1
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Samal RR, Subudhi U. Modulation of antioxidant enzyme by light and heavy rare earth metals: A case study with catalase. Int J Biol Macromol 2024; 283:137820. [PMID: 39566800 DOI: 10.1016/j.ijbiomac.2024.137820] [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: 09/23/2024] [Revised: 11/14/2024] [Accepted: 11/16/2024] [Indexed: 11/22/2024]
Abstract
The present study highlights the hazardous effect of heavy and light rare earth elements (REEs) on bovine liver catalase (BLC) using a combination of spectroscopic and computational methods. The presence of Praseodymium chloride (PrCl3) and Gadolinium chloride (GdCl3) resulted in a substantial reduction in catalytic efficiency of BLC by approximately 1.8 and 2.6 fold, respectively. The compromised activity was further accompanied by conformational rearrangements at the secondary and tertiary levels as evidenced by circular dichroism (CD) and fluorescence spectroscopy. These analyses revealed a significant decrease in α-helical content and a simultaneous increase in random coils, disrupting intramolecular hydrogen bonding. Furthermore, the zeta potential (ζ) of BLC demonstrated a reversal from negative to positive ζ values upon the addition of PrCl3 and GdCl3, indicating BLC-lanthanide complex formation. Isothermal titration calorimetry (ITC) supports spontaneous interaction with negative free energy favouring endothermic reaction. This was further supported by docking studies which revealed the binding of PrCl3 and GdCl3 within the active site of BLC thus interfering with the catalytic ability to degrade hydrogen peroxide (H2O2). Nevertheless, a significant decline in the melting temperature (Tm) of BLC was observed in the presence of lanthanides suggesting the thermal instability of the enzyme. Thus, a similar approach could be applied to evaluate the hazardous effects of lanthanides on structural and functional changes in other proteins or similar biomolecules.
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Affiliation(s)
- Rashmi R Samal
- Biochemistry & Biophysics Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umakanta Subudhi
- Biochemistry & Biophysics Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Fang L, Shi C, Wang Y, Xiong Z, Wang Y. Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials. J Nanobiotechnology 2023; 21:290. [PMID: 37612757 PMCID: PMC10464147 DOI: 10.1186/s12951-023-02071-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.
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Affiliation(s)
- Liuru Fang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Yuhua Wang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China.
| | - Zuzhao Xiong
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Yumei Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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3
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Kar A, Kumari K, Mishra SK, Subudhi U. Self-assembled DNA nanostructure containing oncogenic miRNA-mediated cell proliferation by downregulation of FOXO1 expression. BMC Cancer 2022; 22:1332. [PMID: 36539739 PMCID: PMC9764560 DOI: 10.1186/s12885-022-10423-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.
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Affiliation(s)
- Avishek Kar
- grid.418808.d0000 0004 1792 1607DNA Nanotechnology and Application Laboratory, CSIR-Institute of Minerals and Materials Technology, 751013 Bhubaneswar, India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh 201002 Ghaziabad, India
| | - Kanchan Kumari
- grid.418808.d0000 0004 1792 1607DNA Nanotechnology and Application Laboratory, CSIR-Institute of Minerals and Materials Technology, 751013 Bhubaneswar, India ,grid.12650.300000 0001 1034 3451Department of Molecular Biology, Umea University, Umea, Sweden
| | - Sandip K. Mishra
- grid.418782.00000 0004 0504 0781Cancer Biology Laboratory, Institute of Life Sciences, 751023 Bhubaneswar, India
| | - Umakanta Subudhi
- grid.418808.d0000 0004 1792 1607DNA Nanotechnology and Application Laboratory, CSIR-Institute of Minerals and Materials Technology, 751013 Bhubaneswar, India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh 201002 Ghaziabad, India
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4
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Park S, Tandon A, Raza MT, Lee S, Nguyen TBN, Vu THN, Ha TH, Park SH. Construction and Configuration Analysis of Zelkova Serrata Lenticel-Like Patterns Generated through DNA Algorithmic Self-Assembly. ACS APPLIED BIO MATERIALS 2022; 5:97-104. [PMID: 35014830 DOI: 10.1021/acsabm.1c00455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.
