1
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Oikeh E, Ziebarth J, Dinar MAM, Kirchhoff D, Aronova A, Dziubla TD, Wang Y, DeRouchey JE. DNA Packaging and Polycation Length Determine DNA Susceptibility to Free Radical Damage in Condensed DNA. J Phys Chem B 2024; 128:3329-3339. [PMID: 38557033 DOI: 10.1021/acs.jpcb.3c06116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins: histones in somatic nuclei and protamines in sperm chromatin. The extreme, nearly crystalline packaging of DNA by protamines in spermatozoa is thought to be essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamines is required in sperm, as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to which DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay among polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.
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Affiliation(s)
- Ehigbai Oikeh
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jesse Ziebarth
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Md Abu Monsur Dinar
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel Kirchhoff
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Anastasiia Aronova
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Thomas D Dziubla
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongmei Wang
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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2
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Mitchell RJ, Kriger SM, Fenton AD, Havrylyuk D, Pandeya A, Sun Y, Smith T, DeRouchey JE, Unrine JM, Oza V, Blackburn JS, Wei Y, Heidary DK, Glazer EC. A monoadduct generating Ru(ii) complex induces ribosome biogenesis stress and is a molecular mimic of phenanthriplatin. RSC Chem Biol 2023; 4:344-353. [PMID: 37181632 PMCID: PMC10170627 DOI: 10.1039/d2cb00247g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/01/2023] [Indexed: 03/03/2023] Open
Abstract
Ruthenium complexes are often investigated as potential replacements for platinum-based chemotherapeutics in hopes of identifying systems with improved tolerability in vivo and reduced susceptibility to cellular resistance mechanisms. Inspired by phenanthriplatin, a non-traditional platinum agent that contains only one labile ligand, monofunctional ruthenium polypyridyl agents have been developed, but until now, few demonstrated promising anticancer activity. Here we introduce a potent new scaffold, based on [Ru(tpy)(dip)Cl]Cl (tpy = 2,2':6',2''-terpyridine and dip = 4,7-diphenyl-1,10-phenanthroline) in pursuit of effective Ru(ii)-based monofunctional agents. Notably, the extension of the terpyridine at the 4' position with an aromatic ring resulted in a molecule that was cytotoxic in several cancer cell lines with sub-micromolar IC50 values, induced ribosome biogenesis stress, and exhibited minimal zebrafish embryo toxicity. This study demonstrates the successful design of a Ru(ii) agent that mimics many of the biological effects and phenotypes seen with phenanthriplatin, despite numerous differences in both the ligands and metal center structure.
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Affiliation(s)
- Richard J Mitchell
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Sarah M Kriger
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
| | - Alexander D Fenton
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Dmytro Havrylyuk
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Ankit Pandeya
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Yang Sun
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Tami Smith
- Department of Plant and Soil Sciences, University of Kentucky 1100 S. Limestone St Lexington KY 40546 USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky 1100 S. Limestone St Lexington KY 40546 USA
| | - Viral Oza
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone St. Lexington KY 40536 USA
| | - Jessica S Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky 741 S. Limestone St. Lexington KY 40536 USA
| | - Yinan Wei
- Department of Chemistry, University of Kentucky 505 Rose St. Lexington KY 40506 USA
| | - David K Heidary
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
| | - Edith C Glazer
- Department of Chemistry, North Carolina State University 2620 Yarbrough DriveRaleigh NC 27695 USA
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3
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Shadman H, Gallops CE, Ziebarth JD, DeRouchey JE, Wang Y. Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations. ACS Omega 2022; 7:42083-42095. [PMID: 36440140 PMCID: PMC9685783 DOI: 10.1021/acsomega.2c04227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Protamines are arginine-rich proteins that condense DNA in sperm. Despite their importance in reproduction, information on protamine structure is scarce. We, therefore, used molecular dynamics to examine the structures of salmon, bull P1, and human P1 protamines. The sizes and shapes of each protamine varied widely, indicating that they were disordered with structures covering a broad conformational landscape, from hairpin loop structures to extended coils. Despite their general disorder, the protamines did form secondary structures, including helices and hairpin loops. In eutherians, hairpins may promote disulfide bonding that facilitates protamine-DNA condensation, but the specifics of this bonding is not well established. We examined inter-residue distances in the simulations to predict residue pairs likely to form intramolecular bonds, leading to the identification of bonding pairs consistent with previous results in bull and human. These results support a model for eutherian protamine structures where a highly charged center is surrounded by disulfide-bond-stabilized loops.
