1
|
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
|
2
|
Lansac Y, Degrouard J, Renouard M, Toma AC, Livolant F, Raspaud E. A route to self-assemble suspended DNA nano-complexes. Sci Rep 2016; 6:21995. [PMID: 26912166 PMCID: PMC4766487 DOI: 10.1038/srep21995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/27/2016] [Indexed: 11/29/2022] Open
Abstract
Highly charged polyelectrolytes can self-assemble in presence of condensing agents such as multivalent cations, amphiphilic molecules or proteins of opposite charge. Aside precipitation, the formation of soluble micro- and nano-particles has been reported in multiple systems. However a precise control of experimental conditions needed to achieve the desired structures has been so far hampered by the extreme sensitivity of the samples to formulation pathways. Herein we combine experiments and molecular modelling to investigate the detailed microscopic dynamics and the structure of self-assembled hexagonal bundles made of short dsDNA fragments complexed with small basic proteins. We suggest that inhomogeneous mixing conditions are required to form and stabilize charged self-assembled nano-aggregates in large excess of DNA. Our results should help re-interpreting puzzling behaviors reported for a large class of strongly charged polyelectrolyte systems.
Collapse
Affiliation(s)
- Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France.,Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France.,School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jeril Degrouard
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Madalena Renouard
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Adriana C Toma
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| |
Collapse
|
3
|
Porschke D. Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:413-21. [PMID: 26872482 PMCID: PMC4901124 DOI: 10.1007/s00249-015-1110-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/30/2015] [Accepted: 12/17/2015] [Indexed: 11/05/2022]
Abstract
Because of repeated claims that A-DNA cannot exist without aggregation or condensation, the state of DNA restriction fragments with 84–859 bp has been analyzed in aqueous solutions upon reduction of the water activity. Rotational diffusion times τd measured by electric dichroism at different water activities with a wide variation of viscosities are normalized to values τc at the viscosity of water, which indicate DNA structures at a high sensitivity. For short helices (chain lengths \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ {\ell} $$\end{document}ℓ ≤ persistence length p), cooperative formation of A-DNA is reflected by the expected reduction of the hydrodynamic length; the transition to the A-form is without aggregation or condensation upon addition of ethanol at monovalent salt ≤1 mM. The aggregation boundary, indicated by a strong increase of τc, is shifted to higher monovalent salt (≥4 mM) when ethanol is replaced by trifluoroethanol. The BA transition is not indicated anymore by a cooperative change of τc for \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ {\ell} $$\end{document}ℓ » p; τc values for these long chains decrease upon reduction of the water activity continuously over the full range, including the BA transition interval. This suggests a non-cooperative BC transition, which induces DNA curvature. The resulting wide distribution of global structures hides changes of local length during the BA transition. Free A-DNA without aggregation/condensation is found at low-salt concentrations where aggregation is inhibited and/or very slow. In an intermediate range of solvent conditions, where the A-form starts to aggregate, a time window remains that can be used for analysis of free A-DNA in a quasi-equilibrium state.
Collapse
Affiliation(s)
- Dietmar Porschke
- Max Planck Institut für biophysikalische Chemie, 37077, Göttingen, Germany.
| |
Collapse
|
4
|
|
5
|
Huang Y, Lapitsky Y. Determining the colloidal behavior of ionically cross-linked polyelectrolytes with isothermal titration calorimetry. J Phys Chem B 2013; 117:9548-57. [PMID: 23856000 DOI: 10.1021/jp405384b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mixtures of polyelectrolytes and multivalent counterions can self-assemble into colloidal complexes. These complexes attract widespread interest in applications such as medicine, household product formulations, and separation processes. To facilitate the development of these colloidal dispersions, we examined isothermal titration calorimetry (ITC) as an automated screening tool for identifying the polymer and multivalent counterion compositions that (1) form ionically cross-linked colloidal complexes and (2) lead to their rapid coagulation (and macroscopic phase separation). By studying various polyelectrolyte/multivalent counterion mixtures, we have identified and generalized the features in the ITC data that indicate colloidal complex formation and coagulation. The limitations of this calorimetric screening method were also elucidated. These analyses suggest that ITC can be effective for screening the short-term colloidal behavior of polyelectrolyte/multivalent counterion mixtures but are unreliable in revealing their long-term (equilibrium) properties.
