1
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Alexiou TS, Likos CN. Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency. J Phys Chem B 2023; 127:6969-6981. [PMID: 37493448 PMCID: PMC10424236 DOI: 10.1021/acs.jpcb.3c02216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/12/2023] [Indexed: 07/27/2023]
Abstract
A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.
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Affiliation(s)
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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2
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Olson WK, Li Y, Fenley MO. Insights into DNA solvation found in protein-DNA structures. Biophys J 2022; 121:4749-4758. [PMID: 36380591 PMCID: PMC9808563 DOI: 10.1016/j.bpj.2022.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The proteins that bind double-helical DNA present various microenvironments that sense and/or induce signals in the genetic material. The high-resolution structures of protein-DNA complexes reveal the nature of both the microenvironments and the conformational responses in DNA and protein. Complex networks of interactions within the structures somehow tie the protein and DNA together and induce the observed spatial forms. Here we show how the cumulative buildup of amino acid atoms around the sugars, phosphates, and bases in different protein-DNA complexes produces a binding cloud around the double helix and how different types of atoms fill that cloud. Rather than focusing on the principles of molecular binding and recognition suggested by the arrangements of amino acids and nucleotides in the macromolecular complexes, we consider the proteins in contact with DNA as organized solvents. We describe differences in the mix of atoms that come in closest contact with DNA, subtle sequence-dependent features in the microenvironment of the sugar-phosphate backbone, a direct link between the localized buildup of ionic species and the electrostatic potential surfaces of the DNA bases, and sites of atomic buildup above and below the basepair planes that transmit the unique features of the base environments along the chain backbone. The inferences about solvation that can be drawn from the survey provide new stimuli for improvement of nucleic acid force fields and fresh ideas for exploration of the properties of DNA in solution.
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Affiliation(s)
- Wilma K Olson
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey.
| | - Yun Li
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Marcia O Fenley
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
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3
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Yu B, Bien KG, Wang T, Iwahara J. Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations. Biophys J 2022; 121:3562-3570. [PMID: 35754184 PMCID: PMC9515368 DOI: 10.1016/j.bpj.2022.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Counterions are important constituents for the structure and function of nucleic acids. Using 7Li and 133Cs nuclear magnetic resonance (NMR) spectroscopy, we investigated how ionic radii affect the behavior of counterions around DNA through diffusion measurements of Li+ and Cs+ ions around a 15-bp DNA duplex. Together with our previous data on 23Na+ and 15NH4+ ions around the same DNA under the same conditions, we were able to compare the dynamics of four different monovalent ions around DNA. From the apparent diffusion coefficients at varied concentrations of DNA, we determined the diffusion coefficients of these cations inside and outside the ion atmosphere around DNA (Db and Df, respectively). We also analyzed ionic competition with K+ ions for the ion atmosphere and assessed the relative affinities of these cations for DNA. Interestingly, all cations (i.e., Li+, Na+, NH4+, and Cs+) analyzed by diffusion NMR spectroscopy exhibited nearly identical Db/Df ratios despite the differences in their ionic radii, relative affinities, and diffusion coefficients. These results, along with the theoretical relationship between diffusion and entropy, suggest that the entropy change due to the release of counterions from the ion atmosphere around DNA is also similar regardless of the monovalent ion types. These findings and the experimental diffusion data on the monovalent ions are useful for examination of computational models for electrostatic interactions or ion solvation.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Karina G Bien
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Tianzhi Wang
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas.
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4
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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Catalini S, Vigna J, Mancini I, Mele A, Vacek J, Reha D, Minofar B, Rossi B. Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA revealed by synchrotron-UV Resonance Raman spectroscopy and molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Yu B, Bien KG, Pletka CC, Iwahara J. Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy. Anal Chem 2022; 94:2444-2452. [PMID: 35080384 PMCID: PMC8829827 DOI: 10.1021/acs.analchem.1c04197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by 23Na diffusion nuclear magnetic resonance (NMR) spectroscopy. NMR probe hardware capable of generating strong magnetic field gradients enables 23Na NMR-based diffusion measurements for Na+ ions in solutions of biological macromolecules and their complexes. The dynamic properties of Na+ ions interacting with the macromolecules can be investigated using apparent 23Na diffusion coefficients measured under various conditions. Our diffusion data clearly show that Na+ ions retain high mobility within the ion atmosphere around DNA. The 23Na diffusion NMR method also permits direct observation of the release of Na+ ions from nucleic acids upon protein-nucleic acid association. The entropy change due to the ion release can be estimated from the diffusion data.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Karina G Bien
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068 United States
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6
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Rossi B, Tortora M, Catalini S, Vigna J, Mancini I, Gessini A, Masciovecchio C, Mele A. Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments. Phys Chem Chem Phys 2021; 23:15980-15988. [PMID: 34313275 DOI: 10.1039/d1cp01970h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.