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Affiliation(s)
- Hossain Shadman
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee38154, United States
| | - Caleb Edward Gallops
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee38154, United States
| | - Jesse D. Ziebarth
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee38154, United States
| | - Jason E. DeRouchey
- Department
of Chemistry, The University of Kentucky, Lexington, Kentucky40506, United States
| | - Yongmei Wang
- Department
of Chemistry, The University of Memphis, Memphis, Tennessee38154, United States
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4
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Patel SP, Michael FM, Arif Khan M, Duggan B, Wyse S, Darby DR, Chaudhuri K, Pham JT, Gollihue J, DeRouchey JE, Sullivan PG, Dziubla TD, Rabchevsky AG. Erodible thermogelling hydrogels for localized mitochondrial transplantation to the spinal cord. Mitochondrion 2022; 64:145-155. [DOI: 10.1016/j.mito.2022.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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5
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Uddin N, Warriner LW, Pack DW, DeRouchey JE. Enhanced Gene Delivery and CRISPR/Cas9 Homology-Directed Repair in Serum by Minimally Succinylated Polyethylenimine. Mol Pharm 2021; 18:3452-3463. [PMID: 34387498 DOI: 10.1021/acs.molpharmaceut.1c00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gene therapy aims to treat patients by altering or controlling gene expression. The field of gene therapy has had increasing success in recent years primarily using viral-based approaches; however, there is still significant interest toward the use of polymeric materials due to their potential as flexible, low-cost scaffolds for gene delivery that do not suffer the mutagenesis and immunogenicity concerns of viral vectors. To address the challenges of efficiency and biocompatibility, a series of zwitterion-like polyethylenimine derivatives (zPEIs) were produced via the succinylation of 2-11.5% of polyethylenimine (PEI) amines. With increasing modification, zPEI polyplexes exhibited decreased serum-protein aggregation and dissociated more easily in the presence of a competitor polyanion when compared to unmodified PEI. Surprisingly, the gene delivery mediated in the presence of serum showed that succinylation of as few as 2% of PEI amines resulted in transgene expression 260- to 480-fold higher than that of unmodified PEI and 50- to 65-fold higher than that of commercial PEI-PEG2k in HEK293 and HeLa cells, respectively. Remarkably, the same zPEIs also produced 16-fold greater efficiency of CRISPR/Cas9 gene knock-in compared to unmodified PEI in the presence of serum. In addition, we show that 2% succinylation does not significantly decrease polymer/DNA binding ability or serum protein interaction to a significant extent, yet this small modification is still sufficient to provide a remarkable increase in transgene expression and gene knock-in in the presence of serum.
