1
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Maruyama T, Gong J, Takinoue M. Temporally controlled multistep division of DNA droplets for dynamic artificial cells. Nat Commun 2024; 15:7397. [PMID: 39191726 DOI: 10.1038/s41467-024-51299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Synthetic droplets mimicking bio-soft matter droplets formed via liquid-liquid phase separation (LLPS) in living cells have recently been employed in nanobiotechnology for artificial cells, molecular robotics, molecular computing, etc. Temporally controlling the dynamics of synthetic droplets is essential for developing such bio-inspired systems because living systems maintain their functions based on the temporally controlled dynamics of biomolecular reactions and assemblies. This paper reports the temporal control of DNA-based LLPS droplets (DNA droplets). We demonstrate the timing-controlled division of DNA droplets via time-delayed division triggers regulated by chemical reactions. Controlling the release order of multiple division triggers results in order control of the multistep droplet division, i.e., pathway-controlled division in a reaction landscape. Finally, we apply the timing-controlled division into a molecular computing element to compare microRNA concentrations. We believe that temporal control of DNA droplets will promote the design of dynamic artificial cells/molecular robots and sophisticated biomedical applications.
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Affiliation(s)
- Tomoya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Masahiro Takinoue
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
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2
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Yonezawa N, Shindo T, Oda H, Kimura H, Hiraoka Y, Haraguchi T, Yamagata K. Reconstruction of artificial nuclei with nuclear import activity in living mouse oocytes. Genes Cells 2024. [PMID: 39140385 DOI: 10.1111/gtc.13149] [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: 04/22/2024] [Revised: 07/02/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
In eukaryotes, DNA is housed within the cell nucleus. Molecules required for the formation of a nucleus have been identified using in vitro systems with frog egg extracts and in vivo imaging of somatic cells. However, little is known about the physicochemical factors and conditions required for nuclear formation in mouse oocytes. In this study, using a reconstitution approach with purified DNA, we aimed to determine factors, such as the amount and timing of DNA introduction, required for the formation of nuclei with nuclear transport activity in mouse oocytes. T4 phage DNA (~166 kbp) was microinjected into strontium-activated oocytes to evaluate the conditions appropriate for nuclear formation. Microinjection of 100-500 ng/μL of T4 DNA, but not 20 ng/μL, was sufficient for the formation of nucleus-like structures. Furthermore, microinjection of DNA during metaphase II to telophase II, but not during interphase, was sufficient. Electron and fluorescence microscopy showed that T4 DNA-induced nucleus-like structures had nuclear lamina and nuclear pore complex structures similar to those of natural nuclei, as well as nuclear import activity. These results suggest that exogenous DNA can form artificial nuclei with nuclear transport functions in mouse oocytes, regardless of the sequence or source of the DNA.
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Affiliation(s)
- Nao Yonezawa
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
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3
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Padhy P, Zaman MA, Jensen MA, Cheng YT, Huang Y, Wu M, Galambos L, Davis RW, Hesselink L. Dielectrophoretic bead-droplet reactor for solid-phase synthesis. Nat Commun 2024; 15:6159. [PMID: 39039069 PMCID: PMC11263596 DOI: 10.1038/s41467-024-49284-z] [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: 05/06/2023] [Accepted: 05/29/2024] [Indexed: 07/24/2024] Open
Abstract
Solid-phase synthesis underpins many advances in synthetic and combinatorial chemistry, biology, and material science. The immobilization of a reacting species on the solid support makes interfacing of reagents an important challenge in this approach. In traditional synthesis columns, this leads to reaction errors that limit the product yield and necessitates excess consumption of the mobile reagent phase. Although droplet microfluidics can mitigate these problems, its adoption is fundamentally limited by the inability to controllably interface microbeads and reagent droplets. Here, we introduce Dielectrophoretic Bead-Droplet Reactor as a physical method to implement solid-phase synthesis on individual functionalized microbeads by encapsulating and ejecting them from microdroplets by tuning the supply voltage. Proof-of-concept demonstration of the enzymatic coupling of fluorescently labeled nucleotides onto the bead using this reactor yielded a 3.2-fold higher fidelity over columns through precise interfacing of individual microreactors and beads. Our work combines microparticle manipulation and droplet microfluidics to address a long-standing problem in solid-phase synthesis with potentially wide-ranging implications.
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Affiliation(s)
- Punnag Padhy
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - Mohammad Asif Zaman
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Anthony Jensen
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
| | - Yao-Te Cheng
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Yogi Huang
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Mo Wu
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ludwig Galambos
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ronald Wayne Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Lambertus Hesselink
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
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4
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Schaefer KG, Russell CM, Pyron RJ, Conley EA, Barrera FN, King GM. Polymerization mechanism of the Candida albicans virulence factor candidalysin. J Biol Chem 2024; 300:107370. [PMID: 38750794 PMCID: PMC11193009 DOI: 10.1016/j.jbc.2024.107370] [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: 03/05/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Candida albicans is a commensal fungus that can cause epithelial infections and life-threatening invasive candidiasis. The fungus secretes candidalysin (CL), a peptide that causes cell damage and immune activation by permeation of epithelial membranes. The mechanism of CL action involves strong peptide assembly into polymers in solution. The free ends of linear CL polymers can join, forming loops that become pores upon binding to membranes. CL polymers constitute a therapeutic target for candidiasis, but little is known about CL self-assembly in solution. Here, we examine the assembly mechanism of CL in the absence of membranes using complementary biophysical tools, including a new fluorescence polymerization assay, mass photometry, and atomic force microscopy. We observed that CL assembly is slow, as tracked with the fluorescent marker C-laurdan. Single-molecule methods showed that CL polymerization involves a convolution of four processes. Self-assembly begins with the formation of a basic subunit, thought to be a CL octamer that is the polymer seed. Polymerization proceeds via the addition of octamers, and as polymers grow they can curve and form loops. Alternatively, secondary polymerization can occur and cause branching. Interplay between the different rates determines the distribution of CL particle types, indicating a kinetic control mechanism. This work elucidates key physical attributes underlying CL self-assembly which may eventually evoke pharmaceutical development.
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Affiliation(s)
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Robert J Pyron
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Elizabeth A Conley
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri; Department of Biochemistry, University of Missouri, Columbia, Missouri.
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5
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Raczyłło E, Gołowicz D, Skóra T, Kazimierczuk K, Kondrat S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. NANO LETTERS 2024; 24. [PMID: 38607288 PMCID: PMC11057039 DOI: 10.1021/acs.nanolett.3c05100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.
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Affiliation(s)
- Edyta Raczyłło
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, 20-031 Lublin, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific
Computing and Imaging Institute, University
of Utah, Salt Lake City, Utah 84112, United States
| | | | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute
for Computational Physics, University of
Stuttgart 70569, Stuttgart, Germany
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6
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Seyed N, Taheri T, Rafati S. Live attenuated-nonpathogenic Leishmania and DNA structures as promising vaccine platforms against leishmaniasis: innovations can make waves. Front Microbiol 2024; 15:1326369. [PMID: 38633699 PMCID: PMC11021776 DOI: 10.3389/fmicb.2024.1326369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
Leishmaniasis is a vector-borne disease caused by the protozoan parasite of Leishmania genus and is a complex disease affecting mostly tropical regions of the world. Unfortunately, despite the extensive effort made, there is no vaccine available for human use. Undoubtedly, a comprehensive understanding of the host-vector-parasite interaction is substantial for developing an effective prophylactic vaccine. Recently the role of sandfly saliva on disease progression has been uncovered which can make a substantial contribution in vaccine design. In this review we try to focus on the strategies that most probably meet the prerequisites of vaccine development (based on the current understandings) including live attenuated/non-pathogenic and subunit DNA vaccines. Innovative approaches such as reverse genetics, CRISP/R-Cas9 and antibiotic-free selection are now available to promisingly compensate for intrinsic drawbacks associated with these platforms. Our main goal is to call more attention toward the prerequisites of effective vaccine development while controlling the disease outspread is a substantial need.
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Affiliation(s)
- Negar Seyed
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
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7
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Ito A, Kitabatake S, Furuichi W, Takase N, Nakahara T, Akiyama T, Yoshida S, Kusano Y, Furusawa Y, Hirayama R. LET Dependence of 8-Hydroxy-2'-deoxyguanosine (8-OHdG) Generation in Mammalian Cells under Air-Saturated and Hypoxic Conditions: A Possible Experimental Approach to the Mechanism of the Decreasing Oxygen Effect in the High-LET Region. Radiat Res 2024; 201:189-196. [PMID: 38294870 DOI: 10.1667/rade-23-00046.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
One of the most distinguished features in biological effects of heavy ions would be the decrease of oxygen effect in the high-LET region. This feature has been referred to as the radiobiological basis for the control of hypoxic fraction in cancer radiotherapy. However, mechanisms to explain this phenomenon have not been fully understood. One of the explanations was given by the oxygen in the track hypothesis, which proposes that oxygen is produced along ion tracks even in the hypoxic irradiation condition. In the present study, we designed an experimental approach to support this hypothesis by using 8-hydroxy-2'-deoxyguanosine (8-OHdG) as DNA damage requiring oxygen to produce. The LET dependence of 8-OHdG under hypoxic condition revealed that with increasing LET 8-OHdG yield seems to increase, despite that the yield of OH radical, which is also required for the production of 8-OHdG, decreases in the high-LET region. This result is consistent with the explanation that the local generation of oxygen along ion tracks contributes to the increase of 8-OHdG yield.