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Affiliation(s)
- Barbara Rossi
- Elettra-Sincrotrone Trieste, S. S. 114 km 163.5, Basovizza, 34149, Trieste, Italy.
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7
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Yu B, Iwahara J. Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 2021; 19:2279-2285. [PMID: 33995919 PMCID: PMC8102144 DOI: 10.1016/j.csbj.2021.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/26/2023] Open
Abstract
Ionic interactions are crucial to biological functions of DNA, RNA, and proteins. Experimental research on how ions behave around biological macromolecules has lagged behind corresponding theoretical and computational research. In the 21st century, quantitative experimental approaches for investigating ionic interactions of biomolecules have become available and greatly facilitated examinations of theoretical electrostatic models. These approaches utilize anomalous small-angle X-ray scattering, atomic emission spectroscopy, mass spectrometry, or nuclear magnetic resonance (NMR) spectroscopy. We provide an overview on the experimental methodologies that can quantify and characterize ions within the ion atmospheres around nucleic acids, proteins, and their complexes.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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8
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Abstract
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Molecular association of proteins with nucleic
acids is required
for many biological processes essential to life. Electrostatic interactions
via ion pairs (salt bridges) of nucleic acid phosphates and protein
side chains are crucial for proteins to bind to DNA or RNA. Counterions
around the macromolecules are also key constituents for the thermodynamics
of protein–nucleic acid association. Until recently, there
had been only a limited amount of experiment-based information about
how ions and ionic moieties behave in biological macromolecular processes.
In the past decade, there has been significant progress in quantitative
experimental research on ionic interactions with nucleic acids and
their complexes with proteins. The highly negatively charged surfaces
of DNA and RNA electrostatically attract and condense cations, creating
a zone called the ion atmosphere. Recent experimental studies were
able to examine and validate theoretical models on ions and their
mobility and interactions with macromolecules. The ionic interactions
are highly dynamic. The counterions rapidly diffuse within the ion
atmosphere. Some of the ions are released from the ion atmosphere
when proteins bind to nucleic acids, balancing the charge via intermolecular
ion pairs of positively charged side chains and negatively charged
backbone phosphates. Previously, the release of counterions had been
implicated indirectly by the salt-concentration dependence of the
association constant. Recently, direct detection of counterion
release by NMR spectroscopy
has become possible and enabled more accurate and quantitative analysis
of the counterion release and its entropic impact on the thermodynamics
of protein–nucleic acid association. Recent studies also revealed
the dynamic nature of ion pairs of protein side chains and nucleic
acid phosphates. These ion pairs undergo transitions between two major
states. In one of the major states, the cation and the anion are in
direct contact and form hydrogen bonds. In the other major state,
the cation and the anion are separated by water. Transitions between
these states rapidly occur on a picosecond to nanosecond time scale.
When proteins interact with nucleic acids, interfacial arginine (Arg)
and lysine (Lys) side chains exhibit considerably different behaviors.
Arg side chains show a higher propensity to form rigid contacts with
nucleotide bases, whereas Lys side chains tend to be more mobile at
the molecular interfaces. The dynamic ionic interactions may facilitate
adaptive molecular recognition and play both thermodynamic and kinetic
roles in protein–nucleic acid interactions.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - B. Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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9
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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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10
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Dou X, Meints GA, Sedaghat-Herati R. New Insights into the Interactions of a DNA Oligonucleotide with mPEGylated-PAMAM by Circular Dichroism and Solution NMR. J Phys Chem B 2019; 123:666-674. [PMID: 30562015 DOI: 10.1021/acs.jpcb.8b08517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Dendrimers are well-defined, highly branched, synthetic three-dimensional molecules with a large number of reactive end groups. PAMAM dendrimers form stable complexes with DNA chemistries and constitute an important class of nonviral, cationic vectors in gene delivery. The aim of this study is to examine the interactions of a 12 bp DNA oligonucletide with PAMAM-G2 and mPEG- b-PAMAM-G3 having eight surface amine groups under physiological conditions, using constant DNA concentration but varying dendrimer concentration. 1D 31P NMR, 2D NOESY, and CD spectroscopic methods were employed to investigate the interactions between the dendrimer and the DNA. The CD experiments carried out with a constant DNA concentration of 25 μM and dendrimer concentrations from 0 to 100 μM indicated minimal change to the chirality of the DNA for both types of dendrimers. While the PAMAM-G2 dendrimer caused aggregation of the majority of the DNA, the 2D NMR data of the DNA with an mPEG- b-PAMAM-G3 dendrimer indicated general broadening of the 1D 31P peaks from the DNA phosphates, a small number of 1H chemical shift perturbations (CSPs), and reduction of specific 1H-1H NOE intensities. These data suggest there is minimal structural alteration of the DNA in the complex and indicate preferential binding of the dendrimer to the central AATT region of the DNA sequence. The results herein are the first such results demonstrating a soluble DNA complex with the mPEG- b-PAMAM-G3 dendrimer analyzed by multidimensional NMR.
