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Jeon K, Lee C, Lee JY, Kim DN. DNA Hydrogels with Programmable Condensation, Expansion, and Degradation for Molecular Carriers. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38696548 DOI: 10.1021/acsami.3c17633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Molecular carriers are necessary for the controlled release of drugs and genes to achieve the desired therapeutic outcomes. DNA hydrogels can be a promising candidate in this application with their distinctive sequence-dependent programmability, which allows precise encapsulation of specific cargo molecules and stimuli-responsive release of them at the target. However, DNA hydrogels are inherently susceptible to the degradation of nucleases, making them vulnerable in a physiological environment. To be an effective molecular carrier, DNA hydrogels should be able to protect encapsulated cargo molecules until they reach the target and release them once they are reached. Here, we develop a simple way of controlling the enzyme resistance of DNA hydrogels for cargo protection and release by using cation-mediated condensation and expansion. We found that DNA hydrogels condensed by spermine are highly resistant to enzymatic degradation. They become degradable again if expanded back to their original, uncondensed state by sodium ions interfering with the interaction between spermine and DNA. These controllable condensation, expansion, and degradation of DNA hydrogels pave the way for the development of DNA hydrogels as an effective molecular carrier.
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Affiliation(s)
- Kyounghwa Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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Hara Y, Mayama H, Fujimoto K. Influence of Belousov–Zhabotinsky Substrate Concentrations on Autonomous Oscillation of Polymer Chains with Fe(bpy)3 Catalyst. J Phys Chem B 2014; 118:6931-6. [DOI: 10.1021/jp500824e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yusuke Hara
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-2, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hiroyuki Mayama
- Department of Chemistry, Asahikawa Medical University, 2-1-1-1,
Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Kenji Fujimoto
- Fuji Molecular Planning Co., Ltd., Techno-Core
4F-A, Yokohama-Kanazawa High Tech Center, 1-1-1, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
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Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps. Biophys J 2014; 105:1037-44. [PMID: 23972855 DOI: 10.1016/j.bpj.2013.07.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 12/29/2022] Open
Abstract
The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation.
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Hara Y, Mayama H, Morishima K. Generative Force of Self-Oscillating Gel. J Phys Chem B 2014; 118:2576-81. [DOI: 10.1021/jp412806y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Hara
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-2, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hiroyuki Mayama
- Department
of Chemistry, Asahikawa Medical University, 2-1-1-1 Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Keisuke Morishima
- Department
of Mechanical Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
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Hara Y, Mayama H, Yamaguchi Y, Takenaka Y, Fukuda R. Direct Observation of Periodic Swelling and Collapse of Polymer Chain Induced by the Belousov–Zhabotinsky Reaction. J Phys Chem B 2013; 117:14351-7. [DOI: 10.1021/jp408417h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Hara
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-2, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hiroyuki Mayama
- Department
of Chemistry, Asahikawa Medical University, 2-1-1-1, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Yoshinori Yamaguchi
- Photonics
advanced research center (PARC), Graduate School of Engineering, Osaka University, 2-1
Yamada-oka, Suita-city, Osaka 565-0871, Japan
| | - Yoshiko Takenaka
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Central 5-2, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Ryushi Fukuda
- MEIWAFOSIS
CO., LTD, 1-14-2 Shinju-ku, Tokyo 160-0022, Japan
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Costa D, Queiroz J, Miguel MG, Lindman B. Swelling behavior of a new biocompatible plasmid DNA hydrogel. Colloids Surf B Biointerfaces 2012; 92:106-12. [DOI: 10.1016/j.colsurfb.2011.11.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/31/2011] [Accepted: 11/14/2011] [Indexed: 11/25/2022]
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Higuchi Y, Yoshikawa K, Iwaki T. Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:021924. [PMID: 21929035 DOI: 10.1103/physreve.84.021924] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 07/06/2011] [Indexed: 05/31/2023]
Abstract
We investigated the folding transition between an elongated coil state and a compact state on a single polymer chain confined in a small space with different stiffness with the aid of Monte Carlo simulation. In a flexible polymer, the folding transition is retarded in a confined space. In contrast, the transition is promoted for a semiflexible chain, in which the discontinuity of the volume change occupied by a single chain is diminished by confinement. This unique confinement effect is interpreted in terms of conformational entropy and self-avoiding repulsive interaction.
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Affiliation(s)
- Yuji Higuchi
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Abstract
This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.
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Affiliation(s)
- Tommaso Bellini
- Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, Via F.lli Cervi 93, 20090 Milano, Italy.
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Topuz F, Okay O. Formation of Hydrogels by Simultaneous Denaturation and Cross-Linking of DNA. Biomacromolecules 2009; 10:2652-61. [DOI: 10.1021/bm900585v] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fuat Topuz
- Istanbul Technical University, Department of Chemistry, 34469 Maslak, Istanbul, Turkey
| | - Oguz Okay
- Istanbul Technical University, Department of Chemistry, 34469 Maslak, Istanbul, Turkey
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