1
|
Penkova NA, Sharapov MG, Penkov NV. Hydration Shells of DNA from the Point of View of Terahertz Time-Domain Spectroscopy. Int J Mol Sci 2021; 22:ijms222011089. [PMID: 34681747 PMCID: PMC8538832 DOI: 10.3390/ijms222011089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 11/16/2022] Open
Abstract
Hydration plays a fundamental role in DNA structure and functioning. However, the hydration shell has been studied only up to the scale of 10-20 water molecules per nucleotide. In the current work, hydration shells of DNA were studied in a solution by terahertz time-domain spectroscopy. The THz spectra of three DNA solutions (in water, 40 mm MgCl2 and 150 mM KCl) were transformed using an effective medium model to obtain dielectric permittivities of the water phase of solutions. Then, the parameters of two relaxation bands related to bound and free water molecules, as well as to intermolecular oscillations, were calculated. The hydration shells of DNA differ from undisturbed water by the presence of strongly bound water molecules, a higher number of free molecules and an increased number of hydrogen bonds. The presence of 40 mM MgCl2 in the solution almost does not alter the hydration shell parameters. At the same time, 150 mM KCl significantly attenuates all the found effects of hydration. Different effects of salts on hydration cannot be explained by the difference in ionic strength of solutions, they should be attributed to the specific action of Mg2+ and K+ ions. The obtained results significantly expand the existing knowledge about DNA hydration and demonstrate a high potential for using the THz time-domain spectroscopy method.
Collapse
Affiliation(s)
- Nadezda A. Penkova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Mars G. Sharapov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
| | - Nikita V. Penkov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
- Correspondence:
| |
Collapse
|
2
|
Zhong J, Kankala RK, Wang SB, Chen AZ. Recent Advances in Polymeric Nanocomposites of Metal-Organic Frameworks (MOFs). Polymers (Basel) 2019; 11:E1627. [PMID: 31600886 PMCID: PMC6836088 DOI: 10.3390/polym11101627] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/25/2019] [Accepted: 10/03/2019] [Indexed: 12/25/2022] Open
Abstract
Recently, metal-organic frameworks (MOFs) have garnered enormous attention from researchers owing to their superior physicochemical properties, which are of particular interest in various fields such as catalysis and the diverse areas of biomedicine. Despite their position in the utilization for various applications compared to other innovative nanocarriers such as dendrimers and mesoporous silica nanoparticles (MSNs), in terms of advantageous physicochemical attributes, as well as attractive textural properties, ease of characterization, and abundant surface chemistry for functionalization and other benefits, MOFs yet suffer from several issues such as poor degradability, which might lead to accumulation-induced biocompatibility risk. In addition, some of the MOFs suffer from a shortcoming of poor colloidal stability in the aqueous solution, hindering their applicability in diverse biomedical fields. To address these limitations, several advancements have been made to fabricate polymeric nanocomposites of MOFs for their utility in various biomedical fields. In this review, we aim to provide a brief emphasis on various organic polymers used for coating over MOFs to improve their physicochemical attributes considering a series of recently reported intriguing studies. Finally, we summarize with perspectives.
Collapse
Affiliation(s)
- Jun Zhong
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, China.
| | - Ranjith Kumar Kankala
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, China.
- College of Chemical Engineering Huaqiao University, Xiamen 361021, China.
- Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, China.
| | - Shi-Bin Wang
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, China.
- College of Chemical Engineering Huaqiao University, Xiamen 361021, China.
- Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, China.
| | - Ai-Zheng Chen
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, China.
- College of Chemical Engineering Huaqiao University, Xiamen 361021, China.
- Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, China.
| |
Collapse
|
3
|
Sticking and stacking: Persistent ordering of fragmented DNA analogs. Proc Natl Acad Sci U S A 2018; 115:8652-8654. [PMID: 30093389 DOI: 10.1073/pnas.1810662115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
4
|
Podgornik R, Aksoyoglu MA, Yasar S, Svenšek D, Parsegian VA. DNA Equation of State: In Vitro vs In Viro. J Phys Chem B 2016; 120:6051-60. [DOI: 10.1021/acs.jpcb.6b02017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rudolf Podgornik
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - M. Alphan Aksoyoglu
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Selcuk Yasar
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Daniel Svenšek
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - V. Adrian Parsegian
- Department
of Physics, University of Massachusetts, Amherst, Massachusetts 01003, United States
| |
Collapse
|
5
|
Niessen KA, Xu M, Markelz AG. Terahertz optical measurements of correlated motions with possible allosteric function. Biophys Rev 2015; 7:201-216. [PMID: 28510171 DOI: 10.1007/s12551-015-0168-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/26/2015] [Indexed: 10/23/2022] Open
Abstract
A suggested mechanism for allosteric response is the distortion of the energy landscape with agonist binding changing the protein structure's access to functional configurations. Intramolecular vibrations are indicative of the energy landscape and may have trajectories that enable functional conformational change. Here, we discuss the development of an optical method to measure the intramolecular vibrations in proteins, namely, crystal anisotropy terahertz microscopy, and the various approaches which can be used to identify the spectral data with specific structural motions.
