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Nial PS, Subudhi U. Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA. Int J Biol Macromol 2024; 266:131238. [PMID: 38554916 DOI: 10.1016/j.ijbiomac.2024.131238] [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: 12/16/2023] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Zeta potential is commonly referred as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acids. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, for the first time we discover the zeta potential difference between B-DNA and lanthanum chloride-induced Z-DNA. A series of linear repeat i.e. (CG)n and (GC)n DNA as well as branched DNA (bDNA) structures was used for the B-to-Z DNA transition. Herein, the positive zeta potential of Z-DNA has been demonstrated as a powerful tool to discriminate between B-form and Z-form of DNA. The generality of the approach has been validated both in linear and bDNA nanostructures. Thus, we suggest zeta potential can be used as an ideal signature for the left-handed Z-DNA.
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Affiliation(s)
- Partha S Nial
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment and Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Satapathy SN, Nial PS, Tulsiyan KD, Subudhi U. Light rare earth elements stabilize G-quadruplex structure in variants of human telomeric sequences. Int J Biol Macromol 2024; 254:127703. [PMID: 37918592 DOI: 10.1016/j.ijbiomac.2023.127703] [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: 06/24/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Recently, light rare earth elements (LREEs) are gaining importance in modern-day technologies. Thus, the entry of LREEs into biochemical pathways cannot be ignored, which might affect the conformation of biomacromolecules. Herein, for the first time, we discover the G-quadruplex formation in the human telomeric variants in presence of micromolar concentrations of LREEs. Thermal melting show that the LREE-induced unimolecular G-quadruplex structure. Isothermal titration calorimetry, UV-vis, and CD spectroscopy results suggest the binding stoichiometry of lanthanide ions to telomeric variants is 2:1. The data confirms that the LREE ions coordinate between adjacent G-quartets. The excess LREE ions are most likely binding to quadruplex loops. The CD spectra revealed that the LREE-induced quadruplex in human telomere and its variant have antiparallel orientation. The binding equilibria of LREEs have been studied both in the presence and absence of competing metal cations. Addition of LREEs to the Na+ or K+-induced G-quadruplexes led to conformational change, which may be ascribed to the displacement of K+ or Na+ ions by LREE ions and formation of a more compact LREE-induced G-quadruplex structure in human telomeric variant. Moreover, the thymine in the central loop of the human telomeric sequence stabilizes LREE induced G-quadruplex.
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Affiliation(s)
- Sampat N Satapathy
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Baral B, Panigrahi B, Kar A, Tulsiyan KD, Suryakant U, Mandal D, Subudhi U. Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:493-510. [PMID: 37583574 PMCID: PMC10424151 DOI: 10.1016/j.omtn.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023]
Abstract
Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
- Biopioneer Private Limited, Bhubaneswar 751024, Odisha, India
| | - Avishek Kar
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D. Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Uday Suryakant
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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5
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Bhanjadeo MM, Nial PS, Sathyaseelan C, Singh AK, Dutta J, Rathinavelan T, Subudhi U. Biophysical interaction between lanthanum chloride and (CG) n or (GC) n repeats: A reversible B-to-Z DNA transition. Int J Biol Macromol 2022; 216:698-709. [PMID: 35809677 DOI: 10.1016/j.ijbiomac.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022]
Abstract
The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)n and (GC)n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)6 DNA using millimolar concentration of trivalent lanthanide salt LaCl3. The controlled and reversible transition was seen in (CG)12, and (GC)12 DNA employing CD spectroscopy. While LaCl3 failed to induce B-Z transition in shorter oligonucleotides such as (CG)3 and (GC)3, a smooth B-Z transition was recorded for (CG)6, (CG)12 and (GC)12 sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)6 DNA in presence of LaCl3 and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl3-induced Z-DNA is irreversible which suggest a stronger binding of LaCl3 to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La3+ (of LaCl3) with d(CG)8.d(CG)8 is through the minor groove, wherein, 3 out of 11 La3+ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La3+ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl3-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl3 can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.