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Affiliation(s)
- Xiaozheng Dou
- Department of Chemistry , Missouri State University , Springfield , Missouri 65897 , United States
| | - Gary A Meints
- Department of Chemistry , Missouri State University , Springfield , Missouri 65897 , United States
| | - Reza Sedaghat-Herati
- Department of Chemistry , Missouri State University , Springfield , Missouri 65897 , United States
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11
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Kanellis VG, Dos Remedios CG. A review of heavy metal cation binding to deoxyribonucleic acids for the creation of chemical sensors. Biophys Rev 2018; 10:1401-1414. [PMID: 30229467 DOI: 10.1007/s12551-018-0455-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022] Open
Abstract
Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810-1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample. However, this report raised questions about the mechanism that formed the basis of this quasi-quantitatively test. In this review, we identify the unique and preferred DNA-binding sites of individual metals. We show how highly sensitive and selective DNA-based sensors can be designed that contain multiple binding sites for 21 heavy metal cations that bind to DNA and change its structure, consistent with the release of the DNA-bound dye.
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12
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van Buuren BN, Schleucher J, Wijmenga SS. NMR Structural Studies on a DNA Four-Way Junction: Stacking Preference and Localization of the Metal-ion Binding Site. J Biomol Struct Dyn 2016; 17 Suppl 1:237-43. [PMID: 22607430 DOI: 10.1080/07391102.2000.10506627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked conformer. NOESY spectra showed intermolecular NOE contacts between 4H protons and the ammine protons of the cobalt(III)hexammine complex. These contacts define the metal-ion binding site, located in the vicinity of the junction. The position is similar to the observed site in a recent X-ray structure of a RNA/DNA hybrid 4H and consistent with the position deduced from an uranyl ion photoprobing study on 4Hs with different sequences.
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Affiliation(s)
- B N van Buuren
- a Department of Medical Biochemistry and Biophysics , Umeå University , S-90187 , Umeå , Sweden
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13
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Pan F, Roland C, Sagui C. Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res 2014; 42:13981-96. [PMID: 25428372 PMCID: PMC4267617 DOI: 10.1093/nar/gku1107] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/30/2022] Open
Abstract
The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5'-CGCGCGCGCGCG-3')2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na(+), K(+) and Mg(2 +), with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6](2+) ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6](2+) to distant phosphates, resulting in acute bending of A-RNA; tight 'ion traps' in Z-RNA between C-O2 and the C-O2' atoms in GpC steps; and others.
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Affiliation(s)
- Feng Pan
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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14
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Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014; 10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form and its “null isomer” using molecular dynamics methods. It was found that the phosphate neutralization changes the cation atmosphere around the DNA duplex greatly, increases the major groove width, decreases the minor groove width, and reduces the global bending direction preference. We also noted that the probability of BI phosphate linkages increases significantly because of the charge reduction in the backbone phosphate groups. More importantly, we found that the electrostatic effect on the DNA conformational flexibility is dependent on the sequence; that is, the phosphate backbone neutralization induces the global dynamic bending to be less flexible for GC-rich sequences but more flexible for AT-rich sequences.
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15
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Mandal PK, Venkadesh S, Gautham N. Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1420-6. [PMID: 23192018 PMCID: PMC3509959 DOI: 10.1107/s1744309112041759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 10/05/2012] [Indexed: 11/10/2022]
Abstract
Crystal structures of the hexanucleotide d(CACGCG)·d(CGCGTG) were determined in two crystal lattices when different concentrations of the counterion Mn2+ were used in crystallization. The availability of Mn2+ during the crystallization process appears to play an important role in inducing different crystal packings that lead to crystals belonging to the two space groups P2(1) and P6(5). Analysis of the molecular interactions of Mn2+ with the Z-form duplexes shows direct coordination to the purine residues G and A.
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Affiliation(s)
- P. K. Mandal
- CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - S. Venkadesh
- CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - N. Gautham
- CAS in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
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16
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Mandal PK, Venkadesh S, Gautham N. Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:393-9. [PMID: 22505405 PMCID: PMC3325805 DOI: 10.1107/s174430911200869x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/27/2012] [Indexed: 11/10/2022]
Abstract
The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.