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Affiliation(s)
- A Ito
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - S Kitabatake
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - W Furuichi
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - N Takase
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - T Nakahara
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - T Akiyama
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - S Yoshida
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
| | - Y Kusano
- Department of Nuclear Engineering, School of Engineering, Tokai University, Kanagawa, Japan
- Section of Medical Physics and Engineering, Kanagawa Cancer Center, Kanagawa, Japan
| | - Y Furusawa
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, National Institutes Quantum Science and Technology, Chiba, Japan
| | - R Hirayama
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, National Institutes Quantum Science and Technology, Chiba, Japan
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8
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Wang Y, Fu Q, Park SY, Lee YS, Park SY, Lee DY, Yoon S. Decoding cellular mechanism of recombinant adeno-associated virus (rAAV) and engineering host-cell factories toward intensified viral vector manufacturing. Biotechnol Adv 2024; 71:108322. [PMID: 38336188 DOI: 10.1016/j.biotechadv.2024.108322] [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: 06/11/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is one of the prominent gene delivery vehicles that has opened promising opportunities for novel gene therapeutic approaches. However, the current major viral vector production platform, triple transfection in mammalian cells, may not meet the increasing demand. Thus, it is highly required to understand production bottlenecks from the host cell perspective and engineer the cells to be more favorable and tolerant to viral vector production, thereby effectively enhancing rAAV manufacturing. In this review, we provided a comprehensive exploration of the intricate cellular process involved in rAAV production, encompassing various stages such as plasmid entry to the cytoplasm, plasmid trafficking and nuclear delivery, rAAV structural/non-structural protein expression, viral capsid assembly, genome replication, genome packaging, and rAAV release/secretion. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production is summarized for each stage. The control strategies from the perspectives of host cell and materials (e.g., AAV plasmids) are proposed as our insights based on the characterization of molecular features and our existing knowledge of the AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.
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Affiliation(s)
- Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America.
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9
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Maeki M, Uno S, Sugiura K, Sato Y, Fujioka Y, Ishida A, Ohba Y, Harashima H, Tokeshi M. Development of Polymer-Lipid Hybrid Nanoparticles for Large-Sized Plasmid DNA Transfection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:2110-2119. [PMID: 38141015 PMCID: PMC10798250 DOI: 10.1021/acsami.3c14714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
RNA and DNA delivery technologies using lipid nanoparticles (LNPs) have advanced significantly, as demonstrated by their successful application in mRNA vaccines. To date, commercially available RNA therapeutics include Onpattro, a 21 bp siRNA, and mRNA vaccines comprising 4300 nucleotides for COVID-19. However, a significant challenge remains in achieving efficient transfection, as the size of the delivered RNA and DNA increases. In contrast to RNA transfection, plasmid DNA (pDNA) transfection requires multiple steps, including cellular uptake, endosomal escape, nuclear translocation, transcription, and translation. The low transfection efficiency of large pDNA is a critical limitation in the development of artificial cells and their cellular functionalization. Here, we introduce polymer-lipid hybrid nanoparticles designed for efficient, large-sized pDNA transfection. We demonstrated that LNPs loaded with positively charged pDNA-polycation core nanoparticles exhibited a 4-fold increase in transfection efficiency for 15 kbp pDNA compared with conventional LNPs, which encapsulate a negatively charged pDNA-polycation core. Based on assessments of the size and internal structure of the polymer-lipid nanoparticles as well as hemolysis and cellular uptake analysis, we propose a strategy to enhance large-sized pDNA transfection using LNPs. This approach holds promise for accelerating the in vivo delivery of large-sized pDNA and advancing the development of artificial cells.
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Affiliation(s)
- Masatoshi Maeki
- Division
of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
- JST
PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Institute
of Materials Structure Science, High Energy
Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Shuya Uno
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Kaisei Sugiura
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yusuke Sato
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 8, Kita-ku, Sapporo 060-0812, Japan
| | - Yoichiro Fujioka
- Department
of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15 Nishi 7, Kita-ku, Sapporo 060-8638, Japan
| | - Akihiko Ishida
- Division
of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yusuke Ohba
- Department
of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Kita 15 Nishi 7, Kita-ku, Sapporo 060-8638, Japan
| | - Hideyoshi Harashima
- Graduate
School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Manabu Tokeshi
- JST
PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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10
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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11
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Sueters J, Xiao F, Roovers JP, Bouman MB, Groenman F, Maas H, Huirne J, Smit T. Creation of a decellularized vaginal matrix from healthy human vaginal tissue for potential vagina reconstruction: experimental studies. Int J Surg 2023; 109:3905-3918. [PMID: 37755377 PMCID: PMC10720790 DOI: 10.1097/js9.0000000000000727] [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: 06/26/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND When a disorder causes the absence of a healthy, full-size vagina, various neovaginal creation methods are available. Sometimes dilation or stretching of the vaginal cavity is sufficient, but intestinal or dermal flap tissue is generally required. However, different inherent tissue properties cause complications. Therefore, a lost body part should be replaced with a similar material. The use of organ-specific acellular vaginal tissue carries great potential, as its similar architecture and matrix composition make it suitable for vaginal regeneration. METHODS The authors developed an optimized protocol for decellularization of healthy human vaginal tissue. Resected colpectomy tissue from 12 healthy transgender patients was used. Successful decellularization was confirmed by applying acellular criteria from in-vivo remodeling reports. Suitability as a tissue-mimicking scaffold for vaginal reconstruction was determined by visible structural features, biocompatibility during stretching, and the presence of visible collagen, elastin, laminin, and fibronectin. RESULTS Histological examination confirmed the preservation of structural features, and minimal cellular residue was seen during fluorescence microscopy, DNA and RNA quantification, and fragment length examination. Biomechanical testing showed decreased peak load (55%, P <0.05), strain at rupture (23%, P <0.01), and ultimate tensile stress (55%, P <0.05) after decellularization, while the elastic modulus (68%) did not decrease significantly. Fluorescence microscopy revealed preserved Fibronectin-I/II/III and Laminin-I/II, while Collagen-I and Ficolin-2B were decreased but mostly retained. CONCLUSIONS The absence of cellular residue, moderately altered biomechanical extracellular matrix properties, and mostly preserved structural proteins appear to make our decellularized human vaginal matrix a suitable tissue-mimicking scaffold for vagina transplantation when tissue survival through vascularization and innervation are accomplished in the future.
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Affiliation(s)
- Jayson Sueters
- Department of Gynaecology, Amsterdam Reproduction and Development
| | - Fangxin Xiao
- Department of Human Movement Sciences, Faculty of Behavioral and Movement Sciences, Vrije Universiteit Amsterdam
- AMS – Musculoskeletal Health, Amsterdam Movement Sciences, VU Research Institutes
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Jan-Paul Roovers
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development
| | - Mark-Bram Bouman
- Department of Plastic, Reconstructive and Hand Surgery, Amsterdam UMC – location VUmc
| | - Freek Groenman
- Department of Obstetrics and Gynecology, Amsterdam Reproduction and Development
| | - Huub Maas
- Department of Plastic, Reconstructive and Hand Surgery, Amsterdam UMC – location VUmc
- Department of Human Movement Sciences, Faculty of Behavioral and Movement Sciences, Vrije Universiteit Amsterdam
| | - Judith Huirne
- Department of Gynaecology, Amsterdam Reproduction and Development
| | - Theo Smit
- Department of Gynaecology, Amsterdam Reproduction and Development
- Department of Medical Biology, Amsterdam UMC – location AMC, Amsterdam, The Netherlands
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12
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Oehler J, Morrow CA, Whitby MC. Gene duplication and deletion caused by over-replication at a fork barrier. Nat Commun 2023; 14:7730. [PMID: 38007544 PMCID: PMC10676400 DOI: 10.1038/s41467-023-43494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Replication fork stalling can provoke fork reversal to form a four-way DNA junction. This remodelling of the replication fork can facilitate repair, aid bypass of DNA lesions, and enable replication restart, but may also pose a risk of over-replication during fork convergence. We show that replication fork stalling at a site-specific barrier in fission yeast can induce gene duplication-deletion rearrangements that are independent of replication restart-associated template switching and Rad51-dependent multi-invasion. Instead, they resemble targeted gene replacements (TGRs), requiring the DNA annealing activity of Rad52, the 3'-flap nuclease Rad16-Swi10, and mismatch repair protein Msh2. We propose that excess DNA, generated during the merging of a canonical fork with a reversed fork, can be liberated by a nuclease and integrated at an ectopic site via a TGR-like mechanism. This highlights how over-replication at replication termination sites can threaten genome stability in eukaryotes.
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Affiliation(s)
- Judith Oehler
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl A Morrow
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Matthew C Whitby
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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13
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Chastagnier L, Marquette C, Petiot E. In situ transient transfection of 3D cell cultures and tissues, a promising tool for tissue engineering and gene therapy. Biotechnol Adv 2023; 68:108211. [PMID: 37463610 DOI: 10.1016/j.biotechadv.2023.108211] [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: 12/15/2022] [Revised: 04/26/2023] [Accepted: 07/09/2023] [Indexed: 07/20/2023]
Abstract
Various research fields use the transfection of mammalian cells with genetic material to induce the expression of a target transgene or gene silencing. It is a tool widely used in biological research, bioproduction, and therapy. Current transfection protocols are usually performed on 2D adherent cells or suspension cultures. The important rise of new gene therapies and regenerative medicine in the last decade raises the need for new tools to empower the in situ transfection of tissues and 3D cell cultures. This review will present novel in situ transfection methods based on a chemical or physical non-viral transfection of cells in tissues and 3D cultures, discuss the advantages and remaining gaps, and propose future developments and applications.
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Affiliation(s)
- Laura Chastagnier
- 3D Innovation Lab - 3d.FAB - ICBMS, University Claude Bernard Lyon 1, Université Lyon 1, CNRS, INSA, CPE-Lyon, UMR 5246, bat. Lederer, 5 rue Gaston Berger, 69100 Villeurbanne, France
| | - Christophe Marquette
- 3D Innovation Lab - 3d.FAB - ICBMS, University Claude Bernard Lyon 1, Université Lyon 1, CNRS, INSA, CPE-Lyon, UMR 5246, bat. Lederer, 5 rue Gaston Berger, 69100 Villeurbanne, France
| | - Emma Petiot
- 3D Innovation Lab - 3d.FAB - ICBMS, University Claude Bernard Lyon 1, Université Lyon 1, CNRS, INSA, CPE-Lyon, UMR 5246, bat. Lederer, 5 rue Gaston Berger, 69100 Villeurbanne, France.