Collapse
Affiliation(s)
- Yan Huang
- Department of Chemical and Environmental Engineering, University of Toledo, Toledo, Ohio 43606, USA
| | | |
Collapse
|
6
|
Bauer DW, Huffman JB, Homa FL, Evilevitch A. Herpes virus genome, the pressure is on. J Am Chem Soc 2013; 135:11216-21. [PMID: 23829592 DOI: 10.1021/ja404008r] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.
Collapse
Affiliation(s)
- David W Bauer
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | |
Collapse
|
7
|
Alabi CA, Love KT, Sahay G, Stutzman T, Young WT, Langer R, Anderson DG. FRET-labeled siRNA probes for tracking assembly and disassembly of siRNA nanocomplexes. ACS NANO 2012; 6:6133-41. [PMID: 22693946 PMCID: PMC3404193 DOI: 10.1021/nn3013838] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The assembly, stability, and timely disassembly of short interfering RNA (siRNA) nanocomplexes have the potential to affect the efficiency of siRNA delivery and gene silencing. As such, the design of new probes that can measure these properties without significantly perturbing the nanocomplexes or their environment may facilitate the study and further development of new siRNA nanocomplexes. Herein, we study Förster resonance energy transfer (FRET)-labeled siRNA probes that can track the assembly, stability, and disassembly of siRNA nanocomplexes in different environments. The probe is composed of two identical siRNAs, each labeled with a fluorophore. Upon nanocomplex formation, the siRNA-bound fluorophores become locally aggregated within the nanocomplex and undergo FRET. A key advantage of this technique is that the delivery vehicle (DV) need not be labeled, thus enabling the characterization of a large variety of nanocarriers, some of which may be difficult or even impossible to label. We demonstrate proof-of-concept by measuring the assembly of various DVs with siRNAs and show good agreement with gel electrophoresis experiments. As a consequence of not having to label the DV, we are able to determine nanocomplex biophysical parameters such as the extracellular apparent dissociation constants (K(D)) and intracellular disassembly half-life for several in-house and proprietary commercial DVs. Furthermore, the lack of DV modification allows for a true direct comparison between DVs as well as correlation between their biophysical properties and gene silencing.
Collapse
Affiliation(s)
- Christopher A. Alabi
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin T. Love
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gaurav Sahay
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Tina Stutzman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Whitney T. Young
- Department of Biological Engineering, University of Toledo, Toledo, OH 43606, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT divison of Health Sciences & Technology, Cambridge, MA 02139, USA
| | - Daniel G. Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT divison of Health Sciences & Technology, Cambridge, MA 02139, USA
| |
Collapse
|
8
|
Moriyama R, Shimada N, Kano A, Maruyama A. The role of cationic comb-type copolymers in chaperoning DNA annealing. Biomaterials 2011; 32:7671-6. [DOI: 10.1016/j.biomaterials.2011.06.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/23/2011] [Indexed: 02/05/2023]
|
9
|
Makita N, Yoshikawa Y, Takenaka Y, Sakaue T, Suzuki M, Watanabe C, Kanai T, Kanbe T, Imanaka T, Yoshikawa K. Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex. J Phys Chem B 2011; 115:4453-9. [PMID: 21446742 DOI: 10.1021/jp111331q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We observed single DNA molecules by fluorescence microscopy to clarify the effect of protamine on their higher-order structure. With an increase in the protamine concentration, the conformation of DNA molecules changes from an elongated coil state to a compact state through an intermediate state. Furthermore, the long-axis length of DNA gradually decreases while maintaining a distribution profile with a single peak. Such behavior is markedly different from the conformational transition of DNA induced by small polyamines such as spermidine and spermine, where individual DNA molecules exhibit an all-or-none transition from a coil to a globule state and the size distribution is characterized by twin peaks around the transition region. Next, we examined the effect of salt on the conformation of the DNA-protamine complex. Interestingly, at a fixed concentration of protamine, DNA tends to shrink with an increase in the NaCl concentration up to 300 mM, and then swells with a further increase in the NaCl concentration, that is, biphasic behavior is generated depending on the salt concentration. For comparison, we examined the effect of salt on DNA compaction induced by the trivalent polyamine spermidine. We confirmed that salt always has an inhibitory effect on spermine-induced compaction. To clarify this biphasic effect of salt on protamine-induced DNA compaction, we performed a numerical simulation on a negatively charged semiflexible polyelectrolyte in the presence of polycations with relatively large numbers of positive charges by taking into account the effect of salt at different concentrations. The results showed that salt promotes compaction up to a certain concentration and then tends to unfold the polyelectrolyte chain, which reproduced the experimental observation in a semiquantitative manner. This biphasic effect is discussed in relation to the specific shielding effect that depends on the salt concentration.