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Affiliation(s)
- Suyoun Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Anshula Tandon
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Tayyab Raza
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sungjin Lee
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Thi Bich Ngoc Nguyen
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Thi Hong Nhung Vu
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Tai Hwan Ha
- Core Facility Management Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Sung Ha Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
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5
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Tandon A, Raza MT, Park S, Lee S, Nguyen TBN, Vu THN, Kim S, Ha TH, Park SH. Configuration Analysis of a Lizard Skin-like Pattern Formed by DNA Self-Assembly. ACS OMEGA 2021; 6:27038-27044. [PMID: 34693123 PMCID: PMC8529593 DOI: 10.1021/acsomega.1c03593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Nature manifests diverse and complicated patterns through efficient physical, chemical, and biological processes. One of the approaches to generate complex patterns, as well as simple patterns, is the use of the cellular automata algorithm. However, there are certain limitations to produce such patterns experimentally due to the difficulty of finding candidate programmable building blocks. Here, we demonstrated the feasibility of generating an ocellated lizard skin-like pattern by simulation considering the probabilistic occurrence of cells and constructed the simulation results on DNA lattices via bottom-up self-assembly. To understand the similarity between the simulated pattern (SP) and the observed pattern (OP) of lizard skin, a unique configuration scheme (unit configuration was composed of 7 cells) was conceived. SPs were generated through a computer with a controlling population of gray and black cells in a given pattern. Experimental patterns (EPs) on DNA lattices, consisting of double-crossover (DX) tiles without and with protruding hairpins, were fabricated and verified through atomic force microscopy (AFM). For analyzing the similarity of the patterns, we introduced deviation of the average configuration occurrence for SP and EP with respect to OP, i.e., σα(SO) and σα(EO). The configuration and deviation provide characteristic information of patterns. We recognized that the minimum values of <σα(SO)> and <σα(EO)> occurred when 50% (55%) of black cells in given SPs (DX tiles with hairpins in given EPs) appeared to be most similar to the OP. Our study provides a novel platform for the applicability of DNA molecules to systematically demonstrate other naturally existing complex patterns or processes with ease.
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Affiliation(s)
- Anshula Tandon
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Muhammad Tayyab Raza
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Suyoun Park
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Sungjin Lee
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Thi Bich Ngoc Nguyen
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Thi Hong Nhung Vu
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Seungjae Kim
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
| | - Tai Hwan Ha
- Core
Facility Management Center, Korea Research
Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Sung Ha Park
- Department
of Physics, Institute of Basic Science, and Sungkyunkwan Advanced
Institute of Nanotechnology (SAINT), Sungkyunkwan
University, Suwon 16419, Korea
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6
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Baral B, Dutta J, Subudhi U. Biophysical interaction between self-assembled branched DNA nanostructures with bovine serum albumin and bovine liver catalase. Int J Biol Macromol 2021; 177:119-128. [PMID: 33609575 DOI: 10.1016/j.ijbiomac.2021.02.095] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/30/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
Branched DNA (bDNA) nanostructures have emerged as self-assembled biomaterials and are being considered for biomedical applications. Herein, we report the biophysical interaction between self-assembled bDNA nanostructure with circulating protein bovine serum albumin (BSA) and cellular enzyme bovine liver catalase (BLC). The binding between bDNA and BSA or BLC was confirmed through the decrease in fluorescence spectra. The Stern-Volmer data supports for non-covalent bonding with ~1 binding site in case of BSA and BLC thus advocating a static binding. Furthermore, FTIR and ITC study confirmed the binding of bDNAs with proteins through hydrogen bonding and van der Waals interaction. The negative free energy observed in ITC represent spontaneous reaction for BLC-bDNA interaction. The biophysical interaction between bDNA nanostructures and proteins was also supported by DLS and zeta potential measurement. With an increase in bDNA concentrations up to 100 nM, no significant change in absorbance and CD spectra was observed for both BLC and BSA which suggests structural stability and unaffected secondary conformation of proteins in presence of bDNA. Furthermore, the catalytic activity of BLC was unaltered in presence of bDNAscr even with increasing the incubation period from 1 h to 24 h. Interestingly, the time-dependent decrease in activity of BLC was protected by bDNAmix. The thermal melting study suggests a higher Tm value for proteins in presence of bDNAmix which demonstrates that interaction with bDNAmix increases the thermal stability of proteins. Collectively these data suggest that self-assembled DNA nanostructure may bind to BSA for facilitating circulation in plasma or binding to intracellular proteins like BLC for stabilization, however the secondary conformation of protein or catalytic activity of enzyme is unaltered in presence of bDNA nanostructure. Thus, the newly established genomic sequence-driven self-assembled DNA nanostructure can be explored for in vitro or in vivo experimental work in recent future.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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7