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14
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Wang W, Tasset A, Pyatnitskiy I, Lin P, Bellamkonda A, Mehta R, Gabbert C, Yuan F, Mohamed HG, Peppas NA, Wang H. Reversible, Covalent DNA Condensation Approach Using Chemical Linkers for Enhanced Gene Delivery. NANO LETTERS 2023; 23:9310-9318. [PMID: 37843021 DOI: 10.1021/acs.nanolett.3c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Nonviral gene delivery has emerged as a promising technology for gene therapy. Nonetheless, these approaches often face challenges, primarily associated with lower efficiency, which can be attributed to the inefficient transportation of DNA into the nucleus. Here, we report a two-stage condensation approach to achieve efficient nuclear transport of DNA. First, we utilize chemical linkers to cross-link DNA plasmids via a reversible covalent bond to form smaller-sized bundled DNA (b-DNA). Then, we package the b-DNA into cationic vectors to further condense b-DNA and enable efficient gene delivery to the nucleus. We demonstrate clear improvements in the gene transfection efficiency in vitro, including with 11.6 kbp plasmids and in primary cultured neurons. Moreover, we also observed a remarkable improvement in lung-selective gene transfection efficiency in vivo by this two-stage condensation approach following intravenous administration. This reversible covalent assembly strategy demonstrates substantial value of nonviral gene delivery for clinical therapeutic applications.
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Affiliation(s)
- Wenliang Wang
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aaron Tasset
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ilya Pyatnitskiy
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Peter Lin
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Arjun Bellamkonda
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Rohan Mehta
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Christian Gabbert
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Feng Yuan
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Heba Galaa Mohamed
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nicholas A Peppas
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Biomaterials, Drug Delivery, and Regenerative Medicine, The University of Texas at Austin, Austin, Texas 78712, United States
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Surgery and Perioperative Care, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Huiliang Wang
- Biomedical Engineering Cockrell School of Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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15
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Casper J, Schenk SH, Parhizkar E, Detampel P, Dehshahri A, Huwyler J. Polyethylenimine (PEI) in gene therapy: Current status and clinical applications. J Control Release 2023; 362:667-691. [PMID: 37666302 DOI: 10.1016/j.jconrel.2023.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Polyethlyenimine (PEI) was introduced 1995 as a cationic polymer for nucleic acid delivery. PEI and its derivatives are extensively used in basic research and as reference formulations in the field of polymer-based gene delivery. Despite its widespread use, the number of clinical applications to date is limited. Thus, this review aims to consolidate the past applications of PEI in DNA delivery, elucidate the obstacles that hinder its transition to clinical use, and highlight potential prospects for novel iterations of PEI derivatives. The present review article is divided into three sections. The first section examines the mechanism of action employed by PEI, examining fundamental aspects of cellular delivery including uptake mechanisms, release from endosomes, and transport into the cell nucleus, along with potential strategies for enhancing these delivery phases. Moreover, an in-depth analysis is conducted concerning the mechanism underlying cellular toxicity, accompanied with approaches to overcome this major challenge. The second part is devoted to the in vivo performance of PEI and its application in various therapeutic indications. While systemic administration has proven to be challenging, alternative localized delivery routes hold promise, such as treatment of solid tumors, application as a vaccine, or serving as a therapeutic agent for pulmonary delivery. In the last section, the outcome of completed and ongoing clinical trials is summarized. Finally, an expert opinion is provided on the potential of PEI and its future applications. PEI-based formulations for nucleic acid delivery have a promising potential, it will be an important task for the years to come to introduce innovations that address PEI-associated shortcomings by introducing well-designed PEI formulations in combination with an appropriate route of administration.
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Affiliation(s)
- Jens Casper
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Susanne H Schenk
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Elahehnaz Parhizkar
- Department of Pharmaceutics, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pascal Detampel
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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16
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Wong S, Jimenez S, Slavcev RA. Construction and characterization of a novel miniaturized filamentous phagemid for targeted mammalian gene transfer. Microb Cell Fact 2023; 22:124. [PMID: 37430278 DOI: 10.1186/s12934-023-02135-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/24/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND As simplistic proteinaceous carriers of genetic material, phages offer great potential as targeted vectors for mammalian transgene delivery. The filamentous phage M13 is a single-stranded DNA phage with attractive characteristics for gene delivery, including a theoretically unlimited DNA carrying capacity, amenability to tropism modification via phage display, and a well-characterized genome that is easy to genetically modify. The bacterial backbone in gene transfer plasmids consists of elements only necessary for amplification in prokaryotes, and, as such, are superfluous in the mammalian cell. These problematic elements include antibiotic resistance genes, which can disseminate antibiotic resistance, and CpG motifs, which are inflammatory in animals and can lead to transgene silencing. RESULTS Here, we examined how M13-based phagemids could be improved for transgene delivery by removing the bacterial backbone. A transgene cassette was flanked by isolated initiation and termination elements from the phage origin of replication. Phage proteins provided in trans by a helper would replicate only the cassette, without any bacterial backbone. The rescue efficiency of "miniphagemids" from these split origins was equal to, if not greater than, isogenic "full phagemids" arising from intact origins. The type of cassette encoded by the miniphagemid as well as the choice of host strain constrained the efficiency of phagemid rescue. CONCLUSIONS The use of two separated domains of the f1 ori improves upon a single wildtype origin while still resulting in high titres of miniphagemid gene transfer vectors. Highly pure lysates of miniaturized phagemids could be rapidly obtained in a straightforward procedure without additional downstream processing.
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Affiliation(s)
- Shirley Wong
- School of Pharmacy, University of Waterloo, Waterloo, Canada.
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, Waterloo, Canada
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17
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Draz MS, Dupouy D, Gijs MAM. Acoustofluidic large-scale mixing for enhanced microfluidic immunostaining for tissue diagnostics. LAB ON A CHIP 2023. [PMID: 37365861 DOI: 10.1039/d3lc00312d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The usage of microfluidics for automated and fast immunoassays has gained a lot of interest in the last decades. This integration comes with certain challenges, like the reconciliation of laminar flow patterns of micro-scale systems with diffusion-limited mass transport. Several methods have been investigated to enhance microfluidic mixing in microsystems, including acoustic-based fluidic streaming. Here, we report both by numerical simulation and experiments on the beneficiary effect of acoustic agitation on the uniformity of immunostaining in large-size and thin microfluidic chambers. Moreover, we investigate by numerical simulation the impact of reducing the incubation times and the concentrations of the biochemical detection reagents on the obtained immunoassay signal. Finally, acoustofluidic mixing was successfully used to reduce by 80% the incubation time of the Her2 (human epidermal growth factor receptor 2) and CK (cytokeratins) biomarkers for the spatial immunostaining of breast cancer cell pellets, or reducing their concentration by 66% and achieving a higher signal-to-background ratio than comparable spatially resolved immunostaining with static incubation.
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Affiliation(s)
- Muaz S Draz
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Diego Dupouy
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Martin A M Gijs
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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18
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Park HH, Choi AA, Xu K. Size-Dependent Suppression of Molecular Diffusivity in Expandable Hydrogels: A Single-Molecule Study. J Phys Chem B 2023; 127:3333-3339. [PMID: 37011131 DOI: 10.1021/acs.jpcb.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
By repurposing the recently popularized expansion microscopy to control the meshwork size of hydrogels, we examine the size-dependent suppression of molecular diffusivity in the resultant tuned hydrogel nanomatrices over a wide range of polymer fractions of ∼0.14-7 wt %. With our recently developed single-molecule displacement/diffusivity mapping (SMdM) microscopy methods, we thus show that with a fixed meshwork size, larger molecules exhibit more impeded diffusion and that, for the same molecule, diffusion is progressively more suppressed as the meshwork size is reduced; this effect is more prominent for the larger molecules. Moreover, we show that the meshwork-induced obstruction of diffusion is uncoupled from the suppression of diffusion due to increased solution viscosities. Thus, the two mechanisms, respectively, being diffuser-size-dependent and independent, may separately scale down molecular diffusivity to produce the final diffusion slowdown in complex systems like the cell.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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19
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Free-flow biomolecular concentration and separation of proteins and nucleic acids using teíchophoresis. Talanta 2023; 255:124198. [PMID: 36580810 DOI: 10.1016/j.talanta.2022.124198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The ability to preconcentrate, separate, and purify biomolecules, such as proteins and nucleic acids, is an important requirement for the next generation of portable diagnostic tools for environmental monitoring and disease detection. Traditionally, such pretreatment has been accomplished using large, centralized liquid- or solid-phase extraction equipment, which can be time-consuming and requires many processing steps. Here, we present a newly developed electrokinetic concentration technique, teíchophoresis (TPE), to concentrate and separate proteins, and to concentrate nucleic acids. In TPE, a free-flowing sample is exposed to a perpendicular electric field in the vicinity of a mass-impermeable conductive wall and a conductive terminating electrolyte (TE), which creates a high electric field strength zone between the lower mobility sample and the no-flux barrier. Unlike a similar electrokinetic concentration method, isotachophoresis (ITP), TPE does not require a leading electrolyte (LE), yet still enables a continuous field-driven electrophoretic ion migration across the channel and a free-flowing biomolecular concentration at the conductive wall. Here, we demonstrate the use of free-flow TPE (FFTPE) to manipulate biomolecular samples containing proteins or nucleic acids. We first use TPE to drive a 6.6-fold concentration increase of avidin-FITC, and also demonstrate protein separation and stacking between ovalbumin-fluorescein and BSA-AlexaFluor 555, both without the use of a conventional LE. Further, we utilize TPE to perform a 21-fold concentration increase of nucleic acids. Our results show that TPE is biocompatible with both proteins and nucleic acids, requires only 10 V DC, produces no significant sample pH changes during operation, and demonstrates that this method can be used as an effective sample pretreatment to prepare biological samples for downstream analysis in a continuous free-flowing microfluidic channel.
