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Ding F, Zhang S, Chen Q, Feng H, Ge Z, Zuo X, Fan C, Li Q, Xia Q. Immunomodulation with Nucleic Acid Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206228. [PMID: 36599642 DOI: 10.1002/smll.202206228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.
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Affiliation(s)
- Fei Ding
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Shuangye Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Chen
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Hao Feng
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiaolei Zuo
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- WLA Laboratories, World Laureates Association, Shanghai, 201203, P. R. China
| | - Qiang Xia
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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2
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Lattuada E, Caprara D, Piazza R, Sciortino F. Spatially uniform dynamics in equilibrium colloidal gels. SCIENCE ADVANCES 2021; 7:eabk2360. [PMID: 34860553 PMCID: PMC8641940 DOI: 10.1126/sciadv.abk2360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Gels of DNA nanostars, besides providing a compatible scaffold for biomedical applications, are ideal model systems for testing the physics of equilibrium colloidal gels. Here, using dynamic light scattering and photon correlation imaging (a recent technique that, by blending light scattering and imaging, provides space-resolved quantification of the dynamics), we follow the process of gel formation over 10 orders of magnitude in time in a model system of tetravalent DNA nanostars in solution, a realization of limited-valence colloids. Such a system, depending on the nanostar concentration, can form either equilibrium or phase separation gels. In stark contrast to the heterogeneity of concentration and dynamics displayed by the phase separation gel, the equilibrium gel shows absence of aging and a remarkable spatially uniform dynamics.
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Affiliation(s)
- Enrico Lattuada
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Debora Caprara
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Roberto Piazza
- Department of Chemistry, Materials Science, and Chemical Engineering (CMIC), Politecnico di Milano, Edificio 6, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
- Corresponding author.
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3
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Abstract
A field theoretic representation of the classical partition function is derived for a system composed of a mixture of anisotropic and isotropic mobile charges that interact via long range Coulomb and short range nematic interactions. The field theory is then solved on a saddle-point approximation level, leading to a coupled system of Poisson–Boltzmann and Maier–Saupe equations. Explicit solutions are finally obtained for a rod-like counterion-only system in proximity to a charged planar wall. The nematic order parameter profile, the counterion density profile and the electrostatic potential profile are interpreted within the framework of a nematic–isotropic wetting phase with a Donnan potential difference.
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4
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Wang L, Urbas AM, Li Q. Nature-Inspired Emerging Chiral Liquid Crystal Nanostructures: From Molecular Self-Assembly to DNA Mesophase and Nanocolloids. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1801335. [PMID: 30160812 DOI: 10.1002/adma.201801335] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/17/2018] [Indexed: 05/22/2023]
Abstract
Liquid crystals (LCs) are omnipresent in living matter, whose chirality is an elegant and distinct feature in certain plant tissues, the cuticles of crabs, beetles, arthropods, and beyond. Taking inspiration from nature, researchers have recently devoted extensive efforts toward developing chiral liquid crystalline materials with self-organized nanostructures and exploring their potential applications in diverse fields ranging from dynamic photonics to energy and safety issues. In this review, an account on the state of the art of emerging chiral liquid crystalline nanostructured materials and their technological applications is provided. First, an overview on the significance of chiral liquid crystalline architectures in various living systems is given. Then, the recent significant progress in different chiral liquid crystalline systems including thermotropic LCs (cholesteric LCs, cubic blue phases, achiral bent-core LCs, etc.) and lyotropic LCs (DNA LCs, nanocellulose LCs, and graphene oxide LCs) is showcased. The review concludes with a perspective on the future scope, opportunities, and challenges in these truly advanced functional soft materials and their promising applications.