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Kumari K, Kar A, Nayak AK, Mishra SK, Subudhi U. miRNA-mediated alteration of sulfatase modifying factor 1 expression using self-assembled branched DNA nanostructures. RSC Adv 2021; 11:10670-10680. [PMID: 35423539 PMCID: PMC8695627 DOI: 10.1039/d0ra10733f] [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: 12/22/2020] [Accepted: 03/04/2021] [Indexed: 01/05/2023] Open
Abstract
Sulfatase enzymes catalyze sulfate ester hydrolysis, thus deficiencies of sulfatases lead to the accumulation of biomolecules resulting in several disorders. One of the important sulfatases is estrone sulfatase that converts inactive estrone sulfate to active estradiol. Posttranslational modification of highly conserved cysteine residue leads to unique formylglycine in the active site of sulfatases being critical for its catalytic activity. The essential factor responsible for this modification of sulfatase is Sulfatase-Modifying Factor 1 (SUMF1). The role of estrone sulfatase is well evident in breast cancer progression. However, the function and regulation of SUMF1 in cancer are not studied. In the present study, for the first time, we have assessed the expression of SUMF1 in breast cancer and report the oncogenic behavior upon overexpression of SUMF1. Although increased expression or activity of SUMF1 is anticipated based on its function, the expression of SUMF1 was found to be reduced in breast cancer cells at both mRNA and protein levels. An estrogen receptor (ER) dependent expression of SUMF1 was observed and higher SUMF1 expression is associated with improved breast cancer patient survival in ER-positive cases. However, high SUMF1 expression leads to reduced median survival in ER-negative breast cancer patients. Putative binding sites for miRNAs-106b-5p, 128-3p and 148b-3p were found at 3′-UTR of SUMF1. Since self-assembled branched DNA (bDNA) structures have emerged as a highly efficient strategy for targeting multiple miRNAs simultaneously, we studied the alteration in SUMF1 expression using bDNA nanostructures with a complementary sequence to miRNAs. The findings suggest the involvement of co-regulators and repressors in miRNA-mediated SUMF1 expression in breast cancer cells and reveal the therapeutic potential of SUMF1 in endocrine-related malignancies. Reduced expression of SUMF1 was evidenced in MCF-7 cells transfected with antimiR-bDNA. Expression of miRNA-106 and 148 have positive correlation with the expression of SUMF1. miRNA-106 and 148 blocks the repressor protein controls SUMF-1 expression.![]()
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Affiliation(s)
- Kanchan Kumari
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar
- India
- Department of Molecular Biology
| | - Avishek Kar
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar
- India
| | - Ashok K. Nayak
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar
- India
| | - Sandip K. Mishra
- Cancer Biology Laboratory
- Institute of Life Sciences
- Bhubaneswar
- India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar
- India
- Academy of Scientific & Innovative Research (AcSIR)
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8
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Xiao YP, Zhang J, Liu YH, Huang Z, Guo Y, Yu XQ. Bioinspired pyrimidine-containing cationic polymers as effective nanocarriers for DNA and protein delivery. J Mater Chem B 2020; 8:2275-2285. [PMID: 32100787 DOI: 10.1039/c9tb02528f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cationic polymers have shown great potential in the delivery of nucleic acids and proteins. In this study, a series of pyrimidine-based cationic polymers were synthesized via the Michael addition reaction from pyrimidine-based linkages and low molecular weight polyethyleneimine (PEI). The structure-activity relationship (SAR) of these materials in DNA and protein delivery was investigated. These materials could condense both DNA and protein into nanoparticles with proper sizes and zeta-potentials. In vitro experiments indicated that such polymers were efficient in transporting DNA and proteins into cells. Furthermore, the bioactivity of the genes and proteins encapsulated in these polymers were maintained during the delivery processes. Among the polymers, U-PEI600 synthesized from a uracil-containing linker and PEI 600 Da mediated comparable gene expression to PEI 25 kDa. Moreover, the activities of β-galactosidase delivered by U-PEI600 were well maintained after entering the cells. Evaluation using an immune response assay showed that the U-PEI600/OVA polyplex could stimulate greater production of immune factors with low cytotoxicity. Our study provides a strategy for the construction of cationic polymeric gene and cytosolic protein vectors with high efficiency and low toxicity.
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Affiliation(s)
- Ya-Ping Xiao
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Ji Zhang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Zheng Huang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Yu Guo
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China.
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9
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Bhanjadeo MM, Baral B, Subudhi U. Sequence-specific B-to-Z transition in self-assembled DNA: A biophysical and thermodynamic study. Int J Biol Macromol 2019; 137:337-345. [DOI: 10.1016/j.ijbiomac.2019.06.166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/17/2019] [Accepted: 06/23/2019] [Indexed: 12/20/2022]
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10
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Nayak AK, Rath SK, Subudhi U. Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly. J Phys Chem B 2019; 123:3591-3597. [DOI: 10.1021/acs.jpcb.9b00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashok Kumar Nayak
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Sakti Kanta Rath
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India
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11
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Gong C, Sun S, Zhang Y, Sun L, Su Z, Wu A, Wei G. Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications. NANOSCALE 2019; 11:4147-4182. [PMID: 30806426 DOI: 10.1039/c9nr00218a] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.
