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León-Paz-de-Rodríguez GE, Rodríguez-León E, Iñiguez-Palomares R. DNA Hyperstructure. ACS OMEGA 2024; 9:9013-9026. [PMID: 38434827 PMCID: PMC10905968 DOI: 10.1021/acsomega.3c07379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/29/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
This study presents a new procedure to condense DNA molecules and precipitate them onto a glass slide. The resulting DNA molecules undergo autonomous self-assembly, creating closed superstructures on the micrometer scale, which are called DNA hyperstructures. These structures can be observed using low-magnification (4×) light microscopy. Precisely controlling the alcohol/glacial acetic acid ratio and DNA concentration during precipitation enabled the regulation of structure compaction on the slide. The alcohol/glacial acetic acid ratio is inversely proportional to the DNA concentration to achieve optimal compaction on the slide. Confocal microscopy fluorescence analysis of DNA extracts stained with DAPI shows that nucleic acids self-assemble to form structures during precipitation on the slide. This methodology is relevant since it facilitates the precipitation and visualization of DNA, regardless of its origin or molecular weight. To confirm its versatility, results with DNA extracted from human peripheral blood, the Lambda virus, and plasmid pBR322 are presented. The study examined the morphological features of DNA hyperstructures in both healthy individuals and those diagnosed with different medical conditions or illnesses, revealing distinct patterns specific to each case. This innovative technology has potential for disease detection in peripheral blood samples, ranging from cancer and Alzheimer's disease to determining the gender of the gestational product at an early stage.
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Chen R, Song Y, Wang Z, Ji H, Du Z, Ma Q, Yang Y, Liu X, Li N, Sun Y. Developments in small-angle X-ray scattering (SAXS) for characterizing the structure of surfactant-macromolecule interactions and their complex. Int J Biol Macromol 2023; 251:126288. [PMID: 37582436 DOI: 10.1016/j.ijbiomac.2023.126288] [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: 04/19/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
The surfactant-macromolecule interactions (SMI) are one of the most critical topics for scientific research and industrial application. Small-angle X-ray scattering (SAXS) is a powerful tool for comprehensively studying the structural and conformational features of macromolecules at a size ranging from Angstroms to hundreds of nanometers with a time-resolve in milliseconds scale. The SAXS integrative techniques have emerged for comprehensively analyzing the SMI and the structure of their complex in solution. Here, the various types of emerging interactions of surfactant with macromolecules, such as protein, lipid, nuclear acid, polysaccharide and virus, etc. have been systematically reviewed. Additionally, the principle of SAXS and theoretical models of SAXS for describing the structure of SMI as well as their complex has been summarized. Moreover, the recent developments in the applications of SAXS for charactering the structure of SMI have been also highlighted. Prospectively, the capacity to complement artificial intelligence (AI) in the structure prediction of biological macromolecules and the high-throughput bioinformatics sequencing data make SAXS integrative structural techniques expected to be the primary methodology for illuminating the self-assembling dynamics and nanoscale structure of SMI. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Yang Song
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhichun Wang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Hang Ji
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Zhongyao Du
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Qingwen Ma
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Ying Yang
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Xingxun Liu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Na Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, Yunnan, China.
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Halder S, Paul M, Dyagala S, Aggrawal R, Aswal VK, Biswas S, Saha SK. Role of Gemini Surfactants with Variable Spacers and SiO 2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/ In Vivo Gene Delivery. ACS APPLIED BIO MATERIALS 2023. [PMID: 37277159 DOI: 10.1021/acsabm.3c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO2 nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO2 NPs. While 50% ct-DNA compaction in the presence of SiO2 NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 μM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO2 NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO2 NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO2 NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO2 has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO2 NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.
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Affiliation(s)
- Sayantan Halder
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Milan Paul
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Shalini Dyagala
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Rishika Aggrawal
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, Maharashtra 400085, India
| | - Swati Biswas
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
| | - Subit K Saha
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India
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Ceccarini MR, Ripanti F, Raggi V, Paciaroni A, Petrillo C, Comez L, Donato K, Bertelli M, Beccari T, Valentini L. Development of Salmon Sperm DNA/Regenerated Silk Bio-Based Films for Biomedical Studies on Human Keratinocyte HaCaT Cells under Solar Spectrum. J Funct Biomater 2023; 14:jfb14050280. [PMID: 37233390 DOI: 10.3390/jfb14050280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
In this study, we fabricated adhesive patches from silkworm-regenerated silk and DNA to safeguard human skin from the sun's rays. The patches are realized by exploiting the dissolution of silk fibers (e.g., silk fibroin (SF)) and salmon sperm DNA in formic acid and CaCl2 solutions. Infrared spectroscopy is used to investigate the conformational transition of SF when combined with DNA; the results indicated that the addition of DNA provides an increase in the SF crystallinity. UV-Visible absorption and circular dichroism spectroscopy showed strong absorption in the UV region and the presence of B-form of DNA once dispersed in the SF matrix, respectively. Water absorption measurements as well as thermal dependence of water sorption and thermal analysis, suggested the stability of the fabricated patches. Biological results on cellular viability (MTT assay) of keratinocyte HaCaT cells after exposures to the solar spectrum showed that both SF and SF/DNA patches are photo-protective by increasing the cellular viability of keratinocytes after UV component exposure. Overall, these SF/DNA patches promise applications in wound dressing for practical biomedical purposes.
