1
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England CJ, Gray TC, Malla SRL, Oliveira SA, Martin BR, Beall GW, Lewis LK. pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions. Anal Biochem 2021; 616:114099. [PMID: 33388294 PMCID: PMC7849029 DOI: 10.1016/j.ab.2020.114099] [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: 11/13/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 10/22/2022]
Abstract
Precipitation of DNA is performed frequently in molecular biology laboratories for the purpose of purification and concentration of samples and also for transfer of DNA into cells. Metal ions are used to facilitate these processes, though their precise functions are not well characterized. In the current study we have investigated the precipitation of double-stranded DNA by group 1 and group 2 metal ions. Double-stranded DNAs were not sedimented efficiently by metals alone, even at high concentrations. Increasing the pH to 11 or higher caused strong DNA precipitation in the presence of the divalent group 2 metals magnesium, calcium, strontium and barium, but not group 1 metals. Group 2 sedimentation profiles were distinctly different from that of the transition metal zinc, which caused precipitation at pH 8. Analysis of DNAs recovered from precipitates formed with calcium revealed that structural integrity was retained and that sedimentation efficiency was largely size-independent above 400 bp. Several tests supported a model whereby single-stranded DNA regions formed by denaturation at high pH became bound by the divalent metal cations. Neutralization of negative surface charges reduced the repulsive forces between molecules, leading to formation of insoluble aggregates that could be further stabilized by cation bridging (ionic crosslinking).
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Affiliation(s)
- Corbin J England
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Tanner C Gray
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Shubha R L Malla
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - Samantha A Oliveira
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Benjamin R Martin
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - Gary W Beall
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA.
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2
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Kumar MMA, Biju VMN. A Quick Responsive Chitosan‐Oxine Based Thin Film to Recognize and Remove Zn
2+
Ions from Potable Water. ChemistrySelect 2020. [DOI: 10.1002/slct.202002302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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3
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Nayak AK, Rath SK, Subudhi U. Preparation of Stable Branched DNA Nanostructures: Process of Cooperative Self-Assembly. J Phys Chem B 2019; 123:3591-3597. [DOI: 10.1021/acs.jpcb.9b00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashok Kumar Nayak
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Sakti Kanta Rath
- Department of Biotechnology, Ravenshaw University, Cuttack 753 003, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751 013, India
- Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India
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4
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Saxena S, Joshi S, Shankaraswamy J, Tyagi S, Kukreti S. Magnesium and molecular crowding of the cosolutes stabilize the i-motif structure at physiological pH. Biopolymers 2018; 107. [PMID: 28295161 DOI: 10.1002/bip.23018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 11/09/2022]
Abstract
Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In this study, we used three C-rich oligonucleotides (11Py, 21Py, and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis. The CD spectra revealed that 11Py and 21Py form i-motif structures at acidic pH values of 4.5 and 5.7 in the presence of 100 mM NaCl but remain unstructured at pH 7.0. However, 21Py can form stable i-motif structure even at neutral pH in presence of 1 mM MgCl2 . UV-thermal melting studies showed stabilization of 21Py i-motif at pH 5.7 in the presence of Na+ or K+ with increasing concentration of MgCl2 or CaCl2 from 1 to 10 mM. Significant shift in the CD peak of HTPy sequence was observed as the positive peak from 286 nm shifted to 276 nm while the negative peak from 265 to 254 nm. Further, inevitable necessity of 1 mM Mg2+ to form i-motif structure at neutral pH was observed. Under similar ionic conditions and neutral pH, all the three C-rich sequences were able to form stable i-motif structures (11Py, 21Py) or altered i-motif/homoduplex structures (HTPy) in the presence of MgCl2 and cell mimicking molecular crowding conditions of 40 wt% PEG 200. It is concluded that presence of Mg2+ ions and molecular crowding agents induce and stabilize i-motif structures at physiological solution environment.