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Affiliation(s)
- Ling Wang
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, OH, 44242, USA
| | - Augustine M Urbas
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, 45433, USA
| | - Quan Li
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, OH, 44242, USA
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5
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Sun X, Liu H. Nucleic Acid Nanostructure Assisted Immune Modulation. ACS APPLIED BIO MATERIALS 2020; 3:2765-2778. [DOI: 10.1021/acsabm.9b01195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaoli Sun
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Haipeng Liu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
- Department of Oncology, Wayne State University, Detroit, Michigan 48201, United States
- Tumor Biology and Microenvironment Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
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6
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Control and optical mapping of mechanical transitions in polymer networks and DNA-based soft materials. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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7
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Yevdokimov YM, Skuridin SG, Salyanov VI, Bobrov YA, Bucharsky VA, Kats EI. New optical evidence of the cholesteric packing of DNA molecules in “re-entrant” phase. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Sticking and stacking: Persistent ordering of fragmented DNA analogs. Proc Natl Acad Sci U S A 2018; 115:8652-8654. [PMID: 30093389 DOI: 10.1073/pnas.1810662115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Zhang L, Maity S, Liu K, Liu Q, Göstl R, Portale G, Roos WH, Herrmann A. Nematic DNA Thermotropic Liquid Crystals with Photoresponsive Mechanical Properties. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701207. [PMID: 28696523 DOI: 10.1002/smll.201701207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Over the last decades, water-based lyotropic liquid crystals of nucleic acids have been extensively investigated because of their important role in biology. Alongside, solvent-free thermotropic liquid crystals (TLCs) from DNA are gaining great interest, owing to their relevance to DNA-inspired optoelectronic applications. Up to now, however, only the smectic phase of DNA TLCs has been reported. The development of new mesophases including nematic, hexagonal, and cubic structures for DNA TLCs remains a significant challenge, which thus limits their technological applications considerably. In this work, a new type of DNA TLC that is formed by electrostatic complexation of anionic oligonucleotides and cationic surfactants containing an azobenzene (AZO) moiety is demonstrated. DNA-AZO complexes form a stable nematic mesophase over a temperature range from -7 to 110 °C and retain double-stranded DNA structure at ambient temperature. Photoisomerization of the AZO moieties from the E- to the Z-form alters the stiffness of the DNA-AZO hybrid materials opening a pathway toward the development of DNA TLCs as stimuli-responsive biomaterials.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Sourav Maity
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
| | - Qing Liu
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Robert Göstl
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Giuseppe Portale
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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11
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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.
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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.
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12
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Abstract
Liquid crystals play an important role in biology because the combination of order and mobility is a basic requirement for self-organisation and structure formation in living systems. Cholesteric liquid crystals are omnipresent in living matter under both in vivo and in vitro conditions and address the major types of molecules essential to life. In the animal and plant kingdoms, the cholesteric structure is a recurring design, suggesting a convergent evolution to an optimised left-handed helix. Herein, we review the recent advances in the cholesteric organisation of DNA, chromatin, chitin, cellulose, collagen, viruses, silk and cholesterol ester deposition in atherosclerosis. Cholesteric structures can be found in bacteriophages, archaea, eukaryotes, bacterial nucleoids, chromosomes of unicellular algae, sperm nuclei of many vertebrates, cuticles of crustaceans and insects, bone, tendon, cornea, fish scales and scutes, cuttlebone and squid pens, plant cell walls, virus suspensions, silk produced by spiders and silkworms, and arterial wall lesions. This article specifically aims at describing the consequences of the cholesteric geometry in living matter, which are far from being fully defined and understood, and discusses various perspectives. The roles and functions of biological cholesteric liquid crystals include maximisation of packing efficiency, morphogenesis, mechanical stability, optical information, radiation protection and evolution pressure.
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Affiliation(s)
- Michel Mitov
- Centre d'Elaboration de Matériaux et d'Etudes Structurales (CEMES), CNRS, BP 94347, 29 rue Jeanne-Marvig, F-31055 Toulouse Cedex 4, France.
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13
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Saurabh S, Lansac Y, Jang YH, Glaser MA, Clark NA, Maiti PK. Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA. Phys Rev E 2017; 95:032702. [PMID: 28415169 DOI: 10.1103/physreve.95.032702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Indexed: 06/07/2023]
Abstract
Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.