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Affiliation(s)
- Madhabi M Bhanjadeo
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Ajit K Singh
- Structural Biology Laboratory, DBT-Institute of Life Sciences, Bhubaneswar 751023, India; Department of Pharmacology, University of Vermont College of Medicine, Burlington 05405, USA
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India; Homi Bhaba National Institute, Mumbai 400094, India
| | | | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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6
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Liu M, Cui Y, Zhang Y, An R, Li L, Park S, Sugiyama H, Liang X. Single base-modification reports and locates Z-DNA conformation on a Z-B-chimera formed by topological constraint. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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7
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Li L, Zhang Y, Ma W, Chen H, Liu M, An R, Cheng B, Liang X. Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint. Nucleic Acids Res 2021; 50:684-696. [PMID: 34967416 PMCID: PMC8789069 DOI: 10.1093/nar/gkab1283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 11/14/2022] Open
Abstract
In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)n sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers. Here, by the strong topological constraint caused by hybridization of two complementary short circular ssDNAs, left-handed duplex part was generated for various sequences, and their characteristics were investigated by using gel-shift after binding to specific proteins, CD and Tm analysis, and restriction enzyme cleavage. Under the strong topological constraint, non-APP sequences can also form left-handed DNA duplex as stable as that of APP sequences. As compared with non-APP sequences, the thermal stability difference for APP sequences between Z-form and B-form is smaller, which may be the reason that Z-DNA forms preferentially for APP ones. This result can help us to understand why nature selected APP sequences to regulate gene expression by transient Z-DNA formation, as well as why polymer with chirality can usually form both duplexes with left- or right-handed helix.
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Affiliation(s)
- Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wanzhi Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Bingxiao Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
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8
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Yau HCL, Malekpour AK, Momin NG, Morales-García AL, Willats WGT, Lant NJ, Jones CY. Removal of eDNA from fabrics using a novel laundry DNase revealed using high-resolution imaging. Sci Rep 2021; 11:21542. [PMID: 34728780 PMCID: PMC8563969 DOI: 10.1038/s41598-021-98939-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
Washed textiles can remain malodorous and dingy due to the recalcitrance of soils. Recent work has found that 'invisible' soils such as microbial extracellular DNA (eDNA) play a key role in the adhesion of extracellular polymeric substances that form matrixes contributing to these undesirable characteristics. Here we report the application of an immunostaining method to illustrate the cleaning mechanism of a nuclease (DNase I) acting upon eDNA. Extending previous work that established a key role for eDNA in anchoring these soil matrixes, this work provides new insights into the presence and effective removal of eDNA deposited on fabrics using high-resolution in-situ imaging. Using a monoclonal antibody specific to Z-DNA, we showed that when fabrics are washed with DNase I, the incidence of microbial eDNA is reduced. As well as a quantitative reduction in microbial eDNA, the deep cleaning benefits of this enzyme are shown using confocal microscopy and imaging analysis of T-shirt fibers. To the best of our knowledge, this is the first time the use of a molecular probe has been leveraged for fabric and homecare-related R&D to visualize eDNA and evaluate its removal from textiles by a new-to-laundry DNase enzyme. The approaches described in the current work also have scope for re-application to identify further cleaning technology.
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Affiliation(s)
- Hamish C L Yau
- Procter and Gamble, Newcastle Innovation Centre, Whitley Road, Newcastle upon Tyne, NE12 9BZ, UK
| | - Adam K Malekpour
- Procter and Gamble, Newcastle Innovation Centre, Whitley Road, Newcastle upon Tyne, NE12 9BZ, UK
| | - Nazarmohammad G Momin
- Procter and Gamble, Newcastle Innovation Centre, Whitley Road, Newcastle upon Tyne, NE12 9BZ, UK
| | - Ana L Morales-García
- Procter and Gamble, Newcastle Innovation Centre, Whitley Road, Newcastle upon Tyne, NE12 9BZ, UK
| | - William G T Willats
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne, NE1 7RU, UK.
| | - Neil J Lant
- Procter and Gamble, Newcastle Innovation Centre, Whitley Road, Newcastle upon Tyne, NE12 9BZ, UK.
| | - Catherine Y Jones
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle upon Tyne, NE1 7RU, UK.
