Reconstitutable nanoparticle superlattices. NANO LETTERS 2014; 14:2162-2167. [PMID: 24641553 DOI: 10.1021/nl500473t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal self-assembly predominantly results in lattices that are either: (1) fixed in the solid state and not amenable to additional modification, or (2) in solution, capable of dynamic adjustment, but difficult to transition to other environments. Accordingly, approaches to both dynamically adjust the interparticle spacing of nanoparticle superlattices and reversibly transfer superlattices between solution-phase and solid state environments are limited. In this manuscript, we report the reversible contraction and expansion of nanoparticles within immobilized monolayers, surface-assembled superlattices, and free-standing single crystal superlattices through dehydration and subsequent rehydration. Interestingly, DNA contraction upon dehydration occurs in a highly uniform manner, which allows access to spacings as small as 4.6 nm and as much as a 63% contraction in the volume of the lattice. This enables one to deliberately control interparticle spacings over a 4-46 nm range and to preserve solution-phase lattice symmetry in the solid state. This approach could be of use in the study of distance-dependent properties of nanoparticle superlattices and for long-term superlattice preservation.
Collapse
Affiliation(s)
- Boya Radha
- Department of Chemistry, ‡International Institute for Nanotechnology, §Department of Materials Science and Engineering, and ∥Department of Chemical and Biological Engineering, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | | | | | | | | | | | | |
Collapse
|
16
|
Simulation study on dynamics of A- to B-form transition in aqueous DNA solution: Effect of alkali metal counterions. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4959-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
17
|
Yu Y, Fujimoto S. Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution. Sci China Chem 2013. [DOI: 10.1007/s11426-012-4825-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Kohlstedt KL, Olvera de la Cruz M, Schatz GC. Controlling Orientational Order in 1-D Assemblies of Multivalent Triangular Prisms. J Phys Chem Lett 2013; 4:203-208. [PMID: 26291232 DOI: 10.1021/jz301953k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Multivalent nanostructures are becoming an increasingly important player in the self-assembly of supramolecular lattices. Understanding the role that shape plays in the coordination of the assemblies is crucial for the functional response of the material. We develop a simple design rule for the assembly of multivalent Au triangular nanoprisms into 1-D ordered arrays based on both the length of the valent DNA and the aspect ratio of the prism. Using MD simulations, we describe an order parameter that captures the short-range order of the assembly controlled by the design parameters. The order parameter shows that even short chains (N = 4) of prisms have a high degree of orientational order that transitions to no orientational order when the DNA length is similar to the prism length. Unlike isotropic polyvalent assemblies, we find that the highly oriented chains of prisms lose orientational order in discrete steps during melting as the prisms in the arrays dissociate.
Collapse
Affiliation(s)
- Kevin L Kohlstedt
- †Department of Chemistry and ‡Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- †Department of Chemistry and ‡Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - George C Schatz
- †Department of Chemistry and ‡Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
19
|
Doni G, Nkoua Ngavouka MD, Barducci A, Parisse P, De Vita A, Scoles G, Casalis L, Pavan GM. Structural and energetic basis for hybridization limits in high-density DNA monolayers. NANOSCALE 2013; 5:9988-93. [PMID: 23996015 DOI: 10.1039/c3nr01799k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Giovanni Doni
- Department of Physics, King's College London, London WC2R 2LS, UK
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Michele LD, Eiser E. Developments in understanding and controlling self assembly of DNA-functionalized colloids. Phys Chem Chem Phys 2013; 15:3115-29. [DOI: 10.1039/c3cp43841d] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|