Collapse
Affiliation(s)
- Katherine A Niessen
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA
| | - Mengyang Xu
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA
| | - A G Markelz
- Department of Physics, University at Buffalo (SUNY), Buffalo, NY, 14260, USA.
| |
Collapse
|
6
|
Yasar S, Podgornik R, Valle-Orero J, Johnson MR, Parsegian VA. Continuity of states between the cholesteric → line hexatic transition and the condensation transition in DNA solutions. Sci Rep 2014; 4:6877. [PMID: 25371012 PMCID: PMC4220286 DOI: 10.1038/srep06877] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/12/2014] [Indexed: 11/25/2022] Open
Abstract
A new method of finely temperature-tuning osmotic pressure allows one to identify the cholesteric → line hexatic transition of oriented or unoriented long-fragment DNA bundles in monovalent salt solutions as first order, with a small but finite volume discontinuity. This transition is similar to the osmotic pressure-induced expanded → condensed DNA transition in polyvalent salt solutions at small enough polyvalent salt concentrations. Therefore there exists a continuity of states between the two. This finding, together with the corresponding empirical equation of state, effectively relates the phase diagram of DNA solutions for monovalent salts to that for polyvalent salts and sheds some light on the complicated interactions between DNA molecules at high densities.
Collapse
Affiliation(s)
- Selcuk Yasar
- Department of Physics, University of Massachusetts, Amherst, MA 01003, United States
| | - Rudolf Podgornik
- 1] Department of Physics, University of Massachusetts, Amherst, MA 01003, United States [2] Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia [3] Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jessica Valle-Orero
- 1] Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France [2] Laboratoire de Physique, Ecole Normale Superiéure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mark R Johnson
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP156 38042, Grenoble, France
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, MA 01003, United States
| |
Collapse
|
7
|
Kahouli A, Valle-Orero J, Garden JL, Peyrard M. Ionic mobility in DNA films studied by dielectric spectroscopy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2014; 37:39. [PMID: 25260324 DOI: 10.1140/epje/i2014-14082-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/14/2014] [Accepted: 09/08/2014] [Indexed: 06/03/2023]
Abstract
Double-helix DNA molecules can be found under different conformational structures driven by ionic and hydration surroundings. Usually, only the B-form of DNA, which is the only form stable in aqueous solution, can be studied by dielectric measurements. Here, the dielectric responses of DNA molecules in the A- and B-form, oriented co-linearly within fibres assembled in a film have been analyzed. The dielectric dispersion, permittivity and dissipation factor, have been measured as a function of frequency, strength voltage, time, temperature and nature of the counter-ions. Besides a high electrode polarization component, two relaxation peaks have been observed and fitted by two Cole-Cole relaxation terms. In the frequency range that we investigated (0.1 Hz to 5 ·10(6) Hz) the dielectric properties are dominated by the mobility and diffusivity of the counter-ions and their interactions with the DNA molecules, which can therefore be characterized for the A- and B-forms of DNA.
Collapse
Affiliation(s)
- Abdelkader Kahouli
- Grenoble Electrical Engineering Laboratory (G2ELab), Université Joseph Fourier, 25 rue des Martyrs, 38042, Grenoble cedex 9, France
| | | | | | | |
Collapse
|
8
|
Koontz C, Lee S. Low-frequency Raman scattering study of six nucleosides. J Biomol Struct Dyn 2014; 32:1148-54. [DOI: 10.1080/07391102.2013.802996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
9
|
Longo M, Marconi M, Orecchini A, Petrillo C, Monaco G, Calvitti M, Pirisinu I, Romani R, Sacchetti F, Sebastiani F, Zanatta M, Paciaroni A. Terahertz Dynamics in Human Cells and Their Chromatin. J Phys Chem Lett 2014; 5:2177-2181. [PMID: 26279530 DOI: 10.1021/jz500918w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.
Collapse
Affiliation(s)
- M Longo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ‡Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - M Marconi
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Orecchini
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - C Petrillo
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - G Monaco
- §Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - M Calvitti
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - I Pirisinu
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - R Romani
- ∥Dipartimento di Medicina Sperimentale, Università degli Studi di Perugia, Sant'Andrea delle Fratte, I-06132 Perugia, Italy
| | - F Sacchetti
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - F Sebastiani
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
- ⊥CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - M Zanatta
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| | - A Paciaroni
- †Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli I-06123 Perugia, Italy
| |
Collapse
|
10
|
Kulkarni M, Mukherjee A. Sequence dependent free energy profiles of localized B- to A-form transition of DNA in water. J Chem Phys 2014; 139:155102. [PMID: 24160545 DOI: 10.1063/1.4825175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA carries an inherent polymorphism, which surfaces under various external conditions. While B-form remains predominant under normal physiological conditions for most of the DNA sequences, low humidity and increased ion concentration cause B- to A-form transition. Certain proteins and molecules also sometimes cause local deformation of the DNA to the specific A-form. Previous experimental and computational studies focused on the overall B- to A-form transition. Here for the first time we investigated thermodynamics and mechanism of B- to A-form transition in water for various DNA sequences at a local dinucleotide base pair level. We introduced a new reaction coordinate Zp', based on the unique order parameter Zp, to drive B- to A-form transition locally and thereby calculate free energy profiles for the same for all the ten different dinucleotide steps embedded in a twelve base pair DNA. Results show that the trend of "A" and "B" philicity observed in experiment is preserved even at this local dinucleotide level, indicating its localized origin. Higher free energy cost obtained here is attributed to the cost of creating B∕A junctions along with formation of B->A transition at dimer level. We find that while water energetically stabilizes A-form for all the ten different dinucleotide steps to various extents, entropy acts against it. Therefore, we find that the stability of B-form DNA in water is entropic in origin. Mechanism of the conversion appears to be triggered by Slide; however, backbone parameters change concertedly.