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20
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Draz MS, Uning K, Dupouy D, Gijs MAM. Efficient AC electrothermal flow (ACET) on-chip for enhanced immunoassays. LAB ON A CHIP 2023; 23:1637-1648. [PMID: 36644814 DOI: 10.1039/d2lc01147f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Biochemical reaction rates in microfluidic systems are known to be limited by the diffusional transport of reagents, leading often to lowered sensitivity and/or longer detection times in immunoassays. Several methods, including electrically powering electrodes to generate AC electrothermal flow (ACET) on-chip, have been adopted to enhance the mass transport of the reagents and improve microfluidic mixing. Here, we report a novel ACET electrode design concept for generating in-plane microfluidic mixing vortices that act over a large volume close to the reaction surface of interest. This is different from the traditional ACET parallel electrode design that provides rather local vertical mixing vortices directly above the electrodes. Both numerical simulation and experimental studies were performed to validate the new design. Moreover, numerical simulation was carried out to show the effects of experimental factors such as the reaction kinetics (association constant) and the reagent concentration on the ACET-enhanced surface-based assays. As a proof of concept, the new design for the ACET-enhanced immunoassays was used to improve the immunostaining signal of the HER2 (human epidermal growth factor receptor 2) cancer biomarker on breast cancer cells. Finally, the concept of scaling up the design has been validated by experiments (immunoassays on breast cancer cells for different ACET power and different assay times). In particular, we show that larger ACET in-plane designs can agitate and mix the fluid over large microfluidic volumes, which further enhances the immunoassay's output. We have achieved a 6-times enhancement in the assay signal with a 75% reduction in assay time.
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Affiliation(s)
- Muaz S Draz
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Kevin Uning
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Diego Dupouy
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Martin A M Gijs
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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21
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De Silva S, Ocaña-Rios I, Cagliero C, Gostel MR, Johnson G, Anderson JL. Isolation of DNA from plant tissues using a miniaturized matrix solid-phase dispersion approach featuring ionic liquid and magnetic ionic liquid solvents. Anal Chim Acta 2023; 1245:340858. [PMID: 36737141 DOI: 10.1016/j.aca.2023.340858] [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: 11/19/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The isolation of high-quality plant genomic DNA is a major prerequisite in many plant biomolecular analyses involving nucleic acid amplification. Conventional plant cell lysis and DNA extraction methods involve lengthy sample preparation procedures that often require large amounts of sample and chemicals, high temperatures and multiple liquid transfer steps which can introduce challenges for high throughput applications. In this study, a simple, rapid, miniaturized ionic liquid (IL)-based extraction method was developed for the isolation of genomic DNA from milligram fragments of Arabidopsis thaliana plant tissue. This method is based on a modification of vortex-assisted matrix solid-phase dispersion (VA-MSPD) in which the trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide ([P6,6,6,14+][NTf2-]) IL or trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(hfacac)3-]) magnetic IL (MIL) was directly applied to treated plant tissue (∼1.5 mg) and dispersed in an agate mortar to facilitate plant cell lysis and DNA extraction, followed by recovery of the mixture with a qPCR compatible co-solvent. This study represents the first approach to use ILs and MILs in a MSPD procedure to facilitate plant cell lysis and DNA extraction. The DNA-enriched IL- and MIL-cosolvent mixtures were directly integrated into the qPCR buffer without inhibiting the reaction while also circumventing the need for additional purification steps prior to DNA amplification. Under optimum conditions, the IL and MIL yielded 2.87 ± 0.28 and 1.97 ± 0.59 ng of DNA/mg of plant tissue, respectively. Furthermore, the mild extraction conditions used in the method enabled plant DNA in IL- and MIL-cosolvent mixtures to be preserved from degradation at room temperature.
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Affiliation(s)
- Shashini De Silva
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Iran Ocaña-Rios
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, I-10125, Turin, Italy
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA
| | | | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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22
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Asad N, Smith E, Shakya S, Stegman S, Timmons L. Sustainable Methodologies for Efficient Gel Electrophoresis and Streamlined Screening of Difficult Plasmids. Methods Protoc 2023; 6:mps6020025. [PMID: 36961045 PMCID: PMC10037626 DOI: 10.3390/mps6020025] [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: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
We describe a workflow for efficient, environmentally attentive, and sustainable practices related to routine agarose gel electrophoresis. The methods reduce plastic waste and improve efficiency, especially for the exhaustive screening of difficult-to-obtain plasmids. Sustainability is increased when agarose is used ten times over by virtue of a thorough recycling regimen. The workflow optimizes workspaces and standardizes lab practices for handling potentially hazardous waste, minimizing environmental harm. Safety, efficiency, and sustainability improve laboratory productivity, help minimize environmental contamination, and increase cost-effectiveness.
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Affiliation(s)
- Nadeem Asad
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Biochemistry and Molecular Medicine, 64 Medical Center Drive, University of West Virginia Health Science Center, Morgantown, WV 26506, USA
| | - Emily Smith
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, CA 95618, USA
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618, USA
- Center for Neuroscience, University of California, Davis, CA 95618, USA
| | - Sudeep Shakya
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sutton Stegman
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Lisa Timmons
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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23
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Wang H, Stehr AM, Singh J, Zlatar L, Hartmann A, Evert K, Naschberger E, von Stillfried S, Boor P, Muñoz LE, Knopf J, Stürzl M, Herrmann M. Anti-DNA-IgM Favors the Detection of NET-Associated Extracellular DNA. Int J Mol Sci 2023; 24:ijms24044101. [PMID: 36835515 PMCID: PMC9958910 DOI: 10.3390/ijms24044101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
During inflammatory responses, neutrophils enter the sites of attack where they execute various defense mechanisms. They (I) phagocytose microorganisms, (II) degranulate to release cytokines, (III) recruit various immune cells by cell-type specific chemokines, (IV) secrete anti-microbials including lactoferrin, lysozyme, defensins and reactive oxygen species, and (V) release DNA as neutrophil extracellular traps (NETs). The latter originates from mitochondria as well as from decondensed nuclei. This is easily detected in cultured cells by staining of DNA with specific dyes. However, in tissues sections the very high fluorescence signals emitted from the condensed nuclear DNA hamper the detection of the widespread, extranuclear DNA of the NETs. In contrast, when we employ anti-DNA-IgM antibodies, they are unable to penetrate deep into the tightly packed DNA of the nucleus, and we observe a robust signal for the extended DNA patches of the NETs. To validate anti-DNA-IgM, we additionally stained the sections for the NET-markers histone H2B, myeloperoxidase, citrullinated histone H3, and neutrophil elastase. Altogether, we have described a fast one-step procedure for the detection of NETs in tissue sections, which provides new perspectives to characterize neutrophil-associated immune reactions in disease.
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Affiliation(s)
- Han Wang
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Antonia Margarethe Stehr
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jeeshan Singh
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Leticija Zlatar
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Katja Evert
- Institut für Pathologie, Universität Regensburg, 93053 Regensburg, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | | | - Peter Boor
- Institute of Pathology, University Clinic of the RWTH Aachen, 52074 Aachen, Germany
| | - Luis E. Muñoz
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Martin Herrmann
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Correspondence:
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24
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Ghanem R, Berchel M, Haute T, Buin X, Laurent V, Youf R, Bouraoui A, Le Gall T, Jaffrès PA, Montier T. Gene transfection using branched cationic amphiphilic compounds for an aerosol administration in cystic fibrosis context. Int J Pharm 2023; 631:122491. [PMID: 36529361 DOI: 10.1016/j.ijpharm.2022.122491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
For cystic fibrosis gene therapy, the aerosolization of genetic materials is the most relevant delivery strategy to reach the airway epithelium. However, aerosolized formulations have to resist shear forces while maintaining the integrity of plasmid DNA (pDNA) during its journey from the nebulization to the epithelial cells. Herein, we compared the efficiency of gene delivery by aerosolization of two types of formulations: (i) BSV163, a branched cationic amphiphilic compound, co-formulated with different DOPE ratios (mol/mol) and DMPE-PEG5000 and (ii) 25 KDa branched polyethylenimine (b-PEI)-based formulation used as control. This study also aims to determine whether BSV163-based formulations possess the ability to resist the nebulization mechanisms and protect the nucleic acids (pDNA) cargo. Therefore, two CpG free plasmids (pGM144 or pGM169) encoding either the luciferase reporter gene or hCFTR respectively were used. Air-Liquid Interface (ALI) cell-culture was selected as an in-vitro model for aerosol experiments due to its closer analogy with in vivo morphology. Results highlighted that DOPE ratio influences the capacity of the BSV163 based-formulations to mediate high transfection efficacies. Furthermore, we proved that addition of DMPE-PEG5000 upon the formation of the BSV163/DOPE (1/1) lipid film instead of post-insertion led to a higher transgene expression. The aerosolization of this formulation on ALI cell-culture was more efficient than the use of b-PEI-based formulation.
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Affiliation(s)
- Rosy Ghanem
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Mathieu Berchel
- Univ Brest, CNRS, CEMCA UMR 65216, Avenue Victor, Le Gorgeu, F-29238 Brest, France
| | - Tanguy Haute
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Xavier Buin
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | | | - Raphaëlle Youf
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Amal Bouraoui
- Univ Brest, CNRS, CEMCA UMR 65216, Avenue Victor, Le Gorgeu, F-29238 Brest, France
| | - Tony Le Gall
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Paul-Alain Jaffrès
- Univ Brest, CNRS, CEMCA UMR 65216, Avenue Victor, Le Gorgeu, F-29238 Brest, France
| | - Tristan Montier
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France; CHRU de Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Centre de Référence des Maladies Rares Maladies Neuromusculaires, 29200 Brest, France.