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Affiliation(s)
- Coucong Gong
- Faculty of Production Engineering and Center for Environmental Research and Sustainable technology (UFT), University of Bremen, D-28359 Bremen, Germany.
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12
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Zhang X, Gong C, Akakuru OU, Su Z, Wu A, Wei G. The design and biomedical applications of self-assembled two-dimensional organic biomaterials. Chem Soc Rev 2019; 48:5564-5595. [DOI: 10.1039/c8cs01003j] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.
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Affiliation(s)
- Xiaoyuan Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
- Faculty of Physics and Astronomy
- University of Jena
| | - Coucong Gong
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
| | - Ozioma Udochukwu Akakuru
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- China
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering
- CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province
- Ningbo Institute of Materials Technology and Engineering
- Chinese Academy of Sciences
- Ningbo
| | - Gang Wei
- Faculty of Production Engineering
- University of Bremen
- Bremen
- Germany
- Cixi Institute of Biomedical Engineering
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13
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Mitta SB, Han S, Vellampatti S, Tandon A, Shin J, Ha TH, Park SH. Streptavidin-Decorated Algorithmic DNA Lattices Constructed by Substrate-Assisted Growth Method. ACS Biomater Sci Eng 2018; 4:3617-3623. [PMID: 33450799 DOI: 10.1021/acsbiomaterials.8b00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultimate goal of DNA computing is to store information at higher density and solve complex problems with less computational time and minimal error. Most algorithmic DNA lattices have been constructed using the free-solution growth (FSG) annealing method, and hairpin-embedded DNA rule tiles have been introduced in most algorithmic implementations to differentiate 0- and 1-bit information. Here, we developed streptavidin (SA)-decorated algorithmic COPY (produced line-like patterns with biotinylated 1-bit rule tiles) and XOR (triangle-like patterns) lattices constructed by a substrate-assisted growth (SAG) method and FSG. SA decoration in algorithmic lattices provides an efficient platform for visualizing bit information, and the SAG method in algorithmic assembly offers full coverage of algorithmic lattices on a substrate with a relatively lower DNA concentration than previous methods. The algorithmic COPY and XOR lattices assembled with various ratios of 0- and 1-bit rule tiles were verified by atomic force microscopy. We found that even asymmetric DNA patterns produced by certain algorithmic logic gates could be easily constructed by SAG. Finally, we evaluated sorting factors and error rates of algorithmic COPY and XOR lattices to determine the bit population and quality of the algorithmic assembly. Because of the catalytic effect of the substrate, the sorting factor of algorithmic DX-DNA lattices did not greatly influence the specific rules (i.e., COPY and XOR logic gates) annealed by SAG. Additionally, we found that the overall error rates of algorithmic DX-DNA lattices prepared by the FSG and SAG methods were low, within the range of 1-3%. Hence, the self-assembled algorithmic patterns generated with DNA molecules may serve as a scaffold for molecular demultiplexing circuits and computing.
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Affiliation(s)
- Sekhar Babu Mitta
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Sungguk Han
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Srivithya Vellampatti
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Anshula Tandon
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Jihoon Shin
- Hazards Monitoring BNT Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Tai Hwan Ha
- Hazards Monitoring BNT Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
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Pu F, Ren J, Qu X. Nucleobases, nucleosides, and nucleotides: versatile biomolecules for generating functional nanomaterials. Chem Soc Rev 2017; 47:1285-1306. [PMID: 29265140 DOI: 10.1039/c7cs00673j] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The incorporation of biomolecules into nanomaterials generates functional nanosystems with novel and advanced properties, presenting great potential for applications in various fields. Nucleobases, nucleosides and nucleotides, as building blocks of nucleic acids and biological coenzymes, constitute necessary components of the foundation of life. In recent years, as versatile biomolecules for the construction or regulation of functional nanomaterials, they have stimulated interest in researchers, due to their unique properties such as structural diversity, multiplex binding sites, self-assembly ability, stability, biocompatibility, and chirality. In this review, strategies for the synthesis of nanomaterials and the regulation of their morphologies and functions using nucleobases, nucleosides, and nucleotides as building blocks, templates or modulators are summarized alongside selected applications. The diverse applications range from sensing, bioimaging, and drug delivery to mimicking light-harvesting antenna, the construction of logic gates, and beyond. Furthermore, some perspectives and challenges in this emerging field are proposed. This review is directed toward the broader scientific community interested in biomolecule-based functional nanomaterials.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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