Collapse
Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | | |
Collapse
|
11
|
Lee SA, Pinnick DA, Anderson A. A study of the eigenvectors of the low-frequency vibrational modes in crystalline adenosine via high pressure Raman spectroscopy. J Biomol Struct Dyn 2013; 32:2051-7. [PMID: 24127792 DOI: 10.1080/07391102.2013.845855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
High-pressure Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline adenosine at 295 K by evaluating the logarithmic derivative of the vibrational frequency with respect to pressure: [Formula: see text]. Crystalline samples of molecular materials such as adenosine will have vibrational modes that are localized within a molecular unit ("internal" modes) as well as modes in which the molecular units vibrate against each other ("external" modes). The value of the logarithmic derivative is found to be a diagnostic probe of the nature of the eigenvector of the vibrational modes. Stretching modes which are predominantly internal to the molecule have low logarithmic derivatives while external modes have higher logarithmic derivatives. Particular interest is paid to the low-frequency (≤150 cm(-1)) modes. Based on the pressure dependence of its logarithmic derivative, a mode near 49 cm(-1) is identified as internal mode. The other modes below 400 cm(-1) have pressure dependences of their logarithmic derivatives consistent with being either (1) modes which are mainly external, meaning that the molecules of the unit cell vibrate against each other in translational or librational motions (or linear combinations thereof), or (2) torsional or bending modes involving a large number of atoms, mainly within a molecule. The modes above 400 cm(-1) all have pressure dependences of their logarithmic derivatives consistent with being mainly internal modes.
Collapse
Affiliation(s)
- Scott A Lee
- a Department of Physics & Astronomy , University of Toledo , Toledo , OH 43606 , USA
| | | | | |
Collapse
|
12
|
Kaur P, Plochberger B, Costa P, Cope SM, Vaiana SM, Lindsay S. Hydrophobicity of methylated DNA as a possible mechanism for gene silencing. Phys Biol 2012. [PMID: 23196865 DOI: 10.1088/1478-3975/9/6/065001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
AFM images show that chromatin reconstituted on methylated DNA (meDNA) is compacted when imaged under water. Chromatin reconstituted on unmethylated DNA is less compacted and less sensitive to hydration. These differences must reflect changes in the physical properties of DNA on methylation, but prior studies have not revealed large differences between methylated and unmethylated DNA. Quasi-elastic light scattering studies of solutions of methylated and unmethylated DNA support this view. In contrast, AFM images of molecules at a water/solid interface yield a persistence length that nearly doubles (to 92.5 ± 4 nm) when 9% of the total DNA is methylated. This increase in persistence length is accompanied by a decrease in contour length, suggesting that a significant fraction of the meDNA changes into the stiffer A form as the more hydrophobic meDNA is dehydrated at the interface. This suggests a simple mechanism for gene silencing as the stiffer meDNA is more difficult to remove from nucleosomes.
Collapse
Affiliation(s)
- Parminder Kaur
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | | | | | | | | | | |
Collapse
|
13
|
Lee SA, Tao NJ, Rupprecht A. A Raman scattering study of the interactions of DNA with its water of hydration. J Biomol Struct Dyn 2012; 31:1337-42. [PMID: 23140399 DOI: 10.1080/07391102.2012.736759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The ∼ 3450 cm(-1) molecular O-H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3 Å shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.
Collapse
Affiliation(s)
- Scott A Lee
- a Department of Physics & Astronomy , University of Toledo , M.S. #111, Toledo , OH , 43606 , USA
| | | | | |
Collapse
|
14
|
Hanczyc P, Akerman B, Nordén B. Short oligonucleotides aligned in stretched humid matrix: secondary DNA structure in poly(vinyl alcohol) environment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6662-6669. [PMID: 22452613 DOI: 10.1021/la300960q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins.
Collapse
Affiliation(s)
- Piotr Hanczyc
- Department of Chemical and Biological Engineering, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | | | | |
Collapse
|
15
|
Wildes A, Theodorakopoulos N, Valle-Orero J, Cuesta-López S, Garden JL, Peyrard M. Structural correlations and melting of B-DNA fibers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061923. [PMID: 21797419 DOI: 10.1103/physreve.83.061923] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Indexed: 05/31/2023]
Abstract
Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured. These results, complemented by a differential calorimetry study of the melting of B-DNA fibers as well as electrophoresis and optical observation data, are analyzed in terms of a one-dimensional mesoscopic model of DNA.
Collapse
|
16
|
Asenbaum A, Pruner C, Schröer H, Plätzer K, Bieler L, Brandstetter H, Schirmacher W, Schulte A, Wilhelm E. Rayleigh and Brillouin scattering in a lysozyme–water mixture: An unusual behavior around 343K. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2010.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Smith MS, Lee SA, Rupprecht A. The Stability of the B Conformation in Wet-spun Films of CaDNA: A Raman Study as a Function of Water Content. J Biomol Struct Dyn 2009; 27:105-10. [DOI: 10.1080/07391102.2009.10507300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
18
|
Yoneda S, Sugawara Y, Urabe H. Analysis of low-frequency phonons in guanosine dihydrate based on molecular dynamics simulations. J Phys Chem A 2008; 112:7055-63. [PMID: 18610952 DOI: 10.1021/jp8017277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fourier analysis, using the atomic trajectory calculated by molecular dynamics simulation at 300 K, is applied to the study of low-frequency phonons of guanine dihydrate. The vibrational modes of guanine bases are analyzed, and the optically active modes associated with the guanine moieties are extracted. There are a few significant peaks in the low-frequency region. A possible assignment of the Raman active mode near 27 cm(-1), whose origin would be common to the S-mode of DNA double helices, is discussed.