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Affiliation(s)
- Nasir Uddin
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Logan W Warriner
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel W Pack
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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6
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Saintilnord WN, Tenlep SYN, Preston JD, Duregon E, DeRouchey JE, Unrine JM, de Cabo R, Pearson KJ, Fondufe-Mittendorf YN. Chronic Exposure to Cadmium Induces Differential Methylation in Mice Spermatozoa. Toxicol Sci 2021; 180:262-276. [PMID: 33483743 PMCID: PMC8041459 DOI: 10.1093/toxsci/kfab002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cadmium exposure is ubiquitous and has been linked to diseases including cancers and reproductive defects. Since cadmium is nonmutagenic, it is thought to exert its gene dysregulatory effects through epigenetic reprogramming. Several studies have implicated germline exposure to cadmium in developmental reprogramming. However, most of these studies have focused on maternal exposure, while the impact on sperm fertility and disease susceptibility has received less attention. In this study, we used reduced representation bisulfite sequencing to comprehensively investigate the impact of chronic cadmium exposure on mouse spermatozoa DNA methylation. Adult male C57BL/J6 mice were provided water with or without cadmium chloride for 9 weeks. Sperm, testes, liver, and kidney tissues were collected at the end of the treatment period. Cadmium exposure was confirmed through gene expression analysis of metallothionein-1 and 2, 2 well-known cadmium-induced genes. Analysis of sperm DNA methylation changes revealed 1788 differentially methylated sites present at regulatory regions in sperm of mice exposed to cadmium compared with vehicle (control) mice. Furthermore, most of these differential methylation changes positively correlated with changes in gene expression at both the transcription initiation stage as well as the splicing levels. Interestingly, the genes targeted by cadmium exposure are involved in several critical developmental processes. Our results present a comprehensive analysis of the sperm methylome in response to chronic cadmium exposure. These data, therefore, highlight a foundational framework to study gene expression patterns that may affect fertility in the exposed individual as well as their offspring, through paternal inheritance.
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Affiliation(s)
- Wesley N Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Sara Y N Tenlep
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Joshua D Preston
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA,Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Eleonora Duregon
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 20892, USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 20892, USA
| | - Kevin J Pearson
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536-0509, USA,To whom correspondence should be addressed at Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536-0509, USA. E-mail: ; Department of Molecular and Cellular Biochemistry, University of Kentucky, 800 Rose Street, 273 BBSRB, Lexington, KY 40536-0509, USA. E-mail:
| | - Yvonne N Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0509, USA,To whom correspondence should be addressed at Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536-0509, USA. E-mail: ; Department of Molecular and Cellular Biochemistry, University of Kentucky, 800 Rose Street, 273 BBSRB, Lexington, KY 40536-0509, USA. E-mail:
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7
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Powell CD, Kirchoff DC, DeRouchey JE, Moseley HNB. Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines. BMC Genomics 2020; 21:277. [PMID: 32245406 PMCID: PMC7126135 DOI: 10.1186/s12864-020-6681-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. RESULTS Protamine sequences from UniProt's databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. CONCLUSIONS High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.
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Affiliation(s)
- Christian D. Powell
- Department of Chemistry, University of Kentucky, 161 Jacobs Science Building, Lexington, 40506 USA
- Markey Cancer Center, University of Kentucky, 800 Rose Street, Pavilion CC, Lexington, 40536 USA
| | - Daniel C. Kirchoff
- Department of Chemistry, University of Kentucky, 161 Jacobs Science Building, Lexington, 40506 USA
| | - Jason E. DeRouchey
- Department of Chemistry, University of Kentucky, 161 Jacobs Science Building, Lexington, 40506 USA
| | - Hunter N. B. Moseley
- Markey Cancer Center, University of Kentucky, 800 Rose Street, Pavilion CC, Lexington, 40536 USA
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, 40508 USA
- Institute for Biomedical Informatics, University of Kentucky, Lexington, 40536 USA
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8
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Warriner LW, Duke JR, Pack DW, DeRouchey JE. Succinylated Polyethylenimine Derivatives Greatly Enhance Polyplex Serum Stability and Gene Delivery In Vitro. Biomacromolecules 2018; 19:4348-4357. [DOI: 10.1021/acs.biomac.8b01248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Hansing J, Duke JR, Fryman EB, DeRouchey JE, Netz RR. Particle Diffusion in Polymeric Hydrogels with Mixed Attractive and Repulsive Interactions. Nano Lett 2018; 18:5248-5256. [PMID: 29947212 DOI: 10.1021/acs.nanolett.8b02218] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
All biogels are heterogeneous, consisting of functional groups with different biophysical properties arrayed on spatially disordered polymer networks. Nanoparticles diffusing in such biogels experience a mixture of attractive and repulsive interactions. Here, we present experimental and theoretical studies of charged particle diffusion in gels with a random distribution of attractive and repulsive electrostatic interaction sites inside the gel. In addition to interaction disorder, we theoretically investigate the effect of spatial disorder of the polymer network. Our coarse-grained simulations reveal that attractive interactions primarily determine the diffusive behavior of the particles in systems with mixed attractive and repulsive interactions. As a consequence, charged particles of either sign are immobilized in mixed cationic/anionic gels because they are trapped near oppositely charged interaction sites, whereas neutral particles diffuse rapidly. Even small fractions of oppositely charged interaction sites lead to strong trapping of a charged particle. Translational diffusion coefficients of charged probe molecules in gels consisting of mixed cationic and anionic dextran polymers are determined by fluorescence correlation spectroscopy and quantitatively confirm our theoretical predictions.
