1
|
Xie S, Yue C, Ye S, Li Z. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys 2024; 26:10408-10418. [PMID: 38502252 DOI: 10.1039/d3cp05957j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assemblies. Despite its significance, the physicochemical property and the molecular mechanism followed by TNP1 for histone replacement and DNA condensation are still poorly understood. This study reports the first-time in vitro expression and purification of human TNP1 and investigates the hierarchical dynamics of TNP1-DNA interaction using a combination of computational simulations, biochemical assays, fluorescence imaging, and atomic force microscopy. We explored three crucial facets of TNP1-DNA interactions. Initially, we delve into the molecular binding process that entails fuzzy interactions between TNP1 and DNA at the atomistic scale. Subsequently, we analyze how TNP1 binding affects the electrostatic and mechanical characteristics of DNA and influences its morphology. Finally, we study the biomolecular condensation of TNP1-DNA when subjected to high concentrations. The findings of our study set the foundation for comprehending the potential involvement of TNP1 in histone replacement and DNA condensation in spermatogenesis.
Collapse
Affiliation(s)
- Shangqiang Xie
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Congran Yue
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
| | - Sheng Ye
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| | - Zhenlu Li
- School of Life Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, 92 Weijin Road, Tianjin 300072, China
| |
Collapse
|
2
|
de la Iglesia A, Jodar M, Oliva R, Castillo J. Insights into the sperm chromatin and implications for male infertility from a protein perspective. WIREs Mech Dis 2023; 15:e1588. [PMID: 36181449 DOI: 10.1002/wsbm.1588] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
Male germ cells undergo an extreme but fascinating process of chromatin remodeling that begins in the testis during the last phase of spermatogenesis and continues through epididymal sperm maturation. Most of the histones are replaced by small proteins named protamines, whose high basicity leads to a tight genomic compaction. This process is epigenetically regulated at many levels, not only by posttranslational modifications, but also by readers, writers, and erasers, in a context of a highly coordinated postmeiotic gene expression program. Protamines are key proteins for acquiring this highly specialized chromatin conformation, needed for sperm functionality. Interestingly, and contrary to what could be inferred from its very specific DNA-packaging function across protamine-containing species, human sperm chromatin contains a wide spectrum of protamine proteoforms, including truncated and posttranslationally modified proteoforms. The generation of protamine knock-out models revealed not only chromatin compaction defects, but also collateral sperm alterations contributing to infertile phenotypes, evidencing the importance of sperm chromatin protamination toward the generation of a new individual. The unique features of sperm chromatin have motivated its study, applying from conventional to the most ground-breaking techniques to disentangle its peculiarities and the cellular mechanisms governing its successful conferment, especially relevant from the protein point of view due to the important epigenetic role of sperm nuclear proteins. Gathering and contextualizing the most striking discoveries will provide a global understanding of the importance and complexity of achieving a proper chromatin compaction and exploring its implications on postfertilization events and beyond. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.
Collapse
Affiliation(s)
- Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Mukherjee A, Saurabh S, Olive E, Jang YH, Lansac Y. Protamine Binding Site on DNA: Molecular Dynamics Simulations and Free Energy Calculations with Full Atomistic Details. J Phys Chem B 2021; 125:3032-3044. [DOI: 10.1021/acs.jpcb.0c09166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arnab Mukherjee
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Suman Saurabh
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - Enrick Olive
- GREMAN, CNRS UMR 7347, Université de Tours, 37200 Tours, France
| | - 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
| |
Collapse
|
5
|
Brandariz-Nuñez A, Robinson SJ, Evilevitch A. Pressurized DNA state inside herpes capsids-A novel antiviral target. PLoS Pathog 2020; 16:e1008604. [PMID: 32702029 PMCID: PMC7377361 DOI: 10.1371/journal.ppat.1008604] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/05/2020] [Indexed: 01/25/2023] Open
Abstract
Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, "turns off" capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target-suppressing pressure-driven viral genome ejection-that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.
Collapse
Affiliation(s)
- Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Scott J. Robinson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alex Evilevitch
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| |
Collapse
|
6
|
Gupta S, Tiwari N, Munde M. A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation. Sci Rep 2019; 9:5891. [PMID: 30971720 PMCID: PMC6458161 DOI: 10.1038/s41598-019-41975-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 11/21/2022] Open
Abstract
DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.