Collapse
Affiliation(s)
- Shigetaka Yoneda
- School of Science, Kitasato University, Kitasato, Sagamihara, Kanagawa 228-8555, Japan.
| | | | | |
Collapse
|
19
|
|
20
|
Rudd L, Lee DJ, Kornyshev AA. The role of electrostatics in the B to A transition of DNA: from solution to assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:416103. [PMID: 28192335 DOI: 10.1088/0953-8984/19/41/416103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
On the basis of a wealth of published experimental data and computer simulations, we build a simple physical model that allows us to rationalize the A to B transition of DNA in solution and in aggregates. In both cases we find that the electrostatic interactions are strong enough, alone, to induce the transition independently of other energetic contributions, e.g. those related to hydration. On the basis of this analysis we conclude that in ethanol/water mixtures, the effect responsible for the transition is the reduction of dielectric constant in the mixture. This is manifested in electrostatic self-energy terms that include the interaction of phosphate charges with condensed counterions. But in dense aggregates, electrostatics plays a dual role, giving rise to two competing effects. In the absence of groove localized counterions the electrostatic self-energy favours the B form, and the electrostatic interaction energy between neighbouring DNA favours the A form. However, the addition of enough counterions localized in the narrow groove reverses this. In dry aggregates of DNA both terms, in most cases, conspire to keep DNA in the A form. The analysis gives a broad picture of the B to A transition and sets a number of new research goals, particularly concerning simulations that may test our simple model for aggregates.
Collapse
Affiliation(s)
- Laura Rudd
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ London, UK
| | | | | |
Collapse
|
21
|
Douki T, Setlow B, Setlow P. Effects of the Binding of α/β-type Small, Acid-soluble Spore Proteins on the Photochemistry of DNA in Spores of Bacillus subtilis and In Vitro¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb01536.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Samoc A, Miniewicz A, Samoc M, Grote JG. Refractive-index anisotropy and optical dispersion in films of deoxyribonucleic acid. J Appl Polym Sci 2007. [DOI: 10.1002/app.26082] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
23
|
Affiliation(s)
- X. Fang
- a Department of Polymer Science , The University of Akron , Akron, Ohio, 44325-3909
| | - D. H. Reneker
- a Department of Polymer Science , The University of Akron , Akron, Ohio, 44325-3909
| |
Collapse
|
24
|
Woods KN, Lee SA, Holman HYN, Wiedemann H. The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films. J Chem Phys 2006; 124:224706. [PMID: 16784300 DOI: 10.1063/1.2200349] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infrared spectroscopy is used to probe the dynamics of in vitro samples of DNA prepared as solutions and as solid unoriented films. The lowest frequency DNA mode identified in the far-infrared spectra of the DNA samples is found to shift in frequency when the solvent influence in the hydration shell is altered. The lowest frequency mode also has characteristics that are similar to beta-relaxations identified in other glass forming polymers.
Collapse
Affiliation(s)
- K N Woods
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
| | | | | | | |
Collapse
|
25
|
Douki T. Effect of denaturation on the photochemistry of pyrimidine bases in isolated DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2005; 82:45-52. [PMID: 16243533 DOI: 10.1016/j.jphotobiol.2005.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 08/11/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
The influence of denaturation on DNA photochemistry was studied by quantifying the yield of formation of all possible bipyrimidine photolesions within isolated genomic DNA samples exposed to UVC radiation. Effects of DNA melting was studied either by carrying out irradiation over a wide range of temperature (0-90 degrees C) or by decreasing the ionic strength of the solution at 30 degrees C. A first observation was a much larger decrease in the photoreactivity upon increasing the temperature in single-stranded than in double-stranded DNA. Secondly, formation of trans,syn cyclobutane dimers and, to a lesser extent, modification in the ratio between the yields of cyclobutane dimers and (6-4) photoproducts, were found to be other main features associated with denaturation. These results emphasize the modulating role of structure in the yield and nature of UV-induced DNA damage.
Collapse
Affiliation(s)
- Thierry Douki
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E 3 CEA-UJF, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 38054 Grenoble Cedex 9, France.
| |
Collapse
|
26
|
Nakamae S, Cazayous M, Sacuto A, Monod P, Bouchiat H. Intrinsic low temperature paramagnetism in B-DNA. PHYSICAL REVIEW LETTERS 2005; 94:248102. [PMID: 16090581 DOI: 10.1103/physrevlett.94.248102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Indexed: 05/03/2023]
Abstract
We present an experimental study of magnetization in lambda-DNA in conjunction with structural measurements. The results show the surprising interplay between the molecular structures and their magnetic property. In the B-DNA state, lambda-DNA exhibits paramagnetic behavior below 20 K that is nonlinear in an applied magnetic field whereas, in the A-DNA state, it remains diamagnetic down to 2 K. We propose orbital paramagnetism as the origin of the observed phenomena and discuss its relation to the existence of long range coherent transport in B-DNA at low temperature.
Collapse
Affiliation(s)
- S Nakamae
- Laboratoire de Matériaux et Phénomène Quantiques (UMR 7162), Université Paris 7-Denis-Diderot, Paris, France
| | | | | | | | | |
Collapse
|
27
|
Kutnjak Z, Lahajnar G, Filipic C, Podgornik R, Nordenskiöld L, Korolev N, Rupprecht A. Electrical conduction in macroscopically oriented deoxyribonucleic and hyaluronic acid samples. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 71:041901. [PMID: 15903695 DOI: 10.1103/physreve.71.041901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Indexed: 05/02/2023]
Abstract
Measurements of the quasistatic and frequency dependent electrical conductivity below 1 MHz were carried out on wet-spun, macroscopically oriented, calf thymus deoxyribonucleic (DNA) and umbilical cord hyaluronic acid (HA) bulk samples. The frequency dependence of the electrical conductivity in the frequency range of approximately 10(-3) - 10(6) Hz of both materials is surprisingly rather similar. Temperature dependence of the quasistatic electrical conductivity above the low temperature saturation plateau can be well described by the activated Arrhenius law with the activation energy of approximately 0.8 eV for both DNA and HA. We discuss the meaning of these findings for the possible conduction mechanism in these particular charged polyelectrolytes.