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Affiliation(s)
- Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Savita Joshi
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
| | - J Shankaraswamy
- Amity International Centre for Post Harvest Technology and Cold Chain Management, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shikhar Tyagi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Shrikant Kukreti
- Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India
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5
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Asayama S, Matsuda K, Negishi Y, Kawakami H. Intracellular co-delivery of zinc ions and plasmid DNA for enhancing gene transfection activity. Metallomics 2014; 6:82-7. [PMID: 24084762 DOI: 10.1039/c3mt00226h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Zinc ions, methylated poly(1-vinylimidazole) (PVIm-Me) and plasmid DNA (pDNA) have formed ternary complexes for gene delivery. The resulting Zn-PVIm-Me-pDNA complexes have delivered both Zn(2+) ions and pDNA inside cells, leading to the nuclear translocation of the pDNA. By use of the pDNA containing a nuclear protein, NF-κB, binding sequence, the intracellular co-delivery of Zn(2+) ions and pDNA has enhanced gene expression. These results suggest that the intracellular Zn(2+) ions delivered by Zn-PVIm-Me-pDNA complexes activated the NF-κB, enhancing the nuclear translocation of the pDNA. In conclusion, it has been demonstrated that the Zn-PVIm-Me-pDNA complex is capable of enhancing the gene transfection activity by a synergic effect of the PVIm-Me and the co-delivered intracellular Zn(2+) ions.
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Affiliation(s)
- Shoichiro Asayama
- Department of Applied Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
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6
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Lu S. Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner. Sci Rep 2014; 4:5464. [PMID: 24965053 PMCID: PMC4071324 DOI: 10.1038/srep05464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022] Open
Abstract
Zinc is the second most abundant trace element essential for all living organisms. In human body, 30–40% of the total zinc ion (Zn2+) is localized in the nucleus. Intranuclear free Zn2+ sparks caused by reactive oxygen species have been observed in eukaryotic cells, but question if these free Zn2+ outrages could have affected annealing of complementary single-stranded (ss) DNA, a crucial step in DNA synthesis, repair and recombination, has never been raised. Here the author reports that Zn2+ blocks annealing of complementary ssDNA in a sequence-selective manner under near-physiological conditions as demonstrated in vitro using a low-temperature EDTA-free agarose gel electrophoresis (LTEAGE) procedure. Specifically, it is shown that Zn2+ does not block annealing of repetitive DNA sequences lacking CG/GC sites that are the major components of junk DNA. It is also demonstrated that Zn2+ blocks end-joining of double-stranded (ds) DNA fragments with 3′ overhangs mimicking double-strand breaks, and prevents renaturation of long stretches (>1 kb) of denatured dsDNA, in which Zn2+-tolerant intronic DNA provides annealing protection on otherwise Zn2+-sensitive coding DNA. These findings raise a challenging hypothesis that Zn2+-ssDNA interaction might be among natural forces driving eukaryotic genomes to maintain the Zn2+-tolerant repetitive DNA for adapting to the Zn2+-rich nucleus.
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Affiliation(s)
- Shunwen Lu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND 58102, USA
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7
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Divalent Metal Cations in DNA–Phospholipid Binding. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-12-418698-9.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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8
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Uhríková D, Kučerka N, Lengyel A, Pullmannová P, Teixeira J, Murugova T, Funari SS, Balgavý P. Lipid bilayer – DNA interaction mediated by divalent metal cations: SANS and SAXD study. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/351/1/012011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Giatrellis S, Nounesis G. Nucleic acid-lipid membrane interactions studied by DSC. JOURNAL OF PHARMACY AND BIOALLIED SCIENCES 2011; 3:70-6. [PMID: 21430956 PMCID: PMC3053523 DOI: 10.4103/0975-7406.76470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 11/04/2022] Open
Abstract
The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely dependent upon the formation mechanisms, the morphology, and the molecular organization of the lipoplexes, that is, the complexes of lipid membranes with DNA. Differential scanning calorimetry (DSC) has emerged as an efficient and relatively easy-to-operate experimental technique that can straightforwardly provide data related to the thermodynamics and the kinetics of the DNA-lipid complexation and especially to the lipid organization and phase transitions within the membrane. In this review, we summarize DSC studies considering nucleic acid-membrane systems, accentuating DSC capabilities, and data analysis. Published work involving cationic, anionic, and zwitterionic lipids as well as lipid mixtures interacting with RNA and DNA of different sizes and conformations are included. It is shown that despite limitations, issues such as DNA- or RNA-induced phase separation and microdomain lipid segregation, liposomal aggregation and fusion, alterations of the lipid long-range molecular order, as well as membrane-induced structural changes of the nucleic acids can be efficiently treated by systematic high-sensitivity DSC studies.