Collapse
Affiliation(s)
- Naoko Makita
- Faculty of Environmental and Information Sciences, Yokkaichi University, Yokkaichi, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Abstract
Toroids are small donut shaped organizational units within sperm chromatin and viruses containing DNA and protein. Investigators first characterized the dimensions of toroids created in vitro, in viruses and in decondensed sperm chromatin using transmission electron and atomic force microscopy. More recent measurements, performed using cryo-electron microscopy, have allowed experimenters to observe the hexagonal organization of DNA within viruses, and toroids created from DNA and cobalt hexammine. However, it has been difficult to obtain information about the assembly of DNA into a toroid, its structure and the biomechanical forces involved because of the limitations of these techniques. Similarly, biophysical studies of toroids utilizing techniques such as circular dichroism or light scattering are difficult to perform and interpret because toroids created using bulk DNA can aggregate and precipitate out of solution even at very low concentrations. The development of optical and magnetic traps has allowed experimenters to manipulate single DNA molecules within microfluidic, multichannel flow cells and measure the structural changes they undergo as they are transformed into toroids. During the past few years investigators have demonstrated that toroids consist of loops of DNA. They have observed the stepwise incorporation of these loops into a toroid that is not in contact with charged surfaces, which might affect its formation. The condensation of a constrained DNA molecule into a toroid was observed to significantly increase its tension, which reduced the size of the DNA loops that form the toroid. This structural information is important for understanding how genomic DNA is assembled and organized within the sperm cell and viruses. In this perspective we discuss what is known about the structure and formation of toroids, what has been learned recently using single molecule techniques and what remaining questions have the potential to be answered using these emerging technologies.
Collapse
Affiliation(s)
- Laurence R Brewer
- The Voiland School of Chemical Engineering and Bioengineering, Center for Reproductive Biology, Washington State University, Pullman, WA 99164-2710, USA.
| |
Collapse
|
11
|
Condensed DNA: condensing the concepts. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 105:208-22. [PMID: 20638406 DOI: 10.1016/j.pbiomolbio.2010.07.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/11/2010] [Indexed: 01/09/2023]
Abstract
DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.