Collapse
Affiliation(s)
- Zdravko Kutnjak
- Department of Condensed Matter Physics, Jozef Stefan Institute, P.O. Box 3000, 1001 Ljubljana, Slovenia
| | | | | | | | | | | | | |
Collapse
|
28
|
Douki T, Setlow B, Setlow P. Effects of the Binding of α/β-type Small, Acid-soluble Spore Proteins on the Photochemistry of DNA in Spores of Bacillus subtilis and In Vitro¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-08-18-ra-278.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
29
|
Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. A molecular dynamics simulation study of polyamine? and sodium?DNA. Interplay between polyamine binding and DNA structure. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2004; 33:671-82. [PMID: 15146298 DOI: 10.1007/s00249-004-0410-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Revised: 04/02/2004] [Accepted: 04/05/2004] [Indexed: 10/26/2022]
Abstract
Four different molecular dynamics (MD) simulations have been performed for infinitely long ordered DNA molecules with different counterions, namely the two natural polyamines spermidine(3+) (Spd3+) and putrescine(2+) (Put2+), the synthetic polyamine diaminopropane(2+) (DAP2+), and the simple monovalent cation Na+. All systems comprised a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charge. The simulation setup mimics the DNA state in oriented DNA fibers, previously studied using NMR and other experimental methods. In this paper the interplay between polyamine binding and local DNA structure is analyzed by investigating how and if the minor groove width of DNA depends on the presence and dynamics of the counterions. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural [spermine(4+), Spd3+, Put2+] and the synthetic (DAP2+) polyamines.
Collapse
Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | | | | | | |
Collapse
|
30
|
Lee SL, Debenedetti PG, Errington JR, Pethica BA, Moore DJ. A Calorimetric and Spectroscopic Study of DNA at Low Hydration. J Phys Chem B 2004. [DOI: 10.1021/jp0311409] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sau Lawrence Lee
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Jeffrey R. Errington
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Brian A. Pethica
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - David J. Moore
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| |
Collapse
|
31
|
Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations. Nucleic Acids Res 2004; 31:5971-81. [PMID: 14530445 PMCID: PMC219480 DOI: 10.1093/nar/gkg802] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Four different molecular dynamics (MD) simulations have been performed for ordered DNA decamers, d(5'-ATGCAGTCAG)*d(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine3+ (Spd3+) and putrescine2+ (Put2+), the synthetic polyamine diaminopropane2+ (DAP2+) and Na+. The simulation set-up corresponds to an infinite array of parallel DNA mimicking the state in oriented DNA fibers or crystals. This work describes general properties of polyamine and Na+ binding to DNA. Simulated diffusion coefficients show satisfactory agreement with experimental NMR diffusion data of comparable systems. The interaction of the polyamines with DNA is dynamic in character and the cations mostly form short-lived contacts with the electronegative binding sites of DNA. Polyamines, Na+ and water interact most frequently with the charged phosphate atoms with preference for association from the minor groove side with O1P over O2P. There is a strong anti-correlation in the cation binding to the electronegative groups of DNA, i.e. the presence of a cation near one of the DNA sites repels other cations from binding to this and to the other sites separated by <7.5 A from each other. In contrast to the other polyamines, DAP2+ is able to form 'bridges' connecting neighboring phosphate groups along the DNA strand. A small fraction of DAP2+ and Put2+ can be found in the major grooves, while Spd3+ is absent there. The results of the MD simulations reveal principal differences in the polyamine-DNA interactions between the natural (Spd3+, Put2+ and spermine4+) and synthetic (DAP2+) polyamines.
Collapse
Affiliation(s)
- Nikolay Korolev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | | | | | | |
Collapse
|
32
|
Rupprecht A, Piškur J, Schultz J, Nordenskiöld L, Song Z, Lahajnar G. Mechanochemical study of conformational transitions and melting of Li-, Na-, K-, and CsDNA fibers in ethanol-water solutions. Biopolymers 2004. [DOI: 10.1002/bip.360340709] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
33
|
Andreasson B, Nordenskiöld L, Eriksson PO, Rupprecht A. Li+counterion self-diffusion in ordered DNA. Biopolymers 2004. [DOI: 10.1002/bip.360341205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
34
|
Weidlich T, Powell JW, Genzel L, Rupprecht A. Counterion effects on the far-IR vibrational spectra of poly(rI) · poly(rC). Biopolymers 2004. [DOI: 10.1002/bip.360300324] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
35
|
Fekete A, Rontó G, Hegedüs M, Módos K, Bérces A, Kovács G, Lammer H, Panitz C. Simulation experiments of the effect of space environment on bacteriophage and DNA thin films. ADVANCES IN SPACE RESEARCH : THE OFFICIAL JOURNAL OF THE COMMITTEE ON SPACE RESEARCH (COSPAR) 2004; 33:1306-1310. [PMID: 15806706 DOI: 10.1016/j.asr.2003.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of the genetic material is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation (lambda=254 nm) and high vacuum (10(-4) Pa). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA.