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Affiliation(s)
- Pradeep Kumar Mandal
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Sarkarai Venkadesh
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Namasivayam Gautham
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
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18
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Fales BS, Fujamade NO, Nei YW, Oomens J, Rodgers MT. Infrared multiple photon dissociation action spectroscopy and theoretical studies of diethyl phosphate complexes: effects of protonation and sodium cationization on structure. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:81-92. [PMID: 21472547 PMCID: PMC3042107 DOI: 10.1007/s13361-010-0007-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including [DEP - H](-), [DEP + H](+), [DEP + Na](+), and [DEP - H + 2Na](+) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) with an electrospray ionization (ESI) source, and theoretical electronic structure calculations. Measured IRMPD spectra are compared to linear IR spectra calculated at the B3LYP/6-31G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral complexes are also performed. These experiments and calculations suggest that specific geometric changes occur upon the binding of protons and/or sodium cations, including changes correlating to nucleic acid backbone geometry, specifically P-O bond lengths and ∠OPO bond angles. Information from these observations may be used to gain insight into the structures of more complex systems, such as nucleotides and solvated nucleic acids.
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Affiliation(s)
- B. S. Fales
- Department of Chemistry, Wayne State University, Detroit, MI 48202 USA
| | - N. O. Fujamade
- Department of Chemistry, Wayne State University, Detroit, MI 48202 USA
| | - Y.-w. Nei
- Department of Chemistry, Wayne State University, Detroit, MI 48202 USA
| | - J. Oomens
- FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Neiuwegein, The Netherlands
- van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, MI 48202 USA
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Wang J, Li H, Zhang L, Bu Y. Unexpected dissociation energetics of the Na(+) counterion from GC motifs in DNA hole-migration. Phys Chem Chem Phys 2010; 12:13099-106. [PMID: 20824253 DOI: 10.1039/b927202j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present here a theoretical investigation of the electronic and energetic properties of Na(+)GC, a DNA motif bound to a sodium ion (Na(+)) at the N(7) and O(6) sites of guanine (G), and its hole-trapped derivative [Na(+)GC](+) using density functional theory calculations. Normally, Na(+)GC has positive dissociation energies along various dissociation channels. However, hole-trapping of the Na(+)GC motif can lead to an unusual energetic phenomenon. Hole-trapping can reduce not only the dissociation barrier by destabilizing the Na(+)GC motif to a metastable state, but also the dissociation energy of the Na(+)N(7)/O(6) bond with an unexpected change from a positive to a negative value (61.51 versus-16.18 kcal mol(-1)). This unexpected negative dissociation energy phenomenon implies that this motif can store energy (∼16 kcal mol(-1)) in the Na(+)N(7)/O(6) bond zone due to hole-trapping. The topological properties of electron densities and the Laplacian values at the bond critical points indicate that this energetic phenomenon mainly originates from additional electrostatic repulsions between two moieties linked via a high-energy bond (Na(+)N(7)/O(6)). Proton transfer from G induced by hole-trapping can expand the negative dissociation energy zone to both Na(+)N(7)/O(6) and Watson-Crick (WC) H-bond zones. Similar phenomena can be observed for the Na(+) binding at the minor groove. Solvation of the hole-trapped Na(+)GC motif can change the negative dissociation energies by varying degrees, depending on the solvent-binding sites and the polarity of the solvents.
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Affiliation(s)
- Jun Wang
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, PR China
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Abstract
It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent 'softening' of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.
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Perepelytsya SM, Volkov SN. Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2010; 31:201-205. [PMID: 20198501 DOI: 10.1140/epje/i2010-10566-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 11/10/2009] [Indexed: 05/28/2023]
Abstract
The Raman intensities of counterion vibrations with respect to the phosphate groups of the double-helix backbone (ion-phosphate modes) in the low-frequency spectra (< 200 cm(-1)) of B -DNA with different alkali metal counterions have been calculated using the model for DNA conformational vibrations and the valence-optic approach. The results have showed that the spectra of DNA with heavy counterions (Rb(+) and Cs(+)) differ from the spectra of DNA with light counterions (Na(+) and K(+)). The calculated spectra of DNA with heavy counterions are characterized by intensive modes of ion-phosphate vibrations that form one united band near 115 cm(-1). Ion-phosphate modes in the spectra of DNA with light counterions are characterized by higher frequencies (near 180 cm(-1)) and much lower intensity. Our calculations explain why the modes of ion-phosphate vibrations are observed in Cs-DNA spectra rather than in Na-DNA. The determined sensitivity of the intensities of DNA low-frequency spectra to the counterion type proves the existence of the ion-phosphate modes.
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Affiliation(s)
- S M Perepelytsya
- Bogolyubov Institute for Theoretical Physics, NAS of Ukraine, 14-b Metrologichna St., 03680, Kiev, Ukraine.