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Affiliation(s)
- Johann Hansing
- Fachbereich für Physik , Freie Universität Berlin , 14195 Berlin , Germany
| | - Joseph R Duke
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Emily B Fryman
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Jason E DeRouchey
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Roland R Netz
- Fachbereich für Physik , Freie Universität Berlin , 14195 Berlin , Germany
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10
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Hutchison JM, Rau DC, DeRouchey JE. Role of Disulfide Bonds on DNA Packaging Forces in Bull Sperm Chromatin. Biophys J 2017; 113:1925-1933. [PMID: 29117517 DOI: 10.1016/j.bpj.2017.08.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 01/06/2023] Open
Abstract
Short arginine-rich proteins called protamines mediate the near crystalline DNA packaging in most vertebrate sperm cells. Protamines are synthesized during spermiogenesis and condense the paternal genome into a transcriptionally inactive state in late-stage spermatids. Protamines from eutherian mammals, including bulls and humans, also contain multiple cysteine residues that form intra- and interprotamine sulfur-sulfur bonds during the final stages of sperm maturation. Although the cross-linked protamine network is known to stabilize the resulting nucleoprotamine structure, little is known about the role of disulfide bonds on DNA condensation in the mammalian sperm. Using small angle x-ray scattering, we show that isolated bull nuclei achieve slightly lower DNA packing densities compared to salmon nuclei despite salmon protamine lacking cysteine residues. Surprisingly, reduction of the intermolecular sulfur-sulfur bonds of bull protamine results in tighter DNA packing. Complete reduction of the intraprotamine disulfide bonds ultimately leads to decondensation, suggesting that disulfide-mediated secondary structure is also critical for proper protamine function. Lastly, comparison of multiple bull collections showed some to have aberrant x-ray scattering profiles consistent with incorrect disulfide bond formation. Together, these observations shed light on the biological functions of disulfide linkages for in vivo DNA packaging in sperm chromatin.
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Affiliation(s)
- James M Hutchison
- Department of Chemistry, University of Kentucky, Lexington, Kentucky; Program in Physical Biology, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Donald C Rau
- Program in Physical Biology, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
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11
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Abstract
Cationic dendrimers are promising vectors for non-viral gene due to their well-defined size and chemistry. We have synthesized a series of succinylated fourth generation (G4) PAMAM dendrimers to control the DNA packaging in dendriplexes, allowing us to probe the role of charge on DNA packaging. The self-assembly of DNA induced by these zwitterionic PAMAM (zPAMAM) was investigated using small-angle x-ray scattering (SAXS). We demonstrate that changing the degree of modification in zPAMAM-DNA significantly alters the packing density of the resulting dendriplexes. Salt sensitivities and pH dependence on the inter-DNA spacing were also examined. The swelling and stability to salt is reduced with increasing degree of PAMAM modification. Lowering the pH leads to significantly tighter hexagonal DNA packaging. In combination, these results show zPAMAM is an effective means to modulate nucleic acid packaging in a deterministic manner.