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Affiliation(s)
- Suman Saurabh
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Yun Hee Jang
- Department of Energy Systems Engineering, DGIST, Daegu 42988, Korea
| | - Matthew A Glaser
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Noel A Clark
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
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14
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Yevdokimov YM, Skuridin SG, Semenov SV, Dadinova LA, Salyanov VI, Kats EI. Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles. J Biol Phys 2017; 43:45-68. [PMID: 28028733 PMCID: PMC5323345 DOI: 10.1007/s10867-016-9433-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/18/2016] [Indexed: 11/24/2022] Open
Abstract
In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)-PEG-with concentrations ranging from 120 mg ml-1 to 300 mg ml-1. In the range of PEG concentrations from 120 mg ml-1 to 220 mg ml-1 at room temperature, we find ds DNA molecule packing, typical of classical cholesterics. The corresponding parameters for dispersion particles obtained at concentrations greater than 220 mg ml-1 indicate hexagonal packing of the ds DNA molecules. However, slightly counter-intuitively, the cholesteric-like packing reappears upon the heating of dispersions with hexagonal packing of ds DNA molecules. This transition occurs when the PEG concentration is larger than 220 mg ml-1. The obtained new cholesteric structure differs from the classical cholesterics observed in the PEG concentration range 120-220 mg ml-1 (hence, the term 're-entrant'). Our conclusions are based on the measurements of circular dichroism spectra, X-ray scattering curves and textures of liquid-crystalline phases. We propose a qualitative (similar to the Lindemann criterion for melting of conventional crystals) explanation of this phenomenon in terms of partial melting of so-called quasinematic layers formed by the DNA molecules. The quasinematic layers change their spatial orientation as a result of the competition between the osmotic pressure of the solvent (favoring dense, unidirectional alignment of ds DNA molecules) and twist Frank orientation energy of adjacent layers (favoring cholesteric-like molecular packing).
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Affiliation(s)
- Yuri M Yevdokimov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia.
| | - Sergey G Skuridin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia
| | - Sergey V Semenov
- National Research Centre 'Kurchatov Institute', Kurchatova Sq. 1, 123182, Moscow, Russia
| | - Ljubov A Dadinova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of the Russian Academy of Sciences, Leninskii Ave. 59, 119333, Moscow, Russia
| | - Viktor I Salyanov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova St. 32, 119991, Moscow, Russia
| | - Efim I Kats
- Landau Institute for Theoretical Physics of the Russian Academy of Sciences, Kosygina St. 2, 119334, Moscow, Russia
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15
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Liu YZ, Manivannan K, Lee AW, Huang YJ, Wei PL, Chen JK. Identification of DNA single-base mismatches by resistivity of poly(N-isopropylacrylamide)-block-ssDNA copolymer brush films at dual temperatures. RSC Adv 2017. [DOI: 10.1039/c6ra28270a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The resistivity of tethered PNIPAAm-b-ssDNA copolymer brushes can be exploited to detect a label-free target by homogeneous complexation and phase separation.
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Affiliation(s)
- Yi-Zu Liu
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
| | - Karthikeyan Manivannan
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
| | - Ai-Wei Lee
- Department of Anatomy and Cell Biology
- School of Medicine
- College of Medicine
- Taipei Medical University
- Taipei 110
| | - Yan-Jiun Huang
- Department of Surgery
- College of Medicine
- Division of Colorectal Surgery
- Taipei Medical University Hospital
- Taipei Medical University
| | - Po-Li Wei
- Cancer Center
- Division of General Surgery
- Department of Surgery
- Taipei Medical University Hospital
- College of Medicine
| | - Jem-Kun Chen
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
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16
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Yevdokimov YM, Skuridin SG, Salyanov VI, Kats EI. Temperature-induced changes of the packing of double-stranded linear DNA molecules in particles of liquid-crystalline dispersions. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916030039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Nava G, Ceccarello E, Giavazzi F, Salina M, Damin F, Chiari M, Buscaglia M, Bellini T, Zanchetta G. Label-free detection of DNA single-base mismatches using a simple reflectance-based optical technique. Phys Chem Chem Phys 2016; 18:13395-402. [PMID: 27122358 DOI: 10.1039/c5cp08017g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid and quantitative detection of the binding of nucleic acids to surface-immobilized probes remains a challenge in many biomedical applications. We investigated the hybridization of a set of fully complementary and defected 12-base long DNA oligomers by using the Reflective Phantom Interface (RPI), a recently developed multiplexed label-free detection technique. Based on the simple measurement of reflected light intensity, this technology enables to quantify the hybridization directly as it occurs on the surface with a sensitivity of 10 pg mm(-2). We found a strong effect of single-base mismatches and of their location on hybridization kinetics and equilibrium binding. In line with previous studies, we found that DNA-DNA binding is weaker on a surface than in the bulk. Our data indicate that this effect is a consequence of weak nonspecific binding of the probes to the surface.