Collapse
|
12
|
Toma AC, de Frutos M, Livolant F, Raspaud E. DNA Condensed by Protamine: A “Short” or “Long” Polycation Behavior. Biomacromolecules 2009; 10:2129-34. [DOI: 10.1021/bm900275s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adriana C. Toma
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Marta de Frutos
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405 Orsay Cedex, France
| |
Collapse
|
13
|
Ye J, Wang A, Liu C, Chen Z, Zhang N. Anionic solid lipid nanoparticles supported on protamine/DNA complexes. NANOTECHNOLOGY 2008; 19:285708. [PMID: 21828742 DOI: 10.1088/0957-4484/19/28/285708] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The objective of this study was to design novel anionic ternary nanoparticles for gene delivery. These ternary nanoparticles were equipped with protamine/DNA binary complexes (150-200 nm) as the support, and the anionic formation was achieved by absorption of anionic solid lipid nanoparticles (≤20 nm) onto the surface of the binary complexes. The small solid lipid nanoparticles (SLNs) were prepared by a modified film dispersion-ultrasonication method, and adsorption of the anionic SLNs onto the binary complexes was typically carried out in water via electrostatic interaction. The formulated ternary nanoparticles were found to be relatively uniform in size (257.7 ± 10.6 nm) with a 'bumpy' surface, and the surface charge inversion from 19.28 ± 1.14 mV to -17.16 ± 1.92 mV could be considered as evidence of the formation of the ternary nanoparticles. The fluorescence intensity measurements from three batches of the ternary nanoparticles gave a mean adsorption efficiency of 96.75 ± 1.13%. Circular dichroism spectra analysis showed that the protamine/DNA complexes had been coated by small SLNs, and that the anionic ternary nanoparticles formed did not disturb the construction of the binary complexes. SYBR Green I analysis suggested that the ternary nanoparticles could protect the DNA from nuclease degradation, and cell viability assay results showed that they exhibit lower cytotoxicity to A549 cells compared with the binary complexes and lipofectamine. The transfection efficiency of the ternary nanoparticles was better than that of naked DNA and the binary complexes, and almost equal to that of lipofectamine/DNA complexes, as revealed by inversion fluorescence microscope observation. These results indicated that the anionic ternary nanoparticles could facilitate gene transfer in cultured cells, and might alleviate the drawbacks of the conventional cationic vector/DNA complexes for gene delivery in vivo.
Collapse
Affiliation(s)
- Jiesheng Ye
- School of Pharmaceutical Science, Shandong University, 44 Wenhua Xi Road, Ji'nan, People's Republic of China
| | | | | | | | | |
Collapse
|
14
|
Wei Y, Qu MH, Wang XS, Chen L, Wang DL, Liu Y, Hua Q, He RQ. Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation. PLoS One 2008; 3:e2600. [PMID: 18596978 PMCID: PMC2432501 DOI: 10.1371/journal.pone.0002600] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 06/03/2008] [Indexed: 11/22/2022] Open
Abstract
Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H2O2/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.
Collapse
Affiliation(s)
- Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Hua Qu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing-Sheng Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lan Chen
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dong-Liang Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qian Hua
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Preclinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Rong-Qiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
15
|
Vorob’ev EA, Nechipurenko YD, Salyanov VI, Evdokimov YM. Description of chitosan binding to DNA at varied ionic strength within the framework of ion condensation and adsorption theories. Biophysics (Nagoya-shi) 2007. [DOI: 10.1134/s0006350907040045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
Teif VB. Ligand-induced DNA condensation: choosing the model. Biophys J 2005; 89:2574-87. [PMID: 16085765 PMCID: PMC1366757 DOI: 10.1529/biophysj.105.063909] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 07/18/2005] [Indexed: 11/18/2022] Open
Abstract
We test and compare different models for ligand-induced DNA condensation. Using 14C-labeled spermidine3+, we measure the binding to condensed DNA at micromolar to molar polyamine concentrations. DNA aggregates at a critical polyamine concentration. Spermidine3+ binding becomes highly cooperative at the onset of aggregation. At higher concentrations, spermidine3+ binding to condensed DNA reaches a plateau with the degree of binding equal to 0.7 (NH(4+)/PO3-). Condensed DNA exists in a wide range of spermidine concentrations with the roughly constant degree of ligand binding. At greater concentrations, the degree of binding increases again. Further spermidine penetration between the double helices causes DNA resolubilization. We show that a simple two-state model without ligand-ligand interactions qualitatively predicts the reentrant aggregation-resolubilization behavior and the dependence on the ligand, Na+, and DNA concentrations. However, such models are inconsistent with the cooperative ligand binding to condensed DNA. Including the contact or long-range ligand-ligand interactions improves the coincidence with the experiments, if binding to condensed DNA is slightly more cooperative than to the starting DNA. For example, in the contact interaction model it is equivalent to an additional McGhee-von Hippel cooperativity parameter of approximately 2. Possible physical mechanisms for the observed cooperativity of ligand binding are discussed.