Collapse
Affiliation(s)
- A Fekete
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
The fundamental intramolecular frequency of a globular protein can be obtained from the measurements of acoustic velocities of bulk protein matter. This lowest frequency for common size molecules is shown to be above several hundred GHz. All modes below this frequency would then be intermolecular modes or bulk modes of the molecule and surrounding matter or tissue. The lowest frequency modes of an extended DNA double helix are also shown to be bulk modes because of interaction with water. Only DNA modes, whose frequency is well above 4 GHz, can be intrahelical modes, that is, confined to the helix rather than in the helix plus surroundings. Near 4 GHz, they are heavily damped and, therefore, not able to resonantly absorb. Modes that absorb radio frequency (RF) below this frequency are bulk modes of the supporting matter. Bulk modes rapidly thermalize all absorbed energy. The implication of these findings for the possibility of athermal RF effects is considered. The applicability of these findings for other biological molecules is discussed.
Collapse
Affiliation(s)
- E W Prohofsky
- Department of Physics Purdue University, W. Lafayette, Indiana 47907, USA.
| |
Collapse
|
37
|
Whitmire SE, Wolpert D, Markelz AG, Hillebrecht JR, Galan J, Birge RR. Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. Biophys J 2003; 85:1269-77. [PMID: 12885670 PMCID: PMC1303244 DOI: 10.1016/s0006-3495(03)74562-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2002] [Accepted: 03/28/2003] [Indexed: 10/21/2022] Open
Abstract
Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.
Collapse
Affiliation(s)
- S E Whitmire
- Physics Department, University at Buffalo, State University of New York, Buffalo, New York, USA
| | | | | | | | | | | |
Collapse
|
38
|
Douki T, Laporte G, Cadet J. Inter-strand photoproducts are produced in high yield within A-DNA exposed to UVC radiation. Nucleic Acids Res 2003; 31:3134-42. [PMID: 12799441 PMCID: PMC162242 DOI: 10.1093/nar/gkg408] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Far-UV irradiation of DNA leads to the dimerization of pyrimidine bases, resulting in the formation of cyclobutane type dimers and (6-4) photoproducts. In the dry state, an additional thymine dimeric photolesion, the spore photoproduct, is also generated. While most photoproducts are expected to be produced between adjacent pyrimidines, little attention has been paid to lesions involving bases located on different DNA strands. Using HPLC- mass spectrometry analysis of enzymatically digested DNA, we observed that, in the dry state, inter-strand dimeric photoproducts represented 30% of the total yield of dimeric thymine lesions. The major inter-strand damage was found to be the spore photoproduct. Formation of inter-strand lesions in significant yield could be obtained in solution upon modification of the DNA conformation as the result of the addition of large amounts of ethanol. In both cases, DNA is in the A-form, which is characterized by a high compaction, likely to favor inter-strand photoreactions. Since the latter DNA conformation is also predominant in bacterial spores, the formation and repair of dimeric photoproducts involving thymine bases located on different DNA strands may thus be relevant in terms of deleterious effects of UV radiation to the latter microorganisms.
Collapse
Affiliation(s)
- Thierry Douki
- Laboratoire 'Lésions des Acides Nucléiques', Service de Chimie Inorganique et Biologique, FRE 2600, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France.
| | | | | |
Collapse
|
39
|
Markelz A, Whitmire S, Hillebrecht J, Birge R. THz time domain spectroscopy of biomolecular conformational modes. Phys Med Biol 2002; 47:3797-805. [PMID: 12452570 DOI: 10.1088/0031-9155/47/21/318] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm(-1) range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules.
Collapse
Affiliation(s)
- Andrea Markelz
- Physics Department, University at Buffalo, Buffalo, NY, USA
| | | | | | | |
Collapse
|
40
|
Haring Bolivar P, Brucherseifer M, Nagel M, Kurz H, Bosserhoff A, Büttner R. Label-free probing of genes by time-domain terahertz sensing. Phys Med Biol 2002; 47:3815-21. [PMID: 12452572 DOI: 10.1088/0031-9155/47/21/320] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A label-free sensing approach for the label-free characterization of genetic material with terahertz (THz) electromagnetic waves is presented. Time-resolved THz analysis of polynucleotides demonstrates a strong dependence of the complex refractive index of DNA molecules in the THz frequency range on their hybridization state. By monitoring THz signals one can thus infer the binding state (hybridized or denatured) of oligo- and polynucleotides, enabling the label-free determination the genetic composition of unknown DNA sequences. A broadband experimental proof-of-principle in a freespace analytic configuration, as well as a higher-sensitivity approach using integrated THz sensors reaching femtomol detection levels and demonstrating the capability to detect single-base mutations, are presented. The potential application for next generation high-throughput label-free genetic analytic systems is discussed.