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Affiliation(s)
- Min An
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | | | - Sean R Parkin
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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12
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DeRouchey JE. DNA in Tight Spaces: Linking Structure, Stability and Protection in Protamine Packaged DNA. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Stocke NA, Zhang X, Hilt JZ, DeRouchey JE. Transport in PEG-Based Hydrogels: Role of Water Content at Synthesis and Crosslinker Molecular Weight. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nathanael A. Stocke
- Department of Chemical and Materials Engineering; University of Kentucky; Lexington KY 40506 USA
| | - Xiaolu Zhang
- Department of Chemistry; University of Kentucky; Lexington KY 40506 USA
| | - J. Zach Hilt
- Department of Chemical and Materials Engineering; University of Kentucky; Lexington KY 40506 USA
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14
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Hansing J, Ciemer C, Kim WK, Zhang X, DeRouchey JE, Netz RR. Nanoparticle filtering in charged hydrogels: Effects of particle size, charge asymmetry and salt concentration. Eur Phys J E Soft Matter 2016; 39:53. [PMID: 27167077 DOI: 10.1140/epje/i2016-16053-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/15/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
The understanding of particle transport mechanisms in biological and synthetic hydrogels is crucial for the development of advanced drug delivery methods. We propose a simple model for the diffusion of charged nanoparticles in cross-linked, charged hydrogels based on a cubic periodic environment and an electrostatic interaction potential of varying range and strength, encompassing attractive and repulsive scenarios. The long-time diffusive properties are investigated by use of Brownian dynamics simulations and analytical methods. A number of experimentally observed phenomena attributed to nonsteric interactions between hydrogel polymers and diffusing particle are naturally reproduced by our model. Charged particles diffuse slower than uncharged particles, regardless of the sign of the surface charge, but with a stronger hindrance effect for attractive electrostatic interactions. This is explained in terms of charged particles sticking to the polymer network in regions of strong opposite charge and their exclusion from similarly charged regions. In the case of attractive interactions between hydrogel polymers and the diffusing particle, smaller charged particles diffuse slower than larger ones. This stands in contrast to a size filtering scenario but is in agreement with experimental findings. In the case of repulsive interactions, a range of differently sized particles diffuse equally fast. We compare our model predictions with published experiments on charged particle diffusion in hydrogels and confirm that electrostatic interactions are a key factor influencing the diffusivity of charged nanoparticles and that oppositely charged gels are much more effective in slowing down a charged particle than similarly charged gels.
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Affiliation(s)
- Johann Hansing
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
| | - Catrin Ciemer
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Won Kyu Kim
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Xiaolu Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
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15
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Zhang X, Hansing J, Netz RR, DeRouchey JE. Particle transport through hydrogels is charge asymmetric. Biophys J 2015; 108:530-9. [PMID: 25650921 PMCID: PMC4317548 DOI: 10.1016/j.bpj.2014.12.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 01/19/2023] Open
Abstract
Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks.
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Affiliation(s)
- Xiaolu Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Johann Hansing
- Fachbereich für Physik, Freie Universität Berlin, Berlin, Germany
| | - Roland R Netz
- Fachbereich für Physik, Freie Universität Berlin, Berlin, Germany
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
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An M, Hutchison JM, Parkin SR, DeRouchey JE. Role of pH on the Compaction Energies and Phase Behavior of Low Generation PAMAM–DNA Complexes. Macromolecules 2014. [DOI: 10.1021/ma5020808] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Min An
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - James M. Hutchison
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Sean R. Parkin
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jason E. DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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17
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Moonschi FH, Effinger AK, Zhang X, Martin WE, Fox AM, Heidary DK, DeRouchey JE, Richards CI. Cell-Derived Vesicles for Single-Molecule Imaging of Membrane Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Moonschi FH, Effinger AK, Zhang X, Martin WE, Fox AM, Heidary DK, DeRouchey JE, Richards CI. Cell-derived vesicles for single-molecule imaging of membrane proteins. Angew Chem Int Ed Engl 2014; 54:481-4. [PMID: 25363667 DOI: 10.1002/anie.201408707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/01/2014] [Indexed: 01/08/2023]
Abstract
A new approach is presented for the application of single-molecule imaging to membrane receptors through the use of vesicles derived from cells expressing fluorescently labeled receptors. During the isolation of vesicles, receptors remain embedded in the membrane of the resultant vesicles, thus allowing these vesicles to serve as nanocontainers for single-molecule measurements. Cell-derived vesicles maintain the structural integrity of transmembrane receptors by keeping them in their physiological membrane. It was demonstrated that receptors isolated in these vesicles can be studied with solution-based fluorescence correlation spectroscopy (FCS) and can be isolated on a solid substrate for single-molecule studies. This technique was applied to determine the stoichiometry of α3β4 nicotinic receptors. The method provides the capability to extend single-molecule studies to previously inaccessible classes of receptors.