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Affiliation(s)
- Sarantis Giatrellis
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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10
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Stoll KE, Draper WE, Kliegman JI, Golynskiy MV, Brew-Appiah RAT, Phillips RK, Brown HK, Breyer WA, Jakubovics NS, Jenkinson HF, Brennan RG, Cohen SM, Glasfeld A. Characterization and structure of the manganese-responsive transcriptional regulator ScaR. Biochemistry 2009; 48:10308-20. [PMID: 19795834 PMCID: PMC3586275 DOI: 10.1021/bi900980g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The streptococcal coaggregation regulator (ScaR) of Streptococcus gordonii is a manganese-dependent transcriptional regulator. When intracellular manganese concentrations become elevated, ScaR represses transcription of the scaCBA operon, which encodes a manganese uptake transporter. A member of the DtxR/MntR family of metalloregulators, ScaR shares sequence similarity with other family members, and many metal-binding residues are conserved. Here, we show that ScaR is an active dimer, with two dimers binding the 46 base pair scaC operator. Each ScaR subunit binds two manganese ions, and the protein is activated by a variety of other metal ions, including Cd(2+), Co(2+), and Ni(2+) but not Zn(2+). The crystal structure of apo-ScaR reveals a tertiary and quaternary structure similar to its homologue, the iron-responsive regulator DtxR. While each DtxR subunit binds a metal ion in two sites, labeled primary and ancillary, crystal structures of ScaR determined in the presence of Cd(2+) and Zn(2+) show only a single occupied metal-binding site that is novel to ScaR. The site analogous to the primary site in DtxR is unoccupied, and the ancillary site is absent from ScaR. Instead, metal ions bind to ScaR at a site labeled "secondary", which is composed of Glu80, Cys123, His125, and Asp160 and lies roughly 5 A away from where the ancillary site would be predicted to exist. This difference suggests that ScaR and its closely related homologues are activated by a mechanism distinct from that of either DtxR or MntR.
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Affiliation(s)
- Kate E. Stoll
- Department of Chemistry, Reed College, Portland, Oregon 97202
| | | | - Joseph I. Kliegman
- Department of Chemistry, Reed College, Portland, Oregon 97202
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0358
| | - Misha V. Golynskiy
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0358
| | | | - Rebecca K. Phillips
- Department of Chemistry, Reed College, Portland, Oregon 97202
- Department of Biochemistry and Molecular Biology, U. T. M. D. Anderson Cancer Center, Unit 1000 Houston, TX 77030
| | - Hattie K. Brown
- Department of Chemistry, Reed College, Portland, Oregon 97202
| | - Wendy A. Breyer
- Department of Chemistry, Reed College, Portland, Oregon 97202
| | | | - Howard F. Jenkinson
- Department of Oral and Dental Science, University of Bristol, Bristol BS1 2LY, UK
| | - Richard G. Brennan
- Department of Biochemistry and Molecular Biology, U. T. M. D. Anderson Cancer Center, Unit 1000 Houston, TX 77030
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0358
| | - Arthur Glasfeld
- Department of Chemistry, Reed College, Portland, Oregon 97202
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11
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Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M. Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) in a water-in-oil microemulsion. Chirality 2008; 20:951-60. [PMID: 18246552 DOI: 10.1002/chir.20531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The thermal behavior of the synthetic, high molecular weight, double stranded polynucleotides poly(dA-dT).poly(dA-dT) [polyAT] and poly(dG-dC).poly(dG-dC) [polyGC] solubilized in the aqueous core of the quaternary water-in-oil cationic microemulsion CTAB|n-pentanol|n-hexane|water in the presence of increasing amounts of NiCl(2) at several constant ionic strength values (NaCl) has been studied by means of circular dichroism and electronic absorption spectroscopies. In the microemulsive medium, both polynucleotides show temperature-induced modifications that markedly vary with both Ni(II) concentration and ionic strength. An increase of temperature causes denaturation of the polyAT duplex at low nickel concentrations, while more complex CD spectral modifications are observed at higher nickel concentrations and ionic strengths. By contrast, thermal denaturation is never observed for polyGC. At low Ni(II) concentrations, the increase of temperature induces conformational transitions from B-DNA to Z-DNA form, or, more precisely, to left-handed helical structures. In some cases, at higher nickel concentrations, the CD spectra suggest the presence of Z'-type forms of the polynucleotide.