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22
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Galindo MA, Amantia D, Martinez-Martinez A, Clegg W, Harrington RW, Moreno Martinez V, Houlton A. Reactions of Pd(II) with Chelate-Tethered 2,6-Diaminopurine Derivatives: N3-Coordination and Reaction of the Purine System. Inorg Chem 2009; 48:11085-91. [DOI: 10.1021/ic901475y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Miguel A. Galindo
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - David Amantia
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Alberto Martinez-Martinez
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - William Clegg
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Ross W. Harrington
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Virtudes Moreno Martinez
- Universidad de Barcelona, Facultad de Quimica, Departamento de Quimica Inorganica, Marti Franqués 1-11, E-08028 Barcelona, Spain
| | - Andrew Houlton
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
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Galindo MA, Amantia D, Martinez Martinez A, Clegg W, Harrington RW, Moreno Martinez V, Houlton A. Probing Metal-Ion Purine Interactions at DNA Minor-Groove Sites. Inorg Chem 2009; 48:10295-303. [DOI: 10.1021/ic9013448] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Miguel A. Galindo
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - David Amantia
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Alberto Martinez Martinez
- Universidad de Barcelona, Facultad de Quimica, Departamento de Quimica Inorganica, Marti Franqués 1-11, E-08028 Barcelona, Spain
| | - William Clegg
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Ross W. Harrington
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Virtudes Moreno Martinez
- Universidad de Barcelona, Facultad de Quimica, Departamento de Quimica Inorganica, Marti Franqués 1-11, E-08028 Barcelona, Spain
| | - Andrew Houlton
- Chemical Nanoscience Laboratory and Crystallography Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
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Abstract
AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.
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25
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Nausner M, Brus J, Häubl M, Müller N, Schoefberger W. Characterization of the sodium binding sites in microcrystalline ATP by 23Na-solid-state NMR and ab initio calculations. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Li H, Cukier RI, Bu Y. Remarkable metal counterion effect on the internucleotide J-couplings and chemical shifts of the N-H...N hydrogen bonds in the W-C base pairs. J Phys Chem B 2008; 112:9174-81. [PMID: 18598072 DOI: 10.1021/jp8030545] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of metal ion binding on the (2h) J(NN)-coupling and delta( (1)H)/Deltadelta( (15)N) chemical shifts of N-H...N H-bond units in internucleotide base pairs were explored by a combination of density functional theory calculations and molecular dynamics (MD) simulations. Results indicate that the NMR parameters vary considerably upon cation binding to the natural GC or AT base pairs, and thus can be used to identify the status of the base pairs, if cation-perturbed. The basic trend is that cation perturbation causes (2h) J(NN) to increase, Deltadelta( (15)N) to decrease, and delta( (1)H) to shift upfield for GC, and in the opposite directions for AT. The magnitudes of variation are closely related to the Lewis acidity of the metal ions. For both base pair series (M(z+)GC and M(z+)AT), these NMR parameters are linearly correlated among themselves. Their values depend strongly on the energy gaps (Delta(ELP-->sigma*)) and the second-order interaction energies ( E(2)) between the donor N lone pair (LP(N)) and the acceptor sigma* N-H localized NBO orbitals. In addition, the (2h) J NN changes are also sensitive to the amount of sigma charge transfer from LP(N) to sigma*(N-H) NBOs or from the purine to the pyrimidine moieties. The different trends are a consequence of the different H-bond patterns combined with the polarization effect of the metal ions in the cationized M(z+)AT series, M(z+) <-- A --> T, and the cationized GC series, M(z+) <-- G <-- C. The predicted cation-induced systematic trends of (2h) J(NN) and delta( (15)N, (1)H) in N-H...N H-bond units may provide a new approach to the determination of H-bond structure and strength in Watson-Crick base pairs, and provide an alternative probe of the heterogeneity of DNA sequences.
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Affiliation(s)
- Huifang Li
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
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27
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Michalkova A, Kosenkov D, Gorb L, Leszczynski J. Thermodynamics and Kinetics of Intramolecular Water Assisted Proton Transfer in Na+-1-Methylcytosine Water Complexes. J Phys Chem B 2008; 112:8624-33. [DOI: 10.1021/jp801807x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Michalkova
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217, and Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kiev 03143, Ukraine
| | - D. Kosenkov
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217, and Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kiev 03143, Ukraine
| | - L. Gorb
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217, and Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kiev 03143, Ukraine
| | - J. Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217, and Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kiev 03143, Ukraine
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28
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Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: setup and analysis. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.10. [PMID: 18428869 DOI: 10.1002/0471142700.nc0710s06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.