Collapse
Affiliation(s)
- Vladimir B Teif
- Laboratory of Nucleoprotein Biophysics and Biochemistry, Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Minsk, Belarus
| |
Collapse
|
17
|
Abstract
The term "chromosomics" is introduced to draw attention to the three-dimensional morphological changes in chromosomes that are essential elements in gene regulation. Chromosomics deals with the plasticity of chromosomes in relation to the three-dimensional positions of genes, which affect cell function in a developmental and tissue-specific manner during the cell cycle. It also deals with species-specific differences in the architecture of chromosomes, which has been overlooked in the past. Chromosomics includes research into chromatin-modification-mediated changes in the architecture of chromosomes, which may influence the functions and life-spans of cells, tissues, organs and individuals. It also addresses the occurrence and prevalence of chromosomal gaps and breaks.
Collapse
Affiliation(s)
- U Claussen
- Institute of Human Genetics and Anthropology, Jena, Germany.
| |
Collapse
|
18
|
Hackl EV, Kornilova SV, Blagoi YP. DNA structural transitions induced by divalent metal ions in aqueous solutions. Int J Biol Macromol 2005; 35:175-91. [PMID: 15811473 DOI: 10.1016/j.ijbiomac.2005.01.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 01/20/2005] [Accepted: 01/20/2005] [Indexed: 10/25/2022]
Abstract
Using methods of IR spectroscopy, light scattering, gel-electrophoresis DNA structural transitions are studied under the action of Cu2+, Zn2+, Mn2+, Ca2+ and Mg2+ ions in aqueous solution. Cu2+, Zn2+, Mn2+ and Ca2+ ions bind both to DNA phosphate groups and bases while Mg2+ ions-only to phosphate groups of DNA. Upon interaction with divalent metal ions studied (except for Mg2+ ions) DNA undergoes structural transition into a compact form. DNA compaction is characterized by a drastic decrease in the volume occupied by DNA molecules with reversible formation of DNA dense particles of well-defined finite size and ordered morphology. The DNA secondary structure in condensed particles corresponds to the B-form family. The mechanism of DNA compaction under Mt2+ ion action is not dominated by electrostatics. The effectiveness of the divalent metal ions studied to induce DNA compaction correlates with the affinity of these ions for DNA nucleic bases: Cu2+>>Zn2+>Mn2+>Ca2+>>Mg2+. Mt2+ ion interaction with DNA bases (or Mt2+ chelation with a base and an oxygen of a phosphate group) may be responsible for DNA compaction. Mt2+ ion interaction with DNA bases can destabilize DNA causing bends and reducing its persistent length that will facilitate DNA compaction.
Collapse
Affiliation(s)
- Elene V Hackl
- B.I. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47 Lenin Avenue, 61164 Kharkov, Ukraine.
| | | | | |
Collapse
|
19
|
Hackl EV, Galkin VL, Blagoi YP. DNA interaction with biologically active divalent metal ions: binding constants calculation. Int J Biol Macromol 2004; 34:303-8. [PMID: 15556232 DOI: 10.1016/j.ijbiomac.2004.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In our previous work we have shown that under the action of Cu2+, Mn2+ and Ca2+ ions DNA is able to transit into a compact state in aqueous solution. In the present work we carried out calculations of binding constants for divalent metal ions interacting with DNA in terms of the macromolecule statistical sum. The formula for calculation of the binding constants and cooperativity parameters was proposed. It was shown that on the "coil state"-"compact (globule) state" transition a single DNA molecule may undergo the first-order phase transition while the transition of the assembly of average DNA chains is of sigmoidal character typical of the cooperative and continuous transition.
Collapse
Affiliation(s)
- Elene V Hackl
- BI Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 61164 Kharkov, Ukraine.
| | | | | |
Collapse
|
20
|
Distler AM, Allison J. Additives for the stabilization of double-stranded DNA in UV-MALDI MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:1129-1137. [PMID: 12322960 DOI: 10.1016/s1044-0305(02)00430-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular complexes such as double-stranded oligonucleotides contain non-covalent bonds that are difficult to maintain in the MALDI experiment. Quantifiers are introduced in order to evaluate, summarize, and compare spectra from experiments in which additives are used to stabilize duplex oligonucleotides. Compounds known to complex with and stabilize duplex molecules can be useful as additives in MALDI. Spermine and methylene blue, present at concentrations similar to the matrix, are detected, bound to the duplex. When peptides are used as additives, the duplex is stabilized when the peptide is present at an amount less than that of the duplex.