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9
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Samal RR, Mishra M, Subudhi U. Differential interaction of cerium chloride with bovine liver catalase: A computational and biophysical study. CHEMOSPHERE 2020; 239:124769. [PMID: 31526997 DOI: 10.1016/j.chemosphere.2019.124769] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 07/25/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
In this study, Cerium chloride-induced conformational changes of Bovine Liver Catalase (BLC) has been investigated by molecular docking and further supported by various biophysical techniques. The temporal change of catalytic activity of BLC has also been studied in presence of Ce(III) with different buffer solution in vitro at 25 °C. The differential binding of Ce(III) to BLC observed by simulation study was well supported by the differential regulation of BLC activity in different buffers. After 1 h of incubation with CeCl3, the reduction in activity of BLC was maximum in MOPS, HEPES and Tris buffer, whereas no change in activity was noticed in phosphate buffer. Isothermal Titration Calorimetric (ITC) study also supports the differential binding of Ce(III) to BLC in different buffers. Ce(III)-induced conformational transition in BLC was followed as a function of concentration. Nevertheless, with 24 h incubation of CeCl3 the activity of BLC was highest with higher molar concentration of CeCl3 suggesting the conformational stability of BLC in presence of Ce(III). The compromised activity of BLC in response to Ce(III) is due to the induced conformational change and the degree of change in secondary conformation of BLC was maximum in MOPS, HEPES and Tris and least in phosphate buffer. Therefore, the reduced activity of BLC is controlled by the direct interaction of Ce(III) in the active site of BLC in Tris buffer or indirect interaction of Ce(III) in the non-active site of BLC in MOPS and HEPES buffer.
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Affiliation(s)
- Rashmi R Samal
- CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, 751 013, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi, 110025, India
| | - Madhusmita Mishra
- CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, 751 013, India
| | - Umakanta Subudhi
- CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, 751 013, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi, 110025, India.
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10
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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11
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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: 1.6] [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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12
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Wang K, Ren XW, Wang XY, Xing SY, Zhu BL, Liu C. DNase I-Responsive Calixpyridinium-Mediated DNA Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10505-10511. [PMID: 31310550 DOI: 10.1021/acs.langmuir.9b01116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, cationic macrocyclic calixpyridinium was employed as a new strategy to condense DNA. Moreover, the degradation of DNA by DNase I could lead to the calixpyridinium-DNA supramolecular aggregates being dissipated. Therefore, the present system is potentially applicable as the targeted drug delivery model at DNase I-overexpressed sites.