Collapse
Affiliation(s)
- P Haring Bolivar
- Institut für Halbleitertechnik, RWTH Aachen, Sommerfeldstr. 24, D-52056 Aachen, Germany.
| | | | | | | | | | | |
Collapse
|
41
|
Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiöld L. On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study. Biophys J 2002; 82:2860-75. [PMID: 12023210 PMCID: PMC1302075 DOI: 10.1016/s0006-3495(02)75628-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The interaction of DNA with the polyamine spermine(4+) (Spm(4+)), sodium ions, and water molecules has been studied using molecular dynamics computer simulations in a system modeling a DNA crystal. The simulation model consisted of three B-DNA decamers in a periodic hexagonal cell, containing 1200 water molecules, 8 Spm(4+), 32 Na(+), and 4 Cl(-) ions. The present paper gives a more detailed account of a recently published report of this system and compares results on this mixed Spm(4+)/Na(+)-cation system with an molecular dynamics simulation carried out for the same DNA decamer under similar conditions with only sodium counterions (Korolev et al., J. Mol. Biol. 308:907). The presence of Spm(4+) makes significant influence on the DNA hydration and on the interaction of the sodium ions with DNA. Spermine pushes water molecules out of the minor groove, whereas Na(+) attracts and organizes water around DNA. The major binding site of the Spm(4+) amino groups and the Na(+) ions is the phosphate group of DNA. The flexible polyamine spermine displays a high presence in the minor groove but does not form long-lived and structurally defined complexes. Sodium ions compete with Spm(4+) for binding to the DNA bases in the minor groove. Sodium ions also have several strong binding sites in the major groove. The ability of water molecules, Spm(4+), and Na(+) to modulate the local structure of the DNA double helix is discussed.
Collapse
Affiliation(s)
- Nikolay Korolev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm, Sweden
| | | | | | | |
Collapse
|
42
|
Nagel M, Bolivar PH, Brucherseifer M, Kurz H, Bosserhoff A, Büttner R. Integrated planar terahertz resonators for femtomolar sensitivity label-free detection of DNA hybridization. APPLIED OPTICS 2002; 41:2074-2078. [PMID: 11936814 DOI: 10.1364/ao.41.002074] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A promising label-free approach for the analysis of genetic material by means of detecting the hybridization of polynucleotides with electromagnetic waves at terahertz (THz) frequencies is presented. Using an integrated waveguide approach, incorporating resonant THz structures as sample carriers and transducers for the analysis of the DNA molecules, we achieve a sensitivity down to femtomolar levels. The approach is demonstrated with time-domain ultrafast techniques based on femtosecond laser pulses for generating and electro-optically detecting broadband THz signals, although the principle can certainly be transferred to other THz technologies.
Collapse
Affiliation(s)
- Michael Nagel
- Institut für Halbleitertechnik, Rheinisch Westfälische Technische Hochschule Aachen, Germany
| | | | | | | | | | | |
Collapse
|
43
|
Abstract
In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic acids. This increase has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions, the availability of faster parallel computers, and the development of well-validated empirical molecular mechanical force fields. With these technologies, it has been demonstrated that simulation is not only capable of consistently reproducing experimental observations of sequence specific fine structure of DNA, but also can give detailed insight into prevalent problems in nucleic acid structure, ion association and specific hydration of nucleic acids, polyadenine tract bending, and the subtle environmental dependence of the A-DNA-B-DNA duplex equilibrium. Despite the advances, there are still issues with the methods that need to be resolved through rigorous controlled testing. In general, these relate to deficiencies of the underlying molecular mechanical potentials or applied methods (such as the imposition of true periodicity in Ewald simulations and the need for energy conservation), and significant limits in effective conformational sampling. In this perspective, we provide an overview of our experiences, provide some cautionary notes, and provide recommendations for further study in molecular dynamics simulation of nucleic acids.
Collapse
Affiliation(s)
- T E Cheatham
- Department of Medicinal Chemistry, University of Utah, 30 South, 2000 East, Skaggs Hall 201, Salt Lake City, UT 84112-5820, USA.
| | | |
Collapse
|
44
|
Marlowe RL, Szabó A, Lee SA, Rupprecht A. Experimental studies on the nature of bonding of DNA*bipyridyl-(ethylenediamine)platinum(II) and DNA*netropsin complexes in solution and oriented wet-spun films. J Biomol Struct Dyn 2002; 19:681-90. [PMID: 11843629 DOI: 10.1080/07391102.2002.10506774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The stability of complexes of NaDNA with bipyridyl- (ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)](2+)) and with netropsin has been studied using two techniques: (i) ultraviolet (UV) melting experiments were done on NaDNA* [(bipy)Pt(en)](2+), showing that the [(bipy)Pt(en)](2+) ligand stabilizes the DNA double helix structure; and (ii) swelling measurements (via optical microscopy) as a function of relative humidity were done on wet-spun oriented films of NaDNA*[(bipy)Pt(en)](2+) and of NaDNA*netropsin. The swelling data shows that an irreversible transition of the films occurs at high relative humidity, first for the NaDNA*netropsin, then for pure NaDNA, and lastly for the NaDNA*[(bipy)Pt(en)](2+). These results are indicative that the [(bipy)Pt(en)](2+) complex stabilizes the intermolecular bonds which mediate the film swelling characteristics. A model is suggested for the binding of [(bipy)Pt(en)](2+) to DNA to explain why the swelling experiments show this ligand as increasing the intermolecular bond strength between the DNA double helices, while netropsin decreases this degree of stabilization.
Collapse
Affiliation(s)
- R L Marlowe
- Department of Physics, Geology, and Astronomy, The University of Tennessee, Chattanooga, TN 37403, USA
| | | | | | | |
Collapse
|
45
|
Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB. Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. Biophys J 2001; 81:3409-21. [PMID: 11721003 PMCID: PMC1301797 DOI: 10.1016/s0006-3495(01)75973-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Experimental data on the sequence-dependent B<-->A conformational transition in 24 oligo- and polymeric duplexes yield optimal dimeric and trimeric scales for this transition. The 10 sequence dimers and the 32 trimers of the DNA duplex were characterized by the free energy differences between the B and A forms in water solution. In general, the trimeric scale describes the sequence-dependent DNA conformational propensities more accurately than the dimeric scale, which is likely related to the trimeric model accounting for the two interfaces between adjacent base pairs on both sides (rather than only one interface in the dimeric model). The exceptional preference of the B form for the AA:TT dimers and AAN:N'TT trimers is consistent with the cooperative interactions in both grooves. In the minor groove, this is the hydration spine that stabilizes adenine runs in B form. In the major groove, these are hydrophobic interactions between the thymine methyls and the sugar methylene groups from the preceding nucleotides, occurring in B form. This interpretation is in accord with the key role played by hydration in the B<-->A transition in DNA. Importantly, our trimeric scale is consistent with the relative occurrences of the DNA trimers in A form in protein-DNA cocrystals. Thus, we suggest that the B/A scales developed here can be used for analyzing genome sequences in search for A-philic motifs, putatively operative in the protein-DNA recognition.