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Affiliation(s)
- Faruk H Moonschi
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA)
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19
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An M, Parkin SR, DeRouchey JE. Intermolecular forces between low generation PAMAM dendrimer condensed DNA helices: role of cation architecture. Soft Matter 2014; 10:590-599. [PMID: 24651934 DOI: 10.1039/c3sm52096j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In recent years, dendriplexes, complexes of cationic dendrimers with DNA, have become attractive DNA delivery vehicles due to their well-defined chemistries. To better understand the nature of the forces condensing dendriplexes, we studied low generation poly(amidoamine) (PAMAM) dendrimer-DNA complexes and compared them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we have investigated the effect of molecular chain architecture on DNA-DNA intermolecular forces that determine the net attraction and equilibrium interhelical distance within these polycation condensed DNA arrays. In order to compact DNA, linear cations are believed to bind in DNA grooves and to interact with the phosphate backbone of apposing helices. We have previously shown a length dependent attraction resulting in higher packaging densities with increasing charge for linear cations. Hyperbranched polycations, such as polycationic dendrimers, presumably would not be able to bind to DNA and correlate their charges in the same manner as linear cations. We show that attractive and repulsive force amplitudes in PAMAM-DNA assemblies display significantly different trends than comparably charged linear arginines resulting in lower DNA packaging densities with increasing PAMAM generation. The salt and pH dependencies of packaging in PAMAM dendrimer-DNA and linear arginine-DNA complexes were also investigated. Significant differences in the force curve behaviour and salt and pH sensitivities suggest that different binding modes may be present in DNA condensed by dendrimers when compared to linear polycations.
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Affiliation(s)
- Min An
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA.
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DeRouchey JE, Rau DC. Role of amino acid insertions on intermolecular forces between arginine peptide condensed DNA helices: implications for protamine-DNA packaging in sperm. J Biol Chem 2011; 286:41985-41992. [PMID: 21994948 PMCID: PMC3234980 DOI: 10.1074/jbc.m111.295808] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/04/2011] [Indexed: 11/06/2022] Open
Abstract
In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads.
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Affiliation(s)
- Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506.
| | - Donald C Rau
- Program in Physical Biology, NICHD, National Institutes of Health, Bethesda, Maryland 20892
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Abstract
Using osmotic stress coupled with X-ray scattering, we have directly examined the salt sensitivity of the intermolecular forces between helices in condensed protamine-DNA arrays. Thermodynamic forces are measured from the dependence of DNA helical interaxial spacings on external salt concentration or the osmotic pressure applied by neutral polymer solutions in equilibrium with the condensed phase. Force curves of salmon protamine-DNA condensates are highly dependent on salt species and concentration, indicating salt binding to protamine-DNA complexes. This dependence of the forces on salt species follows the Hofmeister series for anions. Chaotropic anions bind more tightly to protamine-DNA arrays than kosmotropic anions, thus more greatly disrupting the attractive thermodynamic forces. Variations with cation type are small compared with those observed for anions. Further, osmotic stress is used to estimate the number of ions bound in the condensed phase through a Gibbs-Duhem relationship. We estimate that at equilibrium, ∼1 Br(-) is bound per protamine molecule at 200 mM NaBr concentration. Remarkably, this one bound anion results in a change of ∼12% in the surface-to-surface distance between DNA helices. Potential biological implications of this attractive force salt sensitivity are discussed.
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Affiliation(s)
- Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States.
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