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Affiliation(s)
- Kui Wang
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
| | - Xiao-Wei Ren
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
| | - Xiao-Yan Wang
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
| | - Si-Yang Xing
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
| | - Bo-Lin Zhu
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
| | - Chang Liu
- Tianjin Key Laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry , Tianjin Normal University , Binshuixi Road 393 , Xiqing District, Tianjin 300387 , China
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13
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Kumar S, Gupta SK. Synthesis, spectral and electrochemical studies of mononuclear samarium (II), europium (II) and ytterbium (II) complexes with a NNO donor Schiff base derived from 4-methyl-2,6-dibenzoylphenol and propane-1,3-diamine. INORG NANO-MET CHEM 2019. [DOI: 10.1080/24701556.2019.1606828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sanjay Kumar
- School of Studies in Chemistry, Jiwaji University, Gwalior, India
| | - Sushil K Gupta
- School of Studies in Chemistry, Jiwaji University, Gwalior, India
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14
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Gupta S, Tiwari N, Munde M. A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation. Sci Rep 2019; 9:5891. [PMID: 30971720 PMCID: PMC6458161 DOI: 10.1038/s41598-019-41975-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 11/21/2022] Open
Abstract
DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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15
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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: 1.0] [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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16
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Bhanjadeo MM, Subudhi U. Praseodymium promotes B–Z transition in self-assembled DNA nanostructures. RSC Adv 2019; 9:4616-4620. [PMID: 35520195 PMCID: PMC9060621 DOI: 10.1039/c8ra10164g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/31/2019] [Indexed: 11/21/2022] Open
Abstract
Millimolar concentrations of PrCl3 can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures. Competitive dye binding and thermal kinetics suggest that the phosphate backbone and grooves of bDNA are wrapped with Pr3+ for stabilizing the Z-bDNA. Application of EDTA can convert Z-DNA back to the B-form. Millimolar concentrations of PrCl3 can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures.![]()
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Affiliation(s)
- Madhabi M. Bhanjadeo
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar 751 013
- India
- Academy of Scientific & Innovative Research (AcSIR)
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory
- CSIR-Institute of Minerals & Materials Technology
- Bhubaneswar 751 013
- India
- Academy of Scientific & Innovative Research (AcSIR)
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17
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Sharma S, Samal RR, Subudhi U, Chainy GB. Lanthanum chloride-induced conformational changes of bovine liver catalase: A computational and biophysical study. Int J Biol Macromol 2018; 115:853-860. [DOI: 10.1016/j.ijbiomac.2018.04.116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022]
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18
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Lanthanide-Dependent Regulation of Methylotrophy in Methylobacteriumaquaticum Strain 22A. mSphere 2018; 3:mSphere00462-17. [PMID: 29404411 PMCID: PMC5784242 DOI: 10.1128/msphere.00462-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022] Open
Abstract
Methylobacterium species are representative of methylotrophic bacteria. Their genomes usually encode two types of methanol dehydrogenases (MDHs): MxaF and XoxF. The former is a Ca2+-dependent enzyme, and the latter was recently determined to be a lanthanide-dependent enzyme that is necessary for the expression of mxaF. This finding revealed the unexpected and important roles of lanthanides in bacterial methylotrophy. In this study, we performed transcriptome sequencing (RNA-seq) analysis using M. aquaticum strain 22A grown in the presence of different lanthanides. Expression of mxaF and xoxF1 genes showed a clear inverse correlation in response to La3+. We observed downregulation of formaldehyde oxidation pathways, high formaldehyde dehydrogenase activity, and low accumulation of formaldehyde in the reaction with cells grown in the presence of La3+; this might be due to the direct oxidation of methanol to formate by XoxF1. Lanthanides induced the transcription of AT-rich genes, the function of most of which was unknown, and genes possibly related to cellular survival, as well as other MDH homologues. These results revealed not only the metabolic response toward altered primary methanol oxidation, but also the possible targets to be investigated further in order to better understand methylotrophy in the presence of lanthanides. IMPORTANCE Lanthanides have been considered unimportant for biological processes. In methylotrophic bacteria, however, a methanol dehydrogenase (MDH) encoded by xoxF was recently found to be lanthanide dependent, while the classic-type mxaFI is calcium dependent. XoxF-type MDHs are more widespread in diverse bacterial genera, suggesting their importance for methylotrophy. Methylobacterium species, representative methylotrophic and predominating alphaproteobacteria in the phyllosphere, contain both types and regulate their expression depending on the availability of lanthanides. RNA-seq analysis showed that the regulation takes place not only for MDH genes but also the subsequent formaldehyde oxidation pathways and respiratory chain, which might be due to the direct oxidation of methanol to formate by XoxF. In addition, a considerable number of genes of unknown function, including AT-rich genes, were found to be upregulated in the presence of lanthanides. This study provides first insights into the specific reaction of methylotrophic bacteria to the presence of lanthanides, emphasizing the biological relevance of this trace metal.