Collapse
Affiliation(s)
- M Y Tolstorukov
- Laboratory of Computational and Experimental Biology, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | | | | | | | | |
Collapse
|
46
|
Abstract
A dynamic transition at temperatures ∼200-230K is observed in manyhydrated bio-polymers. It shows up as a sharp increase of the mean-squaredatomic displacements above this temperature range. We present neutronscattering data of DNA at different levels of hydration. The analysis showsthat the dynamic transition in DNA is related to a slow relaxation processin the MHz-GHz frequency range. This slow relaxation process iscompletely suppressed in the dry DNA sample where no dynamic transitionwas observed. The nature of the slow process is discussed. We ascribe it toa global relaxation of DNA molecule that involves cooperative motion ofmany base-pairs and backbone.
Collapse
|
47
|
Korolev N, Lyubartsev AP, Rupprecht A, Nordenskiöld L. Competitive substitution of hexammine cobalt(III) for Na+ and K+ ions in oriented DNA fibers. Biopolymers 2001; 58:268-78. [PMID: 11169387 DOI: 10.1002/1097-0282(200103)58:3<268::aid-bip1004>3.0.co;2-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Competition of the trivalent cation, Co(NH3)(3+)(6), with K+ and Na+ ions in binding to DNA was studied by equilibrating oriented DNA fibers with ethanol/water solutions (65 and 52% v/v EtOH), containing different combinations and concentrations of KCl and NaCl and constant concentration (0.8 mM) of Co(NH3)(6)Cl(3). The degree of Co(NH3)(3+)(6) binding to DNA does not depend significantly on the ethanol concentration or on the kind of univalent cation (Na+ or K+). The ion exchange selectivity coefficient of monovalent-trivalent ion competition, D(1)(c3), increases with the concentration of Me+, C(o)(+), and the monotonic dependence of log D(1)(c3) vs log C(o)(+) has an inflection between 100 and 300 mM that is caused by a structural transformation of DNA from A- to B-form. The ion exchange experimental data are compared with results of grand canonical Monte Carlo (GCMC) simulations of systems of parallel and hexagonally ordered, discretely charged polyions with density and spatial distribution of the charged groups modeling B- and A-forms of DNA. The GCMC method for discretely charged models of the DNA polyion produces a quantitative agreement with experimental data on trivalent-monovalent ion competition in dependence on DNA structural state and salt concentration. Based on this and previous studies it is concluded that the affinity of DNA for the cations decreases in the order Co(NH3)(3+)(6) >> Ca2+ > Mg2+ >> Na+ approximately K+ > Li+. DNA does not exhibit selectivity for Na+ or K+ in ethanol/water solutions either in the absence or in the presence of Co(NH3)(3+)(6), Ca2+, and Mg2+.
Collapse
Affiliation(s)
- N Korolev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | | | | | | |
Collapse
|
48
|
|
49
|
Lee SA, Grimm H, Pohle W, Scheiding W, van Dam L, Song Z, Levitt MH, Korolev N, Szabó A, Rupprecht A. NaDNA-bipyridyl-(ethylenediamine)platinum (II) complex: structure in oriented wet-spun films and fibers. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:7044-7058. [PMID: 11102060 DOI: 10.1103/physreve.62.7044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2000] [Indexed: 05/23/2023]
Abstract
Complexes of NaDNA with bipyridyl-(ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)](2+)) in solid, oriented films, prepared with a wet-spinning method, have been studied using x-ray diffraction, elastic neutron scattering, two-dimensional magic-angle-spinning nuclear magnetic resonance (NMR), infrared (IR) linear dichroism, and IR absorption. All of these experiments indicate that the DNA in this complex is in the B conformation. The neutron diffraction experiments reveal that the rise per residue is 3.31 A, indicating that the [(bipy)Pt(en)](2+) molecular ion causes a small distortion of the B conformation. The neutron data in the direction perpendicular to the helical axis are consistent with a centered orthorhombic unit cell with a=22.65 A and b=32.2 A. The NMR and IR experiments show that the orientation of phosphate groups in the DNA small middle dot[(bipy)Pt(en)](2+) complex is the same as that observed for pure DNA in the B conformation. The IR experiments also show that the [(bipy)Pt(en)](2+) molecular ion stabilizes the B conformation of DNA down to 59% relative humidity, a low water activity. Mechanochemical experiments on wet-spun NaDNA fibers in 68% ethanol with and without [(bipy)Pt(en)](2+) reveal a 9% elongation of the DNA fibers as the complex is formed.
Collapse
Affiliation(s)
- S A Lee
- Department of Physics & Astronomy, University of Toledo, Toledo, Ohio 43606, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Cocco S, Monasson R. Theoretical study of collective modes in DNA at ambient temperature. J Chem Phys 2000. [DOI: 10.1063/1.481646] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|