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Affiliation(s)
- G Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
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19
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Abstract
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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20
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Yevdokimov YM, Skuridin SG, Salyanov VI, Volkov VV, Dadinova LA, Kompanets ON, Kats EI. About the spatial organization of double-stranded DNA molecules in the cholesteric liquid-crystalline phase and dispersion particles of this phase. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915050036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Biffi S, Cerbino R, Nava G, Bomboi F, Sciortino F, Bellini T. Equilibrium gels of low-valence DNA nanostars: a colloidal model for strong glass formers. SOFT MATTER 2015; 11:3132-8. [PMID: 25747102 DOI: 10.1039/c4sm02144d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Kinetic arrest in colloidal dispersions with isotropic attractive interactions usually occurs through the destabilization of the homogeneous phase and the formation of a non-equilibrium network of jammed particles. Theory and simulations predict that a different route to gelation should become available when the valence of each colloidal particle is suitably reduced. Under these conditions, gelation should be achievable through a reversible sequence of equilibrium states. Here we report the reversible dynamic arrest of a dispersion of DNA-based nanoparticles with anisotropic interactions and a coordination number equal to four. As the temperature is decreased, the relaxation time for density fluctuations slows down by about five orders of magnitude, following an Arrhenius scaling in the entire experimentally accessible temperature window. The system is in thermodynamic equilibrium at all temperatures. Gelation in our system mimics the dynamic arrest of networking atomic strong glass formers such as silica, for which it could thus provide a suitable colloidal model.
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Affiliation(s)
- Silvia Biffi
- Department of Medical Biotechnology and Translational Medicine, Universitá degli Studi di Milano, via Fratelli Cervi 93, I-20090 Segrate, MI, Italy.
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22
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Acosta-Reyes FJ, Subirana JA, Pous J, Sánchez-Giraldo R, Condom N, Baldini R, Malinina L, Campos JL. Polymorphic crystal structures of an all-AT DNA dodecamer. Biopolymers 2014; 103:123-33. [DOI: 10.1002/bip.22565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/12/2022]
Affiliation(s)
| | - Juan A. Subirana
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Joan Pous
- Plataforma Automatitzada de Cristal·lografia; IBMB-CSIC and Institut de Recerca Biomédica de Barcelona; 08028 Barcelona Spain
| | - Raquel Sánchez-Giraldo
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Núria Condom
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Roberto Baldini
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Lucy Malinina
- Structural Biology Unit, CIC bioGUNE; Technology Park of Bizkaia; 48160 Derio Bilbao Spain
| | - J. Lourdes Campos
- Departament d'Enginyeria Química; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
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Phase behavior and critical activated dynamics of limited-valence DNA nanostars. Proc Natl Acad Sci U S A 2013; 110:15633-7. [PMID: 24019470 DOI: 10.1073/pnas.1304632110] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Colloidal particles with directional interactions are key in the realization of new colloidal materials with possibly unconventional phase behaviors. Here we exploit DNA self-assembly to produce bulk quantities of "DNA stars" with three or four sticky terminals, mimicking molecules with controlled limited valence. Solutions of such molecules exhibit a consolution curve with an upper critical point, whose temperature and concentration decrease with the valence. Upon approaching the critical point from high temperature, the intensity of the scattered light diverges with a power law, whereas the intensity time autocorrelation functions show a surprising two-step relaxation, somehow reminiscent of glassy materials. The slow relaxation time exhibits an Arrhenius behavior with no signs of criticality, demonstrating a unique scenario where the critical slowing down of the concentration fluctuations is subordinate to the large lifetime of the DNA bonds, with relevant analogies to critical dynamics in polymer solutions. The combination of equilibrium and dynamic behavior of DNA nanostars demonstrates the potential of DNA molecules in diversifying the pathways toward collective properties and self-assembled materials, beyond the range of phenomena accessible with ordinary molecular fluids.
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24
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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25
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Abstract
In biological systems and nanoscale assemblies, the self-association of DNA is typically studied and applied in the context of the evolved or directed design of base sequences that give complementary pairing, duplex formation, and specific structural motifs. Here we consider the collective behavior of DNA solutions in the distinctly different regime where DNA base sequences are chosen at random or with varying degrees of randomness. We show that in solutions of completely random sequences, corresponding to a remarkably large number of different molecules, e.g., approximately 10(12) for random 20-mers, complementary still emerges and, for a narrow range of oligomer lengths, produces a subtle hierarchical sequence of structured self-assembly and organization into liquid crystal (LC) phases. This ordering follows from the kinetic arrest of oligomer association into long-lived partially paired double helices, followed by reversible association of these pairs into linear aggregates that in turn condense into LC domains.
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