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Affiliation(s)
- Marta Airoldi
- Dipartimento di Chimica Inorganica e Analitica Stanislao Cannizzaro, Università di Palermo, 90128 Palermo, Italy
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12
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Hatton B, Rickard D. Nucleic acids bind to nanoparticulate iron (II) monosulphide in aqueous solutions. ORIGINS LIFE EVOL B 2008; 38:257-70. [PMID: 18409029 DOI: 10.1007/s11084-008-9132-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 02/22/2008] [Indexed: 11/27/2022]
Abstract
In the hydrothermal FeS-world origin of life scenarios nucleic acids are suggested to bind to iron (II) monosulphide precipitated from the reaction between hydrothermal sulphidic vent solutions and iron-bearing oceanic water. In lower temperature systems, the first precipitate from this process is nanoparticulate, metastable FeSm with a mackinawite structure. Although the interactions between bulk crystalline iron sulphide minerals and nucleic acids have been reported, their reaction with nanoparticulate FeSm has not previously been investigated. We investigated the binding of different nucleic acids, and their constituents, to freshly precipitated, nanoparticulate FeSm. The degree to which the organic molecules interacted with FeSm is chromosomal DNA > RNA > oligomeric DNA > deoxadenosine monophosphate approximately deoxyadenosine approximately adenine. Although we found that FeSm does not fluoresce within the visible spectrum and there is no quantum confinement effect seen in the absorption, the mechanism of linkage of the FeSm to these biomolecules appears to be primarily electrostatic and similar to that found for the attachment of ZnS quantum dots. The results of a preliminary study of similar reactions with nanoparticulate CuS further supported the suggestion that the interaction mechanism was generic for nanoparticulate transition metal sulphides. In terms of the FeS-world hypothesis, the results of this study further support the idea that sulphide minerals precipitated at hydrothermal vents interact with biomolecules and could have assisted in the formation and polymerisation of nucleic acids.
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Affiliation(s)
- Bryan Hatton
- School of Earth and Ocean Sciences, Cardiff University, Park Place, Cardiff, CF10 3YE, UK.
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13
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Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M. Interaction of the alternating double stranded copolymer poly(dA-dT) x poly(dA-dT) with NiCl(2) and CdCl(2): solution behavior. J Biomol Struct Dyn 2007; 25:77-84. [PMID: 17676940 DOI: 10.1080/07391102.2007.10507157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The thermal denaturation of the synthetic high molecular weight double stranded polynucleotide poly(dA-dT) x poly(dA-dT) has been studied in aqueous buffered solution (Tris 1.0 mM; pH 7.8+/-0.2) in the presence of increasing concentrations of either Ni(2+) (borderline cation) or Cd(2+) (soft cation) at four different constant ionic strength values (NaCl), making use of UV and circular dichroism (CD) spectroscopies. The experimental results show that the B-type double helix of the polymer is stabilized against thermal denaturation in the presence of both cations at low concentrations, relative to the systems where only NaCl is present, in the same conditions of ionic strength and pH. The effect is more pronounced for Ni(2+) than for Cd(2+). At higher concentrations, both cations start to destabilize the double helix, with Cd cations inducing larger variations of T(m). In many cases, when denaturation starts, interstrand cross-linking occurs with formation of aggregates that precipitate.