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Affiliation(s)
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Veronica Raggi
- Polo Scientifico Didattico, University of Perugia, Strada di Pentima 4, 05100 Terni, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Kevin Donato
- MAGI EUREGIO SCS, Via Maso della Pieve, 60/A, 39100 Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, 107 Technology Parkway, Peachtree Corners, GA 30092, USA
| | - Matteo Bertelli
- MAGI EUREGIO SCS, Via Maso della Pieve, 60/A, 39100 Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, 107 Technology Parkway, Peachtree Corners, GA 30092, USA
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Luca Valentini
- Civil and Environmental Engineering Department, University of Perugia, Strada di Pentima 6, 05100 Terni, Italy
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Kuznetsova DA, Kuznetsov DM, Vasileva LA, Amerhanova SK, Valeeva DN, Salakhieva DV, Nikolaeva VA, Nizameev IR, Islamov DR, Usachev KS, Voloshina AD, Zakharova LY. Complexation of Oligo- and Polynucleotides with Methoxyphenyl-Functionalized Imidazolium Surfactants. Pharmaceutics 2022; 14:pharmaceutics14122685. [PMID: 36559178 PMCID: PMC9782993 DOI: 10.3390/pharmaceutics14122685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Interaction between cationic surfactants and nucleic acids attracts much attention due to the possibility of using such systems for gene delivery. Herein, the lipoplexes based on cationic surfactants with imidazolium head group bearing methoxyphenyl fragment (MPI-n, n = 10, 12, 14, 16) and nucleic acids (oligonucleotide and plasmid DNA) were explored. The complex formation was confirmed by dynamic/electrophoretic light scattering, transmission electron microscopy, fluorescence spectroscopy, circular dichroism, and gel electrophoresis. The nanosized lipoplex formation (of about 100-200 nm), contributed by electrostatic, hydrophobic interactions, and intercalation mechanism, has been shown. Significant effects of the hydrocarbon tail length of surfactant and the type of nucleic acid on their interaction was revealed. The cytotoxic effect and transfection ability of lipoplexes studied were determined using M-HeLa, A549 cancer cell lines, and normal Chang liver cells. A selective reduced cytotoxic effect of the complexes on M-HeLa cancer cells was established, as well as a high ability of the systems to be transfected into cancer cells. MPI-n/DNA complexes showed a pronounced transfection activity equal to the commercial preparation Lipofectamine 3000. Thus, it has been shown that MPI-n surfactants are effective agents for nucleic acid condensation and can be considered as potential non-viral vectors for gene delivery.
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Affiliation(s)
- Darya A. Kuznetsova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
- Correspondence:
| | - Denis M. Kuznetsov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Leysan A. Vasileva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Syumbelya K. Amerhanova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Dilyara N. Valeeva
- Institute of Innovation Management, Kazan National Research Technological University, Karl Marx Str. 68, 420015 Kazan, Russia
| | - Diana V. Salakhieva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlyovskaya Str. 18, 420008 Kazan, Russia
| | - Viktoriia A. Nikolaeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kremlyovskaya Str. 18, 420008 Kazan, Russia
| | - Irek R. Nizameev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Daut R. Islamov
- FRC Kazan Scientific Center of RAS, Russian Academy of Sciences, Lobachevsky Street 2/31, 420111 Kazan, Russia
| | - Konstantin S. Usachev
- FRC Kazan Scientific Center of RAS, Russian Academy of Sciences, Lobachevsky Street 2/31, 420111 Kazan, Russia
| | - Alexandra D. Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
| | - Lucia Ya. Zakharova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str. 8, 420088 Kazan, Russia
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Verkh Y, Illa O, Ortuño RM. Synthesis of Chiral Scaffolds Based on Polyfunctional Cyclobutane β‐Amino Acids. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yaroslav Verkh
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola del Vallès, Barcelona Spain
- The Boston Consulting Group RWTH Aachen University 52078 Aachen North Rhine-Westphalia Germany
| | - Ona Illa
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Rosa M. Ortuño
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola del Vallès, Barcelona Spain
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