Collapse
Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
7
|
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] [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.
Collapse
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.
| |
Collapse
|
8
|
An M, Tonga GY, Parkin SR, Rotello VM, DeRouchey JE. Tuning DNA Condensation with Zwitterionic Polyamidoamine (zPAMAM) Dendrimers. Macromolecules 2017; 50:8202-8211. [PMID: 30700915 DOI: 10.1021/acs.macromol.7b01470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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.
Collapse
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
| |
Collapse
|
9
|
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] [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
| |
Collapse
|
10
|
Ausió J, González-Romero R, Woodcock CL. Comparative structure of vertebrate sperm chromatin. J Struct Biol 2014; 188:142-55. [PMID: 25264147 DOI: 10.1016/j.jsb.2014.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/11/2014] [Accepted: 09/17/2014] [Indexed: 12/11/2022]
Abstract
A consistent feature of sperm nuclei is its exceptionally compact state in comparison with somatic nuclei. Here, we have examined the structural organization of sperm chromatin from representatives of three vertebrate lineages, bony fish (Danio rerio), birds (Gallus gallus domesticus) and mammals (Mus musculus) using light and transmission electron microscopy (TEM). Although the three sperm nuclei are all highly compact, they differ in morphology and in the complement of compaction-inducing proteins. Whereas zebrafish sperm retain somatic histones and a nucleosomal organization, in the rooster and mouse, histones are largely replaced by small, arginine-rich protamines. In contrast to the mouse, the rooster protamine contains no cysteine residues and lacks the potential stabilizing effects of S-S bonds. Protamine driven chromatin compaction results in a stable, highly condensed chromatin, markedly different from the somatic nucleosome-based beads-on-a-string architecture, but its structure remains poorly understood. When prepared gently for whole mount TEM, the rooster and mouse sperm chromatin reveal striking rod-like units 40-50 nm in width. Also present in the mouse, which has very flattened sperm nuclei, but not rooster, where nuclei take the form of elongated cylinders, are toroidal shaped structures, with an external diameter of about 90 nm. In contrast, similarly prepared zebrafish sperm exhibit nucleosomal chromatin. We also examined the early stages in the binding of salmine (the salmon protamine) to defined sequence DNA. These images suggest an initial side-by-side binding of linear DNA-protamine complexes leading to the nucleation of thin, flexible rods with the potential to bend, allowing the ends to come into contact and fuse to form toroidal structures. We discuss the relationship between these in vitro observations and the rods and toroids seen in nuclei, and suggest an explanation for the apparent absence of these structures in TEM images of fully condensed sperm nuclei.
Collapse
Affiliation(s)
- Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Rodrigo González-Romero
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | | |
Collapse
|
11
|
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] [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.
Collapse
Affiliation(s)
- Min An
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA.
| | | | | |
Collapse
|
12
|
DeRouchey J, Hoover B, Rau DC. A comparison of DNA compaction by arginine and lysine peptides: a physical basis for arginine rich protamines. Biochemistry 2013; 52:3000-9. [PMID: 23540557 DOI: 10.1021/bi4001408] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protamines are small, highly positively charged peptides used to package DNA at very high densities in sperm nuclei. Tight DNA packing is considered essential for the minimization of DNA damage by mutagens and reactive oxidizing species. A striking and general feature of protamines is the almost exclusive use of arginine over lysine for the positive charge to neutralize DNA. We have investigated whether this preference for arginine might arise from a difference in DNA condensation by arginine and lysine peptides. The forces underlying DNA compaction by arginine, lysine, and ornithine peptides are measured using the osmotic stress technique coupled with X-ray scattering. The equilibrium spacings between DNA helices condensed by lysine and ornithine peptides are significantly larger than the interhelical distances with comparable arginine peptides. The DNA surface-to-surface separation, for example, is some 50% larger with polylysine than with polyarginine. DNA packing by lysine rich peptides in sperm nuclei would allow much greater accessibility to small molecules that could damage DNA. The larger spacing with lysine peptides is caused by both a weaker attraction and a stronger short-range repulsion relative to that of the arginine peptides. A previously proposed model for binding of polyarginine and protamine to DNA provides a convenient framework for understanding the differences between the ability of lysine and arginine peptides to assemble DNA.
Collapse
Affiliation(s)
- Jason DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | | | | |
Collapse
|