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25
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CNS Delivery of Nucleic Acid Therapeutics: Beyond the Blood-Brain Barrier and Towards Specific Cellular Targeting. Pharm Res 2023; 40:77-105. [PMID: 36380168 DOI: 10.1007/s11095-022-03433-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022]
Abstract
Nucleic acid-based therapeutic molecules including small interfering RNA (siRNA), microRNA(miRNA), antisense oligonucleotides (ASOs), messenger RNA (mRNA), and DNA-based gene therapy have tremendous potential for treating diseases in the central nervous system (CNS). However, achieving clinically meaningful delivery to the brain and particularly to target cells and sub-cellular compartments is typically very challenging. Mediating cell-specific delivery in the CNS would be a crucial advance that mitigates off-target effects and toxicities. In this review, we describe these challenges and provide contemporary evidence of advances in cellular and sub-cellular delivery using a variety of delivery mechanisms and alternative routes of administration, including the nose-to-brain approach. Strategies to achieve subcellular localization, endosomal escape, cytosolic bioavailability, and nuclear transfer are also discussed. Ultimately, there are still many challenges to translating these experimental strategies into effective and clinically viable approaches for treating patients.
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26
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Padmakumar S, D'Souza A, Parayath NN, Bleier BS, Amiji MM. Nucleic acid therapies for CNS diseases: Pathophysiology, targets, barriers, and delivery strategies. J Control Release 2022; 352:121-145. [PMID: 36252748 DOI: 10.1016/j.jconrel.2022.10.018] [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: 06/23/2022] [Revised: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 11/08/2022]
Abstract
Nucleic acid therapeutics have emerged as one of the very advanced and efficacious treatment approaches for debilitating health conditions, including those diseases affecting the central nervous system (CNS). Precise targeting with an optimal control over gene regulation confers long-lasting benefits through the administration of nucleic acid payloads via viral, non-viral, and engineered vectors. The current review majorly focuses on the development and clinical translational potential of non-viral vectors for treating CNS diseases with a focus on their specific design and targeting approaches. These carriers must be able to surmount the various intracellular and extracellular barriers, to ensure successful neuronal transfection and ultimately attain higher therapeutic efficacies. Additionally, the specific challenges associated with CNS administration also include the presence of blood-brain barrier (BBB), the complex pathophysiological and biochemical changes associated with different disease conditions and the existence of non-dividing cells. The advantages offered by lipid-based or polymeric systems, engineered proteins, particle-based systems coupled with various approaches of neuronal targeting have been discussed in the context of a variety of CNS diseases. The possibilities of rapid yet highly efficient gene modifications rendered by the breakthrough methodologies for gene editing and gene manipulation have also opened vast avenues of research in neuroscience and CNS disease therapy. The current review also underscores the extensive scientific efforts to optimize specialized, efficacious yet non-invasive and safer administration approaches to overcome the therapeutic delivery challenges specifically posed by the CNS transport barriers and the overall obstacles to clinical translation.
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Affiliation(s)
- Smrithi Padmakumar
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA
| | - Anisha D'Souza
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA; Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 20115, USA
| | - Neha N Parayath
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA
| | - Benjamin S Bleier
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 20115, USA
| | - Mansoor M Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, MA 02115, USA; Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA 02115, USA.
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27
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Oh I, Song J, Hyun HR, Lee SH, Kim JS. Brownian ratchet for directional nanoparticle transport by repetitive stretch-relaxation of DNA. Phys Rev E 2022; 106:054117. [PMID: 36559375 DOI: 10.1103/physreve.106.054117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Brownian motion subject to a periodic and asymmetric potential can be biased by external, nonequilibrium fluctuations, leading to directional movement of Brownian particles. Sequence-dependent flexibility variation along double-stranded DNA has been proposed as a tool to develop periodic and asymmetric potentials for DNA binding of cationic nanoparticles with sizes below tens of nanometers. Here, we propose that repetitive stretching and relaxation of a long, double-stranded DNA molecule with periodic flexibility gradient can induce nonequilibrium fluctuations that tune the amplitude of asymmetric potentials for DNA-nanoparticle binding to result in directional transport of nanometer-sized particles along DNA. Realization of the proposed Brownian ratchet was proven by Brownian dynamics simulations of coarse-grained models of a single, long DNA molecule with flexibility variation and a cationic nanoparticle.
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Affiliation(s)
- Inrok Oh
- LG Chem Ltd, LG Science Park, Seoul 07796, Republic of Korea
| | - Jeongeun Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye Ree Hyun
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang Hak Lee
- Department of Chemistry, Pusan National University, Busan 46241, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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28
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Crowding and confinement act in concert to slow DNA diffusion within cell-sized droplets. iScience 2022; 25:105122. [PMID: 36185357 PMCID: PMC9523355 DOI: 10.1016/j.isci.2022.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/27/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Dynamics of biological macromolecules, such as DNA, in crowded and confined environments are critical to understanding cellular processes such as transcription, infection, and replication. However, the combined effects of cellular confinement and crowding on macromolecular dynamics remain poorly understood. Here, we use differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. We show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion with scaling that is insensitive to the degree of confinement and crowding. However, effective DNA diffusion coefficients Deff decrease up to 2 orders of magnitude as droplet size decreases—an effect that is enhanced by increased crowding. We mathematically model the coupling of crowding and confinement by combining polymer scaling theories with confinement-induced depletion effects. The generality and tunability of our system and models render them applicable to elucidating wide-ranging crowded and confined systems. DNA diffusion measured in cell-sized droplets with differential dynamic microscopy Combination of crowding and confinement leads to subdiffusion and slowing Diffusion coefficients of DNA decrease strongly with decreasing droplet size Polymer scaling theories and depletion effects predict observed dynamics
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29
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Shah KG, Kumar S, Yager P. Near-digital amplification in paper improves sensitivity and speed in biplexed reactions. Sci Rep 2022; 12:14618. [PMID: 36028745 PMCID: PMC9418329 DOI: 10.1038/s41598-022-18937-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
The simplest point-of-care assays are usually paper and plastic devices that detect proteins or nucleic acids at low cost and minimal user steps, albeit with poor limits of detection. Digital assays improve limits of detection and analyte quantification by splitting a sample across many wells (or droplets), preventing diffusion, and performing analyte amplification and detection in multiple small wells. However, truly digital nucleic acid amplification tests (NAATs) require costly consumable cartridges that are precisely manufactured, aligned, and operated to enable low detection limits. In this study, we demonstrate how to implement near-digital NAATs in low-cost porous media while approaching the low limits of detection of digital assays. The near-digital NAAT was enabled by a paper membrane containing lyophilized amplification reagents that automatically, passively meters and distributes a sample over a wide area. Performing a NAAT in the paper membrane while allowing diffusion captures many of the benefits of digital NAATs if the pad is imaged at a high spatial resolution during amplification. We show that the near-digital NAAT is compatible with a low-cost paper and plastic disposable cartridge coupled to a 2-layer rigid printed circuit board heater (the MD NAAT platform). We also demonstrate compatibility with biplexing and imaging with mobile phones with different camera sensors. We show that the near-digital NAAT increased signal-to-noise ratios by ~ 10×, improved limits of detection from above 103 copies of methicillin-resistant Staphylococcus aureus genomic DNA to between 100 and 316 copies in a biplexed reaction containing 105 copies of co-amplifying internal amplification control DNA, and reduced time-to-result from 45 min of amplification to 15-20 min for the positive samples.
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Affiliation(s)
- Kamal G Shah
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sujatha Kumar
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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30
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Angert I, Karuka SR, Mansky LM, Mueller JD. Partitioning of ribonucleoprotein complexes from the cellular actin cortex. SCIENCE ADVANCES 2022; 8:eabj3236. [PMID: 35984883 PMCID: PMC9390997 DOI: 10.1126/sciadv.abj3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The cell cortex plays a crucial role in cell mechanics, signaling, and development. However, little is known about the influence of the cortical meshwork on the spatial distribution of cytoplasmic biomolecules. Here, we describe a fluorescence microscopy method with the capacity to infer the intracellular distribution of labeled biomolecules with subresolution accuracy. Unexpectedly, we find that RNA binding proteins are partially excluded from the cytoplasmic volume adjacent to the plasma membrane that corresponds to the actin cortex. Complementary diffusion measurements of RNA-protein complexes suggest that a rudimentary model based on excluded volume interactions can explain this partitioning effect. Our results suggest the actin cortex meshwork may play a role in regulating the biomolecular content of the volume immediately adjacent to the plasma membrane.
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Affiliation(s)
- Isaac Angert
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Siddarth Reddy Karuka
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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31
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Shin D, Choi J, Lee JH, Bang D. Onepot-Seq: capturing single-cell transcriptomes simultaneously in a continuous medium via transient localization of mRNA. Nucleic Acids Res 2022; 50:12621-12635. [PMID: 35953080 PMCID: PMC9825186 DOI: 10.1093/nar/gkac665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 05/27/2022] [Accepted: 07/25/2022] [Indexed: 01/29/2023] Open
Abstract
The development of single-cell RNA-seq has broadened the spectrum for biological research by providing a high-resolution analysis of cellular heterogeneity. However, the requirement for sophisticated devices for the compartmentalization of cells has limited its widespread applicability. Here, we develop Onepot-Seq, a device-free method, that harnesses the transient localization of mRNA after lysis to capture single-cell transcriptomes simultaneously in a continuous fluid medium. In mixed-species experiments, we obtained high-quality single-cell profiles. Further, cell type-specific poly(A)-conjugated antibodies allow Onepot-Seq to effectively capture target cells in complex populations. Chemical perturbations to cells can be profiled by Onepot-Seq at single-cell resolution. Onepot-Seq should allow routine transcriptional profiling at single-cell resolution, accelerating clinical and scientific discoveries in many fields of science.