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29
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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30
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Ruan C, Huang H, Rodgers MT. Modeling Metal Cation−Phosphate Interactions in Nucleic Acids in the Gas Phase via Alkali Metal Cation−Triethyl Phosphate Complexes. J Phys Chem A 2007; 111:13521-7. [DOI: 10.1021/jp076449x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunhai Ruan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Hai Huang
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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31
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Zhang Y, Huang K. The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine–thymine base pair: A comparative study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Heddi B, Foloppe N, Hantz E, Hartmann B. The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol 2007; 368:1403-11. [PMID: 17395202 DOI: 10.1016/j.jmb.2007.03.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/01/2007] [Accepted: 03/06/2007] [Indexed: 11/17/2022]
Abstract
The influence of monovalent cations on DNA conformation and readout is an open question. This NMR study of DNA with either Na(+) or K(+) at physiological concentrations shows that the nature of the cation affects the (31)P chemical shifts (deltaP) and the sequential distances H2'(i)-H6/8(i+1), H2"(i)-H6/8(i+1), and H6/8(i)-H6/8(i+1). The deltaP and distance variations ascertain that the nature of the cation affects the DNA overall structure, i.e. both the conformational equilibria between the backbone BI (epsilon-zeta <0 degrees ) and BII (epsilon-zeta >0 degrees ) states and the helical parameters, via their strong mechanical coupling. These results reveal that Na(+) and K(+) interactions with DNA are different and sequence-dependent. These ions modulate the overall intrinsic properties of DNA, and possibly its packaging and readout.
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Affiliation(s)
- Brahim Heddi
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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33
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Koudelka GB, Mauro SA, Ciubotaru M. Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2007; 81:143-77. [PMID: 16891171 DOI: 10.1016/s0079-6603(06)81004-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Cooke Hall, North Campus, Buffalo, New York 14260, USA
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35
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Mount AR, Mountford CP, Evans SAG, Su TJ, Buck AH, Dickinson P, Campbell CJ, Keane LM, Terry JG, Beattie JS, Walton AJ, Ghazal P, Crain J. The stability and characteristics of a DNA Holliday junction switch. Biophys Chem 2006; 124:214-21. [PMID: 16716492 DOI: 10.1016/j.bpc.2006.03.020] [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] [Received: 01/17/2006] [Accepted: 03/25/2006] [Indexed: 11/17/2022]
Abstract
A Holliday junction (HJ) consists of four DNA double helices, with a branch point discontinuity at the intersection of the component strands. At low ionic strength, the HJ adopts an open conformation, with four widely spaced arms, primarily due to strong electrostatic repulsion between the phosphate groups on the backbones. At high ionic strength, screening of this repulsion induces a switch to a more compact (closed) junction conformation. Fluorescent labelling with dyes placed on the HJ arms allows this conformational switch to be detected optically using fluorescence resonance energy transfer (FRET), producing a sensitive fluorescent output of the switch state. This paper presents a systematic and quantitative survey of the switch characteristics of such a labelled HJ. A short HJ (arm length 8 bp) is shown to be prone to dissociation at low switching ion concentration, whereas an HJ of arm length 12 bp is shown to be stable over all switching ion concentrations studied. The switching characteristics of this HJ have been systematically and quantitatively studied for a variety of switching ions, by measuring the required ion concentration, the sharpness of the switching transition and the fluorescent output intensity of the open and closed states. This stable HJ is shown to have favourable switch characteristics for a number of inorganic switching ions, making it a promising candidate for use in nanoscale biomolecular switch devices.
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Affiliation(s)
- A R Mount
- School of Chemistry, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JJ, UK.
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36
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Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. Cheminformatics methods for novel nanopore analysis of HIV DNA termini. BMC Bioinformatics 2006; 7 Suppl 2:S22. [PMID: 17118144 PMCID: PMC1683570 DOI: 10.1186/1471-2105-7-s2-s22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis. RESULTS HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus.