Collapse
Affiliation(s)
- Anne M Distler
- Department of Chemistry, Michigan University, East Lansing 48824, USA
| | | |
Collapse
|
21
|
Mikheikin AL, Streltsov SA, Zasedatelev AS, Nabiev IR. Mixed mode of ligand-DNA binding results in S-shaped binding curves. J Biomol Struct Dyn 2001; 18:703-8. [PMID: 11334107 DOI: 10.1080/07391102.2001.10506700] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
S-shaped binding curves often characterize interactions of ligands with nucleic acid molecules as analyzed by different physico-chemical and biophysical techniques. S-shaped experimental binding curves are usually interpreted as indicative of the positive cooperative interactions between the bound ligand molecules. This paper demonstrates that S-shaped binding curves may occur as a result of the "mixed mode" of DNA binding by the same ligand molecule. Mixed mode of the ligand-DNA binding can occur, for example, due to 1) isomerization or dimerization of the ligands in solution or on the DNA lattice, 2) their ability to intercalate the DNA and to bind it within the minor groove in different orientations. DNA-ligand complexes are characterized by the length of the ligand binding site on the DNA lattice (so-called "multiple-contact" model). We show here that if two or more complexes with different lengths of the ligand binding sites could be produced by the same ligand, the dependence of the concentration of the complex with the shorter length of binding site on the total concentration of ligand should be S-shaped. Our theoretical model is confirmed by comparison of the calculated and experimental CD binding curves for bis-netropsin binding to poly(dA-dT) poly(dA-dT). Bis-netropsin forms two types of DNA complexes due to its ability to interact with the DNA as monomers and trimers. Experimental S-shaped bis-netropsin-DNA binding curve is shown to be in good correlation with those calculated on the basis of our theoretical model. The present work provides new insight into the analysis of ligand-DNA binding curves.
Collapse
|
22
|
Brewer LR, Corzett M, Balhorn R. Protamine-induced condensation and decondensation of the same DNA molecule. Science 1999; 286:120-3. [PMID: 10506559 DOI: 10.1126/science.286.5437.120] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The DNA in sperm and certain viruses is condensed by arginine-rich proteins into toroidal subunits, a form of packaging that inactivates their entire genome. Individual DNA molecules were manipulated with an optical trap to examine the kinetics of torus formation induced by the binding of protamine and a subset of its DNA binding domain, Arg6. Condensation and decondensation experiments with lambda-phage DNA show that toroid formation and stability are influenced by the number of arginine-rich anchoring domains in protamine. The results explain why protamines contain so much arginine and suggest that these proteins must be actively removed from sperm chromatin after fertilization.
Collapse
Affiliation(s)
- L R Brewer
- Electronics Engineering Technologies Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | | | | |
Collapse
|
23
|
Stoylov S, Stoylova E, Todorov R, Schmiedel P, Thunig C, Hoffmann H, Roques BP, Le Cam E, Coulaud D, Delain E, Gérard D, Mély Y. Aggregation of polyA–HIV-1 nucleocapsid protein NCp7 complexes and properties of the aggregates. Colloids Surf A Physicochem Eng Asp 1999. [DOI: 10.1016/s0927-7757(98)00674-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
24
|
van Lieshout E, Hemminga MA. NMR study on the binding of d(GGAAATTTCC)2 with a positively charged pentacosapeptide. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1442:137-47. [PMID: 9804928 DOI: 10.1016/s0167-4781(98)00157-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
To obtain a better understanding of the electrostatic nature of protein-nucleic acid interactions, we have investigated the interaction of a double-stranded decamer d(GGAAATTTCC)2 with a synthetic arginine and lysine-rich pentacosapeptide (Pep25), using NMR and optical spectroscopy. The chemical shift data of the decamer under various experimental conditions show that the binding of Pep25 changes the conformation of the decamer in a different way, as compared to the conformational changes induced by a variation in temperature or ionic strength. The chemical shift results are interpreted in terms of ring current effects that emerge into a model for the conformational change, in which the double-stranded helix of the decamer undergoes a decrease of twist and rise to accommodate Pep25. The binding results indicate that the positively charged arginine and lysine side chains of Pep25 not only have a stabilising electrostatic interaction with the negatively charged backbone phosphates of d(GGAAATTTCC)2, but also that a stabilisation of the base pairs of d(GGAAATTTCC)2 by Pep25 takes place.