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Affiliation(s)
| | | | - Ji Hyun Lee
- Correspondence may also be addressed to Ji Hyun Lee.
| | - Duhee Bang
- To whom correspondence should be addressed.
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32
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Plasmid-mediated gene transfer of Cas9 induces vector-related but not SpCas9-related immune responses in human retinal pigment epithelial cells. Sci Rep 2022; 12:13202. [PMID: 35915300 PMCID: PMC9343442 DOI: 10.1038/s41598-022-17269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) system represents a powerful gene-editing tool and could enable treatment of blinding diseases of the retina. As a peptide of bacterial origin, we investigated the immunogenic potential of Cas9 in models of retinal immunocompetent cells: human microglia (IMhu) and ARPE-19 cells. Transfection with Streptococcus pyogenes-Cas9 expression plasmids (SpCas9 plasmid) induced Cas9 protein expression in both cell lines. However, only ARPE-19 cells, not IMhu cells, responded with pro-inflammatory immune responses as evidenced by the upregulation of IL-8, IL-6, and the cellular activation markers HLA-ABC and CD54 (ICAM). These pro-inflammatory responses were also induced through transfection with equally sized non-coding control plasmids. Moreover, viability rates of ARPE-19 cells were reduced after transfection with both the SpCas9 plasmids and the control plasmids. Although these results demonstrate cell type-specific responses to the DNA plasmid vector, they show no evidence of an immunogenic effect due to the presence of Cas9 in models of human retinal pigment epithelial and microglia cells. These findings add another layer of confidence in the immunological safety of potential future Cas9-mediated retinal gene therapies.
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33
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Lee J, Lee S, Lee M, Prakash R, Kim H, Cho G, Lee J. Enhancing Mixing Performance in a Rotating Disk Mixing Chamber: A Quantitative Investigation of the Effect of Euler and Coriolis Forces. MICROMACHINES 2022; 13:mi13081218. [PMID: 36014138 PMCID: PMC9416410 DOI: 10.3390/mi13081218] [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: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023]
Abstract
Lab-on-a-CD (LOCD) is gaining importance as a diagnostic platform due to being low-cost, easy-to-use, and portable. During LOCD usage, mixing and reaction are two processes that play an essential role in biochemical applications such as point-of-care diagnosis. In this paper, we numerically and experimentally investigate the effects of the Coriolis and Euler forces in the mixing chamber during the acceleration and deceleration of a rotating disk. The mixing performance is investigated under various conditions that have not been reported, such as rotational condition, chamber aspect ratio at a constant volume, and obstacle arrangement in the chamber. During disk acceleration and deceleration, the Euler force difference in the radial direction causes rotating flows, while the Coriolis force induces perpendicular vortices. Increasing the maximum rotational velocity improves the maximum rotational displacement, resulting in better mixing performance. A longer rotational period increases the interfacial area between solutions and enhances mixing. Mixing performance also improves when there is a substantial difference between Euler forces at the inner and outer radii. Furthermore, adding obstacles in the angular direction also passively promotes or inhibits mixing by configuration. This quantitative investigation provides valuable information for designing and developing high throughput and multiplexed point-of-care LOCDs.
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Affiliation(s)
- Jihyeong Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (J.L.); (S.L.)
| | - Saebom Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (J.L.); (S.L.)
| | - Minki Lee
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Korea;
| | - Ritesh Prakash
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea;
- Research Engineering Center for R2R Printed Flexible, Sungkyunkwan University, Suwon 16419, Korea
| | - Hyejeong Kim
- School of Mechanical Engineering, Korea University, Seoul 02841, Korea;
| | - Gyoujin Cho
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea;
- Research Engineering Center for R2R Printed Flexible, Sungkyunkwan University, Suwon 16419, Korea
- Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
- Correspondence: (G.C.); (J.L.)
| | - Jinkee Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (J.L.); (S.L.)
- Institute of Quantum Biophysics, Sungkyunkwan University, Suwon 16419, Korea;
- Correspondence: (G.C.); (J.L.)
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34
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Girardin C, Maze D, Gonçalves C, Le Guen YT, Pluchon K, Pichon C, Montier T, Midoux P. Selective attachment of a microtubule interacting peptide to plasmid DNA via a triplex forming oligonucleotide for transfection improvement. Gene Ther 2022; 30:271-277. [PMID: 35794469 DOI: 10.1038/s41434-022-00354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
In nonviral gene therapy approaches, the linkage of signal molecules to plasmid DNA (pDNA) is of interest for guiding its delivery to the nucleus. Here, we report its linkage to a peptide (P79-98) mediating migration on microtubules by using a triplex-forming oligonucleotide (TFO). pDNA of 5 kbp and 21 kbp containing 6 and 36 oligopurine • oligopyrimidine sites (TH), respectively, inserted outside the luciferase gene sequence were used. TFO with a dibenzocyclooctyl (DBCO) group in 3' end comprising some Bridged Nucleic Acid bases was conjugated by click chemistry with the peptide carrying an azide function in the C-terminal end. We found the formation of 6 and 18 triplex with pDNA of 5 kbp and 21 kbp, respectively. A twofold increase of the transfection efficiency was observed in the hind-limbs upon Hydrodynamic Limb Vein (HLV) injection in mice of naked P79-98 -pDNA of 21 kbp. This work paves the way for the selective equipping of pDNA with intracellular targeting molecules while preserving the full expression of the encoded gene.
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Affiliation(s)
- Caroline Girardin
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Delphine Maze
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Cristine Gonçalves
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | | | - Kevin Pluchon
- Univ Brest, INSERM, EFS, UMR 1078, GGB - GTCA Team, F-29200, Brest, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France
| | - Tristan Montier
- Univ Brest, INSERM, EFS, UMR 1078, GGB - GTCA Team, F-29200, Brest, France. .,Service de Génétique Médicale et Biologie de la Reproduction, Centre de référence des maladies rares 'Maladies neuromusculaires', CHRU de Brest, F-29200, Brest, France.
| | - Patrick Midoux
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071, Orléans cedex 02, France.
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35
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Ko W, Porter JJ, Sipple MT, Edwards KM, Lueck JD. Efficient suppression of endogenous CFTR nonsense mutations using anticodon-engineered transfer RNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:685-701. [PMID: 35664697 PMCID: PMC9126842 DOI: 10.1016/j.omtn.2022.04.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Nonsense mutations or premature termination codons (PTCs) comprise ∼11% of all genetic lesions, which result in over 7,000 distinct genetic diseases. Due to their outsized impact on human health, considerable effort has been made to find therapies for nonsense-associated diseases. Suppressor tRNAs have long been identified as a possible therapeutic for nonsense-associated diseases; however, their ability to inhibit nonsense-mediated mRNA decay (NMD) and support significant protein translation from endogenous transcripts has not been determined in mammalian cells. Here, we investigated the ability of anticodon edited (ACE)-tRNAs to suppress cystic fibrosis (CF) causing PTCs in the cystic fibrosis transmembrane regulator (CFTR) gene in gene-edited immortalized human bronchial epithelial (16HBEge) cells. Delivery of ACE-tRNAs to 16HBEge cells harboring three common CF mutations G542XUGA-, R1162XUGA-, and W1282XUGA-CFTR PTCs significantly inhibited NMD and rescued endogenous mRNA expression. Furthermore, delivery of our highly active leucine-encoding ACE-tRNA resulted in rescue of W1282X-CFTR channel function to levels that significantly exceed the necessary CFTR channel function for therapeutic relevance. This study establishes the ACE-tRNA approach as a potential standalone therapeutic for nonsense-associated diseases due to its ability to rescue both mRNA and full-length protein expression from PTC-containing endogenous genes.
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Affiliation(s)
- Wooree Ko
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph J. Porter
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew T. Sipple
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Katherine M. Edwards
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John D. Lueck
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
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36
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Heinemann D, Zabic M, Terakawa M, Boch J. Laser-based molecular delivery and its applications in plant science. PLANT METHODS 2022; 18:82. [PMID: 35690858 PMCID: PMC9188231 DOI: 10.1186/s13007-022-00908-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 05/14/2023]
Abstract
Lasers enable modification of living and non-living matter with submicron precision in a contact-free manner which has raised the interest of researchers for decades. Accordingly, laser technologies have drawn interest across disciplines. They have been established as a valuable tool to permeabilize cellular membranes for molecular delivery in a process termed photoinjection. Laser-based molecular delivery was first reported in 1984, when normal kidney cells were successfully transfected with a frequency-multiplied Nd:YAG laser. Due to the rapid development of optical technologies, far more sophisticated laser platforms have become available. In particular, near infrared femtosecond (NIR fs) laser sources enable an increasing progress of laser-based molecular delivery procedures and opened up multiple variations and applications of this technique.This review is intended to provide a plant science audience with the physical principles as well as the application potentials of laser-based molecular delivery. The historical origins and technical development of laser-based molecular delivery are summarized and the principle physical processes involved in these approaches and their implications for practical use are introduced. Successful cases of laser-based molecular delivery in plant science will be reviewed in detail, and the specific hurdles that plant materials pose will be discussed. Finally, we will give an outlook on current limitations and possible future applications of laser-based molecular delivery in the field of plant science.
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Affiliation(s)
- Dag Heinemann
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany.