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Affiliation(s)
- Marta Airoldi
- Dipartimento di Chimica Inorganica e Analitica "Stanislao Cannizzaro", Universita di Palermo--Viale delle Scienze, Pad.17, 90128 Palermo, Italy
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14
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Seela F, Chittepu P. Oligonucleotides containing 6-aza-2'-deoxyuridine: synthesis, nucleobase protection, pH-dependent duplex stability, and metal-DNA formation. J Org Chem 2007; 72:4358-66. [PMID: 17503846 DOI: 10.1021/jo0702903] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligodeoxyribonucleotides containing the nucleoside 6-aza-2'-deoxyuridine z6Ud (1a) were prepared by using solid-phase synthesis. As the pKa value of this nucleoside is 6.8, unwanted side reactions are observed. Consequently, nitrogen-3 was protected (o-anisoyl protection). The phosphoramidite of 1a prepared on this route was as efficient as the building blocks of canonical nucleosides in allowing multiple incorporations into oligonucleotides. Oligonucleotide duplexes containing 1a show a pH dependence of the Tm value. This is caused by nucleobase deprotonation occurring on compound 1a already under neutral conditions. Metal (M)-DNA formation was studied in the presence of Zn+2 ions. It is demonstrated that 6-azauracil-modified duplexes form M-DNA already in neutral medium while alkaline conditions (above pH 8.5) are required for natural DNA. The conformational analysis of the sugar moiety of the nucleoside 1a and its anisoyl derivative 5a shows a preferred N-conformation in solution while an S-conformation for compound 1a was obtained in the solid state (single-crystal X-ray analysis).
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Affiliation(s)
- Frank Seela
- Laboratory for Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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15
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Lindell J, Girard P, Müller N, Jordan M, Wurm F. Calfection: a novel gene transfer method for suspension cells. ACTA ACUST UNITED AC 2004; 1676:155-61. [PMID: 14746910 DOI: 10.1016/j.bbaexp.2003.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have developed a novel method called Calfection for gene delivery to and protein expression from suspension-cultivated mammalian cells. Plasmid DNA was simply diluted into a calcium chloride solution and then added to the cell culture for transfection. We evaluated and optimized this approach using suspension-adapted HEK293 cells grown in 12-well plates that were shaken on an orbital shaker. Highest expression levels were obtained when cells were transfected at a density of 5x10(5) cells/ml in the presence of 9 mM calcium and 5 microg/ml of plasmid DNA while maintaining a culture pH of 7.6 at the time of transfection. Suspension-adapted BHK 21 and CHO DG 44 cells could also be transfected using this method. Calfection differs from the widely known calcium phosphate coprecipitation technique. The physico-chemical composition of the DNA interacting complexes is not yet known. The transfection cocktail, DNA in a calcium chloride solution, remained highly efficient during long-term storage at temperatures ranging from room temperature to -80 degrees C. In contrast, calcium phosphate-DNA cocktails are only efficient for gene transfer when prepared fresh. Furthermore, passing the calcium-plasmid DNA mixture through a 0.2-microm filter did not compromise protein expression, whereas calcium phosphate-DNA coprecipitates were retained by the filter. High protein expression levels, a limited number of manipulations and the possibility to filter the cocktail make the Calfection approach suitable for both large-scale transfection in bioreactors and for high-throughput transfection experiments in microtiter plates.
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Affiliation(s)
- Jeanette Lindell
- Laboratory of Cellular Biotechnology, Swiss Federal Institute of Technology, Lausanne, CH-1015, Switzerland
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16
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Abstract
A novel method for protection of DNA from high shear induced damage is presented. This method uses simple divalent cations and the lyophilizable alcohol, tert-butanol, to self-assemble DNA into condensed, shear-resistant forms. The DNA used in these studies was a 5600 BP plasmid DNA encoding a therapeutic gene. Various solvents and salts were used to identify optimal conditions to condense plasmid DNA. A stable formulation was identified with plasmid DNA condensed in a cosolvent solution containing 20% (v/v) tert-butanol and 1mM calcium chloride. The DNA was formulated at 100 microg/ml and condensed into rod and toroidal shapes that were approximately 50-300 nm in diameter. The rods were found to be kinetically stable for greater than 24h following their preparation. Condensation of the plasmid DNA in this manner results in nearly 100% of the plasmid DNA remaining intact after 1 min of high shear stress applied by a 50 W probe sonicator. Uncondensed control plasmid DNA is completely fragmented following 30s of identical sonication. It is believed that condensation of DNA in this manner will permit utilization of high shear-stress inducing processing techniques, such as lyophilization or spray-drying without resulting in damage to the DNA.