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19
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Nahar S, Nayak AK, Ghosh A, Subudhi U, Maiti S. Enhanced and synergistic downregulation of oncogenic miRNAs by self-assembled branched DNA. NANOSCALE 2017; 10:195-202. [PMID: 29210414 DOI: 10.1039/c7nr06601e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
miRNAs, a group of small non-coding RNA molecules, regulate the expression of many genes involved in various cellular processes. Acute evidence suggests that one miRNA can regulate many genes as its targets, while one gene can be targeted by many miRNAs that co-operatively regulate the gene. Thus, targeting a single miRNA is not sufficient enough to rescue the disease phenotype but it is also essential to target multiple miRNAs simultaneously. This inspired us to design a novel DNA nanostructure that can concurrently downregulate multiple oncomiRNAs. Here we designed a programmable antimiR branched DNA (antimiR-bDNA) nanostructure having antimiRNAs for selective binding to oncomiRNAs miRNA-27a, 96 and 182 which collectively downregulate FOXO1a expression. The antimiR-bDNAs show enhanced stability compared to naked antimiRNAs in serum and are able to knockdown these miRNAs with up to ∼50% greater repression as compared to antimiRNAs. This synergistic miRNA repression leads to the restoration of FOXO1a protein levels which in turn inhibit G1-S traversion in cancer cells. To the best of our knowledge, this is the first study harnessing the ability of bDNA structures to silence multiple miRNAs simultaneously.
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Affiliation(s)
- S Nahar
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.
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20
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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: 130] [Impact Index Per Article: 18.6] [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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21
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Zou S, Li G, Rees TW, Jin C, Huang J, Chen Y, Ji L, Chao H. Interfering with DNA High-Order Structures using Chiral Ruthenium(II) Complexes. Chemistry 2017; 24:690-698. [PMID: 29112314 DOI: 10.1002/chem.201704403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 12/31/2022]
Abstract
In this work, it was found that DNA can undergo B-Z transformational changes and compaction in the presence of DNA intercalators such as ruthenium(II) polypyridyl complexes. The link between B-Z transition and condensation is weak but can be strengthened under certain circumstances with slight alterations to the structures of the ruthenium(II) complexes. Here, following on from previous research, this work reports a series of ruthenium(II) complexes with imidazophenanthroline ligands, which vary in size and planarity. The complexes exhibit distinct effects on DNA structures, ranging from little impact to the transformation of DNA secondary structures to the formation of higher-order DNA structures. Further studies on DNA morphological changes induced by chiral ruthenium(II) complexes are observed by atomic force microscopy and transmission electron microscopy.
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Affiliation(s)
- Shanshan Zou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Guanying Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Thomas W Rees
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Chengzhi Jin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Juanjuan Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Yu Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
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22
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Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice. Biochem Biophys Res Commun 2017; 485:492-498. [PMID: 28189681 DOI: 10.1016/j.bbrc.2017.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/05/2017] [Indexed: 12/14/2022]
Abstract
DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices.
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23
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Kawara K, Tsuji G, Taniguchi Y, Sasaki S. Synchronized Chiral Induction between [5]Helicene-Spermine Ligand andB-ZDNA Transition. Chemistry 2017; 23:1763-1769. [DOI: 10.1002/chem.201605276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Kensuke Kawara
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Genichiro Tsuji
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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24
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Bhanjadeo MM, Nayak AK, Subudhi U. Cerium chloride stimulated controlled conversion of B-to-Z DNA in self-assembled nanostructures. Biochem Biophys Res Commun 2017; 482:916-921. [DOI: 10.1016/j.bbrc.2016.11.133] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/24/2016] [Indexed: 01/01/2023]
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