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167, Hannover, Germany.
| | - Miroslav Zabic
- Hannover Centre for Optical Technologies, Leibniz University Hannover, Nienburger Str. 17, 30167, Hannover, Germany
- Institute of Horticultural Production Systems, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Mitsuhiro Terakawa
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Jens Boch
- Institute of Plant Genetics, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Karoui H, Patwal PS, Pavan Kumar BVVS, Martin N. Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges. Front Mol Biosci 2022; 9:880525. [PMID: 35720123 PMCID: PMC9199989 DOI: 10.3389/fmolb.2022.880525] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.
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Affiliation(s)
- Hedi Karoui
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
| | - Pankaj Singh Patwal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
| | | | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
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Sachdev S, Potočnik T, Rems L, Miklavčič D. Revisiting the role of pulsed electric fields in overcoming the barriers to in vivo gene electrotransfer. Bioelectrochemistry 2022; 144:107994. [PMID: 34930678 DOI: 10.1016/j.bioelechem.2021.107994] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 12/21/2022]
Abstract
Gene therapies are revolutionizing medicine by providing a way to cure hitherto incurable diseases. The scientific and technological advances have enabled the first gene therapies to become clinically approved. In addition, with the ongoing COVID-19 pandemic, we are witnessing record speeds in the development and distribution of gene-based vaccines. For gene therapy to take effect, the therapeutic nucleic acids (RNA or DNA) need to overcome several barriers before they can execute their function of producing a protein or silencing a defective or overexpressing gene. This includes the barriers of the interstitium, the cell membrane, the cytoplasmic barriers and (in case of DNA) the nuclear envelope. Gene electrotransfer (GET), i.e., transfection by means of pulsed electric fields, is a non-viral technique that can overcome these barriers in a safe and effective manner. GET has reached the clinical stage of investigations where it is currently being evaluated for its therapeutic benefits across a wide variety of indications. In this review, we formalize our current understanding of GET from a biophysical perspective and critically discuss the mechanisms by which electric field can aid in overcoming the barriers. We also identify the gaps in knowledge that are hindering optimization of GET in vivo.
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Affiliation(s)
- Shaurya Sachdev
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Tjaša Potočnik
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Lea Rems
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Damijan Miklavčič
- University of Ljubljana, Faculty of Electrical Engineering, Tržaška cesta 25, 1000 Ljubljana, Slovenia.
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Eitzmann DR, Varona M, Anderson JL. Thin Film Microextraction Enables Rapid Isolation and Recovery of DNA for Downstream Amplification Assays. Anal Chem 2022; 94:3677-3684. [DOI: 10.1021/acs.analchem.1c05380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Derek R. Eitzmann
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
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Kejnovsky E, Jedlicka P. Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components? Bioessays 2022; 44:e2100242. [PMID: 35112737 DOI: 10.1002/bies.202100242] [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: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/07/2022]
Abstract
There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.
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Affiliation(s)
- Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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41
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Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
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Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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42
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Zhang CH, Cai K, Zhang PG, Wu Z, Ma M, Chen B. pH-Responsive DNA nanoassembly for detection and combined therapy of tumor. Biosens Bioelectron 2022; 195:113654. [PMID: 34592499 DOI: 10.1016/j.bios.2021.113654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/08/2021] [Accepted: 09/18/2021] [Indexed: 11/02/2022]
Abstract
We have developed a novel cancer theragnostic nanoassembly with high biocompatibility, stability and low toxicity which are activated rapidly by tumor microenvironment to realize selective fluorescence imaging, chemotherapy as well as chemoenzymatic therapy. The nanoprobes are synthesized by hybridization of fluorophore labeled hairpin DNAs containing a 5-aza-dC at hemimethylated CpG sites and pH-sensitive DNA sequence covalently conjugated with PEGylated GO. The aptamer, which is also covalently conjugated on PEGylated GO, enables to target the tumor site and the weak acid environment of tumor triggers the release of drug loaded by nanoprobes including functionalized DNA and DOXs, effectively activating fluorescence signals and selectively killing the tumor cells. The results revealed that the nanoprobe enables sensitive detection of pH changes within subcellular environment, selectively imaging and great synergy of multicombination therapeutic including chemotherapy and chemoenzymatic therapy, implying that developed pH activatable probe has considerable potential for diagnosis and efficient therapy of cancer.
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Affiliation(s)
- Chong-Hua Zhang
- Institute of Chemical Biology & Nanomedicine, State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ke Cai
- Key Laboratory of Phytochemical R&D of Hunan Province, And Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, 410081, China
| | - Peng-Ge Zhang
- Institute of Chemical Biology & Nanomedicine, State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Zhan Wu
- Key Laboratory of Phytochemical R&D of Hunan Province, And Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, 410081, China.
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, And Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, 410081, China.
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province, And Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, 410081, China
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Marschall ALJ. Targeting the Inside of Cells with Biologicals: Chemicals as a Delivery Strategy. BioDrugs 2021; 35:643-671. [PMID: 34705260 PMCID: PMC8548996 DOI: 10.1007/s40259-021-00500-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
Delivering macromolecules into the cytosol or nucleus is possible in vitro for DNA, RNA and proteins, but translation for clinical use has been limited. Therapeutic delivery of macromolecules into cells requires overcoming substantially higher barriers compared to the use of small molecule drugs or proteins in the extracellular space. Breakthroughs like DNA delivery for approved gene therapies and RNA delivery for silencing of genes (patisiran, ONPATTRO®, Alnylam Pharmaceuticals, Cambridge, MA, USA) or for vaccination such as the RNA-based coronavirus disease 2019 (COVID-19) vaccines demonstrated the feasibility of using macromolecules inside cells for therapy. Chemical carriers are part of the reason why these novel RNA-based therapeutics possess sufficient efficacy for their clinical application. A clear advantage of synthetic chemicals as carriers for macromolecule delivery is their favourable properties with respect to production and storage compared to more bioinspired vehicles like viral vectors or more complex drugs like cellular therapies. If biologicals can be applied to intracellular targets, the druggable space is substantially broadened by circumventing the limited utility of small molecules for blocking protein–protein interactions and the limitation of protein-based drugs to the extracellular space. An in depth understanding of the macromolecular cargo types, carrier types and the cell biology of delivery is crucial for optimal application and further development of biologicals inside cells. Basic mechanistic principles of the molecular and cell biological aspects of cytosolic/nuclear delivery of macromolecules, with particular consideration of protein delivery, are reviewed here. The efficiency of macromolecule delivery and applications in research and therapy are highlighted.
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Affiliation(s)
- Andrea L J Marschall
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Brunswick, Germany.
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44
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Monnery BD. Polycation-Mediated Transfection: Mechanisms of Internalization and Intracellular Trafficking. Biomacromolecules 2021; 22:4060-4083. [PMID: 34498457 DOI: 10.1021/acs.biomac.1c00697] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Polyplex-mediated gene transfection is now in its' fourth decade of serious research, but the promise of polyplex-mediated gene therapy has yet to fully materialize. Only approximately one in a million applied plasmids actually expresses. A large part of this is due to an incomplete understanding of the mechanism of polyplex transfection. There is an assumption that internalization must follow a canonical mechanism of receptor mediated endocytosis. Herein, we present arguments that untargeted (and most targeted) polyplexes do not utilize these routes. By incorporating knowledge of syndecan-polyplex interactions, we can show that syndecans are the "target" for polyplexes. Further, it is known that free polycations (which disrupt cell-membranes by acid-catalyzed hydrolysis of phospholipid esters) are necessary for (untargeted) endocytosis. This can be incorporated into the model to produce a novel mechanism of endocytosis, which fits the observed phenomenology. After membrane translocation, polyplex containing vesicles reach the endosome after diffusing through the actin mesh below the cell membrane. From there, they are acidified and trafficked toward the lysosome. Some polyplexes are capable of escaping the endosome and unpacking, while others are not. Herein, it is argued that for some polycations, as acidification proceeds the polyplexes excluding free polycations, which disrupt the endosomal membrane by acid-catalyzed hydrolysis, allowing the polyplex to escape. The polyplex's internal charge ratio is now insufficient for stability and it releases plasmids which diffuse to the nucleus. A small proportion of these plasmids diffuse through the nuclear pore complex (NPC), with aggregation being the major cause of loss. Those plasmids that have diffused through the NPC will also aggregate, and this appears to be the reason such a small proportion of nuclear plasmids express mRNA. Thus, the structural features which promote unpacking in the endosome and allow for endosomal escape can be determined, and better polycations can be designed.
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Affiliation(s)
- Bryn D Monnery
- Department of Organic and (Bio)Polymer Chemistry, Hasselt University, Building F, Agoralaan 1, B-3590 Diepenbeek, Belgium
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45
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Mangion M, Robert MA, Slivac I, Gilbert R, Gaillet B. Production and Use of Gesicles for Nucleic Acid Delivery. Mol Biotechnol 2021; 64:278-292. [PMID: 34596870 DOI: 10.1007/s12033-021-00389-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 09/08/2021] [Indexed: 12/29/2022]
Abstract
Over-expression of the vesicular stomatitis virus glycoprotein (VSVG) in mammalian cells can induce the formation of VSVG-pseudotyped vesicles (named "gesicles") from membrane budding. Its use as a nucleic acid delivery tool is still poorly documented. Naked-plasmid DNA can be delivered in animal cells with gesicles in presence of hexadimethrine bromide (polybrene). However, little is known about gesicle manufacturing process and conditions to obtain successful nucleic acid delivery. In this study, gesicles production process using polyethylenimine (PEI)-transfected HEK293 cells was developed by defining the VSVG-plasmid concentration, the DNA:PEI mass ratio, and the time of gesicle harvest. Furthermore, parameters described in the literature relevant for nucleic acid delivery such as (i) component concentrations in assembly mixture, (ii) component addition order, (iii) incubation time, and (iv) polybrene concentration were tested by assessing the transfection capacity of the gesicles complexed with a green fluorescent protein (GFP)-coding plasmid. Interestingly, freezing/thawing cycles and storage at + 4 °C, - 20 °C, and - 80 °C did not reduce gesicles' ability to transfer plasmid DNA. Transfection efficiency of 55% and 22% was obtained for HeLa cells and for hard-to-transfect cells such as human myoblasts, respectively. For the first time, gesicles were used for delivery of a large plasmid (18-kb) with 42% of efficiency and for enhanced green fluorescent protein (eGFP) gene silencing with siRNA (up to 60%). In conclusion, gesicles represent attractive bioreagents with great potential to deliver nucleic acids in mammalian cells.