Collapse
Affiliation(s)
- E van Lieshout
- Department of Molecular Physics, Wageningen Agricultural University, Dreijenlaan 3, 6703 HA Wageningen, Netherlands
| | | |
Collapse
|
25
|
Abstract
We have examined the equilibrium binding of a series of synthetic oligoarginines (net charge z = +2 to +6) containing tryptophan to poly(U), poly(A), poly(C), poly(I), and double-stranded (ds) DNA. Equilibrium association constants, K(obs), measured by monitoring tryptophan fluorescence quenching, were examined as functions of monovalent salt (MX) concentration and type, as well as temperature, from which deltaG(standard)obs, deltaH(obs), and deltaS(standard)obs were determined. For each peptide, K(obs) decreases with increasing [K+], and the magnitude of the dependence of K(obs) on [K+], delta log K(obs)/delta log[K+], increases with increasing net peptide charge. In fact, the values of delta log K(obs)/delta log[K+] are equivalent for oligolysines and oligoarginines possessing the same net positive charge. However, the values of K(obs) are systematically greater for oligoarginines binding to all polynucleotides, when compared to oligolysines with the same net charge. The origin of this difference is entirely enthalpic, with deltaH(obs), determined from van't Hoff analysis, being more exothermic for oligoarginine binding. The values of deltaH(obs) are also independent of [K+]; therefore, the salt concentration dependence of deltaG(standard)obs is entirely entropic in origin, reflecting the release of cations from the nucleic acid upon complex formation. These results suggest that hydrogen bonding of arginine to the phosphate backbone of the nucleic acids contributes to the increased stability of these complexes.
Collapse
Affiliation(s)
- D P Mascotti
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | |
Collapse
|
26
|
Werstuck G, Zapp ML, Green MR. A non-canonical base pair within the human immunodeficiency virus rev-responsive element is involved in both rev and small molecule recognition. CHEMISTRY & BIOLOGY 1996; 3:129-37. [PMID: 8807838 DOI: 10.1016/s1074-5521(96)90289-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) replication depends on the interaction of an HIV regulatory protein, Rev, with a viral RNA element (the Rev-responsive element, RRE). The high affinity RRE core region contains a non-canonical base pair (G48:G71) that is important for Rev recognition. Aminoglycoside antibiotics, specifically neomycin B, bind to the RRE and selectively block Rev-RRE interactions in vivo and in vitro. We attempted to generate an in vitro model for the establishment of HIV-1 resistance to neomycin B. RESULTS We have used in vitro genetic selection to evolve RRE variants that bind to Rev in the presence of neomycin B. Most of the RRE variants selected in the presence of 10 microM neomycin B contain a G48:G71 to A48:A71 substitution. Those selected in 100 microM neomycin B contain either C:A or A:A substitutions at this position. Binding constants for the interaction of neomycin B with the wild-type RRE and a subset of the selected RRE variants were determined using a novel ultrafiltration procedure. CONCLUSIONS A purine-purine base pair within the bulge region of the RRE core elements is critical for neomycin B binding as well as Rev binding. RRE variants that survive in high concentrations of neomycin do so either by binding Rev better than wild-type (this correlates with the sequence A48:A71) or by binding neomycin poorly (correlating with the sequence C48:A71). Other sequences must also influence both Rev and neomycin B binding.
Collapse
Affiliation(s)
- G Werstuck
- Program in Molecular Medicine, Howard Hughes Medical Institute, UMASS Medical Center, Worcester, MA, 01605, USA
| | | | | |
Collapse
|