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Affiliation(s)
- Stephen Winters-Hilt
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Matthew Landry
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Mark Akeson
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Maria Tanase
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Iftekhar Amin
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Amy Coombs
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Eric Morales
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - John Millet
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Carl Baribault
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
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37
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Griffiths KK, Russu IM. Specific Interactions of Divalent Metal Ions with a DNA Duplex Containing the d(CA)n/(GT)nTandem Repeat. J Biomol Struct Dyn 2006; 23:667-76. [PMID: 16615812 DOI: 10.1080/07391102.2006.10507091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Divalent metal ions are essential for maintaining functional states of the DNA molecule. Their participation in DNA structure is modulated by the base sequence and varies depending on the nature of the ion. The present investigation addresses the interaction of Ca2+ ions with a tandem repeat of two CA dinucleotides, (CA)2/(TG)2. The binding of Ca2+ to the repeat is monitored by nuclear magnetic resonance (NMR) spectroscopy using chemical shift mapping. Parallel experiments monitor binding of Mg2+ ions to the repeat as well as binding of each ion to a DNA duplex in which the (CA)2/(TG)2 repeat is eliminated. The results reveal that the direction and the magnitude of chemical shift changes induced by Ca2+ ions in the NMR spectra of the repeat are different from those induced by Mg2+ ions. The differences between the two cations are significantly diminished by the elimination of the (CA)2/(TG)2 repeat. These findings suggest a specific interaction of Ca2+ ions with the (CA)2/(TG)2 motif. The specificity of the interaction resides in the two A-T base pairs of the repeat, and it involves the major groove of the first A-T base pair and both grooves of the second A-T base pair.
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Affiliation(s)
- Keren K Griffiths
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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38
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Boudreau EA, Pelczer I, Borer PN, Heffron GJ, LaPlante SR. Changes in drug 13C NMR chemical shifts as a tool for monitoring interactions with DNA. Biophys Chem 2004; 109:333-44. [PMID: 15110931 DOI: 10.1016/j.bpc.2003.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 11/11/2003] [Accepted: 12/11/2003] [Indexed: 10/26/2022]
Abstract
The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to monitor drug 13C NMR chemical shifts changes. The binding mode of netropsin to the minor groove of DNA is well-known, and served as a good model for evaluating the relative sensitivity of 13C chemical shifts to hydrogen bonding. Large downfield shifts were observed for four resonances of carbons that neighbor sites which are known to form hydrogen bond interactions with the DNA minor groove. Many of the remaining resonances of netropsin exhibit shielding or relatively smaller deshielding changes. Based on the model system presented here, large deshielding NMR shift changes of a ligand upon macromolecule binding can likely be attributed to hydrogen bond formation at nearby sites.
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Affiliation(s)
- Eilis A Boudreau
- Health Science Research and Development Program, Portland VA Medical Center, Portland, OR 97239, USA
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39
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Auffinger P, Bielecki L, Westhof E. Anion binding to nucleic acids. Structure 2004; 12:379-88. [PMID: 15016354 DOI: 10.1016/j.str.2004.02.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 12/01/2003] [Accepted: 12/07/2003] [Indexed: 11/20/2022]
Abstract
Nucleic acids are generally considered as efficient cation binders. Therefore, the likelihood that negatively charged ions might intrude their first hydration shell is rarely considered. Here, we show on the basis of (i) a survey of the Nucleic Acid Database, (ii) several structures extracted from the Cambridge Structural Database, and (iii) molecular dynamics simulations, that the nucleotide electropositive edges involving mainly amino, imino, and hydroxyl groups can cast specific anion binding sites. These binding sites constitute also good locations for the binding of the negatively charged groups of the Asp and Glu residues or the nucleic acid phosphate groups. Furthermore, it is observed in several instances that anions, like water molecules and cations, do mediate protein/nucleic acid interactions. Thus, anions as well as negatively charged groups are directly involved in specific recognition and folding phenomena involving polyanionic nucleic acids.
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Affiliation(s)
- Pascal Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15, rue René Descartes, 67084 Strasbourg Cedex, France.
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40
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Ponomarev SY, Thayer KM, Beveridge DL. Ion motions in molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A 2004; 101:14771-5. [PMID: 15465909 PMCID: PMC522050 DOI: 10.1073/pnas.0406435101] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.
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Affiliation(s)
- Sergei Y Ponomarev
- Department of Physics, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA
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41
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Abstract
Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Abstract
Is it by design or by default that water molecules are observed at the interfaces of some protein-DNA complexes? Both experimental and theoretical studies on the thermodynamics of protein-DNA binding overwhelmingly support the extended hydrophobic view that water release from interfaces favors binding. Structural and energy analyses indicate that the waters that remain at the interfaces of protein-DNA complexes ensure liquid-state packing densities, screen the electrostatic repulsions between like charges (which seems to be by design), and in a few cases act as linkers between complementary charges on the biomolecules (which may well be by default). This review presents a survey of the current literature on water in protein-DNA complexes and a critique of various interpretations of the data in the context of the role of water in protein-DNA binding and principles of protein-DNA recognition in general.
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Affiliation(s)
- B Jayaram
- Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.