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Affiliation(s)
- Jefferson D Knight
- Department of Pharmaceutical Research and Development, Pfizer Global Research and Development, Groton Laboratories, MS 8156-26, Groton, CT 06340, USA
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17
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Niedzinski EJ, Olson DC, Chen YJ, Udove JA, Nantz MH, Tseng HC, Bolaffi JL, Bennett MJ. Zinc enhancement of nonviral salivary gland transfection. Mol Ther 2003; 7:396-400. [PMID: 12668135 DOI: 10.1016/s1525-0016(02)00058-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Gene transfer to exocrine glands, including the major salivary glands, presents an attractive method to deliver proteins for therapeutic applications. Previous efforts using nonviral gene delivery to these glands have resulted in limited success. In this report, zinc and other divalent transitions were coadministered with plasmid DNA in an effort to improve nonviral salivary gland transfection efficiency. The inclusion of zinc into plasmid DNA solutions resulted in a 20-fold enhancement in transgene expression without noticeable inflammation compared to a solution of plasmid DNA only. This observed enhancement in transgene expression was dependent upon the DNA dose and correlated with the accumulation of plasmid DNA by salivary gland tissues.
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18
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Kizek R, Trnková L, Sevcíková S, Smarda J, Jelen F. Silver electrode as a sensor for determination of zinc in cell cultivation medium. Anal Biochem 2002; 301:8-13. [PMID: 11811961 DOI: 10.1006/abio.2001.5484] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Use of the silver electrode as a sensor for the monitoring of zinc in cell growth medium is described. Zinc at silver electrodes provides specific voltammetric signal, which is affected by solution components. Signals of zinc ions in phosphate buffer solutions with and without cell growth medium were compared. Common DMEM cell culture medium was used for the cultivation of a cell line of v-myb-transformed chicken monoblasts and its variants expressing v-jun and c-jun in a zinc-dependent manner. Electrochemical results showed zinc concentrations in the medium coincide very well with the jun expression. With respect to the low toxicity of silver for eukaryotic cells, silver electrodes represent promising tools for the determination of zinc concentrations in vivo without the potential risk of a cell culture damage.
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Affiliation(s)
- René Kizek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, 612 65, Czech Republic
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Spanakis E. Human DNA Sampling and Banking. MOLECULAR GENETIC EPIDEMIOLOGY — A LABORATORY PERSPECTIVE 2002. [DOI: 10.1007/978-3-642-56207-5_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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MacLellan SR, Forsberg CW. Properties of the major non-specific endonuclease from the strict anaerobe Fibrobacter succinogenes and evidence for disulfide bond formation in vivo. MICROBIOLOGY (READING, ENGLAND) 2001; 147:315-323. [PMID: 11158348 DOI: 10.1099/00221287-147-2-315] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNase A is a non-specific endonuclease of Fibrobacter succinogenes. The enzyme was purified to homogeneity and its properties studied both in vitro and in vivo. Magnesium but not calcium was essential for nucleolytic activity. Manganese ions substituted for magnesium but were less stimulatory. DNase A activity was markedly inhibited by either NaCl or KCl at concentrations greater than 75 mM. The enzyme had a temperature optimum of 25 degrees C and a pH optimum of about 7.0. Values for K:(m) and K:(cat) were determined to be 61 microM and 330 s(-1) respectively, with a catalytic efficiency approximately threefold greater than bovine pancreatic DNase I, but 10-fold less than the Serratia marcescens NucA. DNase A was localized to the periplasm and probably exists as a monomeric species. The enzyme possessed one or more disulfide bonds. In the reduced form it had an apparent mass of 33 kDa, while in the oxidized form it was 29 kDa as estimated by SDS-PAGE. Reduction of the disulfide bonds by dithiothreitol with or without subsequent alkylation by iodoacetamide strongly inactivated the enzyme. DNase A accumulated in vivo had an apparent mass of 29 kDa, indicating that it was in an oxidized form. This is the first indication in a strict anaerobe of a functional periplasmic disulfide bond forming system, phenotypically similar to Dsb systems in facultative and aerobic bacteria.
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Affiliation(s)
- Shawn R MacLellan
- Department of Microbiology, University of Guelph, Guelph, Ontario, CanadaN1G 2W11
| | - Cecil W Forsberg
- Department of Microbiology, University of Guelph, Guelph, Ontario, CanadaN1G 2W11
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