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Affiliation(s)
- Mathias Mangion
- Chemical Engineering Department, Laval University, Pouliot Building, 1065 Avenue de la Médecine, Québec, QC, G1V0A6, Canada.,PROTEO: The Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Vachon Building, local 3403, 1045 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.,ThéCell: FRQS Cell and Tissue Therapy Network, LOEX, Aile R, local R-125, Hôpital de l'Enfant-Jésus, 1401 18e rue, Québec, QC, G1J 1Z4, Canada
| | - Marc-André Robert
- Chemical Engineering Department, Laval University, Pouliot Building, 1065 Avenue de la Médecine, Québec, QC, G1V0A6, Canada.,PROTEO: The Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Vachon Building, local 3403, 1045 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.,ThéCell: FRQS Cell and Tissue Therapy Network, LOEX, Aile R, local R-125, Hôpital de l'Enfant-Jésus, 1401 18e rue, Québec, QC, G1J 1Z4, Canada.,Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Avenue Royalmount, Montréal, QC, H4P 2R2, Canada
| | - Igor Slivac
- Chemical Engineering Department, Laval University, Pouliot Building, 1065 Avenue de la Médecine, Québec, QC, G1V0A6, Canada.,PROTEO: The Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Vachon Building, local 3403, 1045 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada.,ThéCell: FRQS Cell and Tissue Therapy Network, LOEX, Aile R, local R-125, Hôpital de l'Enfant-Jésus, 1401 18e rue, Québec, QC, G1J 1Z4, Canada
| | - Rénald Gilbert
- ThéCell: FRQS Cell and Tissue Therapy Network, LOEX, Aile R, local R-125, Hôpital de l'Enfant-Jésus, 1401 18e rue, Québec, QC, G1J 1Z4, Canada.,Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Avenue Royalmount, Montréal, QC, H4P 2R2, Canada
| | - Bruno Gaillet
- Chemical Engineering Department, Laval University, Pouliot Building, 1065 Avenue de la Médecine, Québec, QC, G1V0A6, Canada. .,PROTEO: The Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Vachon Building, local 3403, 1045 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada. .,ThéCell: FRQS Cell and Tissue Therapy Network, LOEX, Aile R, local R-125, Hôpital de l'Enfant-Jésus, 1401 18e rue, Québec, QC, G1J 1Z4, Canada.
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Sparrenberg LT, Greiner B, Mathis HP. The Mean Single Molecule Rate (mSMR) in the Analysis of Fluorescence Fluctuations: Measurements on DNA Mixtures of Defined Composition. J Fluoresc 2021; 31:1883-1894. [PMID: 34529200 PMCID: PMC8547212 DOI: 10.1007/s10895-021-02803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022]
Abstract
We present a method for the evaluation of fluorescence fluctuations on the basis of Mandel’s Q parameter, using sampling time-dependent factorial cumulants. By relating the Q parameter to the sampling time, we obtain the mean single molecule rate (mSMR), an easy to interpret expression that provides both brightness and diffusion information. The model is suitable for the widely used confocal setups with single photon excitation and a single detection channel. We present a way to correct the mSMR for afterpulsing, dead time and background noise. To account for photokinetic effects at short sampling times, we expand the model by a simple on/off isomerization term, which is similar to the well-known triplet model. The functionality of the mSMR is shown using Monte Carlo simulations. The correction mechanisms and the experimental applicability of the model are then demonstrated by DNA measurements of defined composition. By systematically analyzing DNA mixtures, we can show that at large sampling times, the mSMR correctly describes the single molecule brightness rates and the diffusive properties of DNA molecules. At short sampling times, the photokinetic effects of isomerization are accurately described by the mSMR model. Since additionally the mSMR can easily be corrected for measurement artefacts such as detector dead time, afterpulsing and background noise, this is a valuable advantage over the standard method of fluorescence correlation spectroscopy.
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Affiliation(s)
- Lorenz T Sparrenberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany. .,Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany.
| | - Benjamin Greiner
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
| | - Harald P Mathis
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
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Mukherjee A, de Izarra A, Degrouard J, Olive E, Maiti PK, Jang YH, Lansac Y. Protamine-Controlled Reversible DNA Packaging: A Molecular Glue. ACS NANO 2021; 15:13094-13104. [PMID: 34328301 DOI: 10.1021/acsnano.1c02337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 106-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.
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Affiliation(s)
- Arnab Mukherjee
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Ambroise de Izarra
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Jeril Degrouard
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay, 91405 Orsay, France
| | - Enrick Olive
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Yves Lansac
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay, 91405 Orsay, France
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Mostafa A, Ganguli A, Berger J, Rayabharam A, Saavedra C, Aluru NR, Bashir R. Culture-free biphasic approach for sensitive detection of Escherichia coli O157:H7 from beef samples. Biotechnol Bioeng 2021; 118:4516-4529. [PMID: 34415570 DOI: 10.1002/bit.27920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022]
Abstract
Foodborne illnesses are a major threat to public health also leading to significant mortality and financial and reputational damage to industry. It is very important to detect pathogen presence in food products early, rapidly, and accurately to avoid potential outbreaks and economic loss. However, "gold standard" culture methods, including enrichment of pathogens, can take up to several days. Moreover, the food matrix often interferes with nucleic acid amplification methods of detection, requiring DNA extraction from the sample for successful molecular detection of pathogens. Here, we introduce a "biphasic" amplification method that can achieve high sensitivity detection with background noise from ground beef food samples without culture or other extraction methods in 2.5 h. Homogenized ground beef is dried resulting in an increase in porosity of the dried food matrix to allowing amplification enzymes and primers to access the target DNA and initiate the reaction within the dried food matrix. Using Loop Mediated Isothermal Amplification, we demonstrate the detection of 1-3 cfu of Escherichia coli bacteria in 30 mg of dried food matrix. Our approach significantly lowers the time to result to less than a few hours and have a pronounced impact on reduction of instrumentation complexity and costs.
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Affiliation(s)
- Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Archith Rayabharam
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Carlos Saavedra
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Narayana R Aluru
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Carle Illinois College of Medicine, Urbana, Illinois, USA
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Mezei A, Pons R. MWNTs or PEG as Stability Enhancers for DNA-Cationic Surfactant Gel Particles. Int J Mol Sci 2021; 22:ijms22168801. [PMID: 34445500 PMCID: PMC8395904 DOI: 10.3390/ijms22168801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/25/2022] Open
Abstract
Cationic surfactants interact with DNA (Deoxyribonucleic acid), forming surfactant-DNA complexes that offer particularly efficient control for encapsulation and release of DNA from DNA gel particles. In the present work, DNA-based particles were prepared using CTAB (Cetyltrimethylammonium bromide) as the cationic surfactant and modified using two different additives: (Multi-Walled Carbon Nanotubes) MWNT or PEG (Poly Ethylene Glycol). The use of both additives to form composites increased the stability of the gel particles. The stability was monitored by the release of DNA and CTAB in different pH solutions. However, not much is known about the influence of pH on DNA–surfactant interaction and the release of DNA and surfactant from gel particles. It was observed that the solubilization of DNA occurs only in very acid media, while that of CTAB does not depend on pH and gets to a plateau after about 8 h. Within 2 h in contact with a pH = 2 solution, about 1% DNA and CTAB was released. Complete destruction for the gel particles was observed in pH = 2 solution after 17 days for PEG and 20 days for MWNT. The composite particles show a considerably enlarged sustained release span compared to the unmodified ones. The dehydration-rehydration studies show that the structure of the composite gel particles, as determined from SAXS (Small-Angle-X-Ray-Scattering) experiments, is similar to that of the unmodified ones. These studies will allow a better knowledge of these particles’ formation and evolution in view of possible applications in drug delivery and release.
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50
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Sharma D, Arora S, Singh J, Layek B. A review of the tortuous path of nonviral gene delivery and recent progress. Int J Biol Macromol 2021; 183:2055-2073. [PMID: 34087309 PMCID: PMC8266766 DOI: 10.1016/j.ijbiomac.2021.05.192] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Gene therapy encompasses the transfer of exogenous genetic materials into the patient's target cells to treat or prevent diseases. Nevertheless, the transfer of genetic material into desired cells is challenging and often requires specialized tools or delivery systems. For the past 40 years, scientists are mainly pursuing various viruses as gene delivery vectors, and the overall progress has been slow and far from the expectation. As an alternative, nonviral vectors have gained substantial attention due to their several advantages, including superior safety profile, enhanced payload capacity, and stealth abilities. Since nonviral vectors encounter multiple extra- and intra-cellular barriers limiting the transfer of genetic payload into the target cell nucleus, we have discussed these barriers in detail for this review. A direct approach, utilizing physical methods like electroporation, sonoporation, gene gun, eliminate the requirement for a specific carrier for gene delivery. In contrast, chemical methods of gene transfer exploit natural or synthetic compounds as carriers to increase cellular targeting and gene therapy effectiveness. We have also emphasized the recent advancements aimed at enhancing the current nonviral approaches. Therefore, in this review, we have focused on discussing the current evolving state of nonviral gene delivery systems and their future perspectives.
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Affiliation(s)
- Divya Sharma
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo 58105, ND, USA
| | - Sanjay Arora
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo 58105, ND, USA
| | - Jagdish Singh
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo 58105, ND, USA
| | - Buddhadev Layek
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo 58105, ND, USA.
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