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Beveridge DL, Dixit SB, Barreiro G, Thayer KM. Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. Biopolymers 2004; 73:380-403. [PMID: 14755574 DOI: 10.1002/bip.20019] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent studies of DNA axis curvature and flexibility based on molecular dynamics (MD) simulations on DNA are reviewed. The MD simulations are on DNA sequences up to 25 base pairs in length, including explicit consideration of counterions and waters in the computational model. MD studies are described for ApA steps, A-tracts, for sequences of A-tracts with helix phasing. In MD modeling, ApA steps and A-tracts in aqueous solution are essentially straight, relatively rigid, and exhibit the characteristic features associated with the B'-form of DNA. The results of MD modeling of A-tract oligonucleotides are validated by close accord with corresponding crystal structure results and nuclear magnetic resonance (NMR) nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC) structures of d(CGCGAATTCGCG) and d(GGCAAAAAACGG). MD simulation successfully accounts for enhanced axis curvature in a set of three sequences with phased A-tracts studied to date. The primary origin of the axis curvature in the MD model is found at those pyrimidine/purine YpR "flexible hinge points" in a high roll, open hinge conformational substate. In the MD model of axis curvature in a DNA sequence with both phased A-tracts and YpR steps, the A-tracts appear to act as positioning elements that make the helix phasing more precise, and key YpR steps in the open hinge state serve as curvature elements. Our simulations on a phased A-tract sequence as a function of temperature show that the MD simulations exhibit a premelting transition in close accord with experiment, and predict that the mechanism involves a B'-to-B transition within A-tracts coupled with the prediction of a transition in key YpR steps from the high roll, open hinge, to a low roll, closed hinge substate. Diverse experimental observations on DNA curvature phenomena are examined in light of the MD model with no serious discrepancies. The collected MD results provide independent support for the "non-A-tract model" of DNA curvature. The "junction model" is indicated to be a special case of the non-A-tract model when there is a Y base at the 5' end of an A-tract. In accord with crystallography, the "ApA wedge model" is not supported by MD.
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Affiliation(s)
- D L Beveridge
- Department of Chemistry, Wesleyan University, Middletown CT 06459, USA.
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Bandyopadhyay D, Bhattacharyya D. Different Modes of Interaction Between Hydrated Magnesium Ion and DNA Functional Groups: Database Analysis and ab initio Studies. J Biomol Struct Dyn 2003; 21:447-58. [PMID: 14616039 DOI: 10.1080/07391102.2003.10506939] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Role of Magnesium ion is well substantiated in DNA structure and function though the appropriate nature of DNA magnesium interaction is still not fully established. We have analyzed available DNA crystal structures in presence of magnesium ion, which show the experimental evidences for various interaction modes between DNA molecule and magnesium ion. Two preferred modes are found: direct coordinating interaction between magnesium ion and electronegative DNA atoms, and the secondary mode of interaction via formation of hydrogen bonds. This qualitative data is further supported by ab initio quantum chemical calculations using restricted Hartree-Fock and Density Functional Theory. We have analyzed the energies and partial charges of different DNA fragments and hydrated magnesium ions, following restrained and unrestrained geometry optimizations along the reaction coordinate. The restrained optimizations for the systems generally show two energy minima separated by an energy barrier, the height ranges from about 5 to 15 kcal/mol, which is in agreement with experimental observations. All these analyses suggest that both modes of interactions occur almost with equal probability, although water mediated secondary mode of interaction is preferred in most cases, which was so far neglected.
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Affiliation(s)
- Debashree Bandyopadhyay
- Biophysics Division, Saha Institute of Nuclear Physics, 37 Belgachia Road, Kolkata 700037, India
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Subirana JA, Soler-Lopez M. Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:27-45. [PMID: 12598364 DOI: 10.1146/annurev.biophys.32.110601.141726] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cations are bound to nucleic acids in a solvated state. High-resolution X-ray diffraction studies of oligonucleotides provide a detailed view of Mg2+, and occasionally other ions bound to DNA. In a survey of several such structures, certain general observations emerge. First, cations bind preferentially to the guanine base in the major groove or to phosphate group oxygen atoms. Second, cations interact with DNA most frequently via water molecules in their primary solvation shell, direct ion-DNA contacts being only rarely observed. Thus, the solvated ions should be viewed as hydrogen bond donors in addition to point charges. Finally, ion interaction sites are readily exchangeable: The same site may be occupied by any ion, including spermine, as well as by a water molecule.
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Affiliation(s)
- Juan A Subirana
- Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, Barcelona, Spain.
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Madhumalar A, Bansal M. Structural insights into the effect of hydration and ions on A-tract DNA: a molecular dynamics study. Biophys J 2003; 85:1805-16. [PMID: 12944294 PMCID: PMC1303353 DOI: 10.1016/s0006-3495(03)74609-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
DNA structure is known to be sensitive to hydration and ionic environment. To explore the dynamics, hydration, and ion binding features of A-tract sequences, a 7-ns Molecular dynamics (MD) study has been performed on the dodecamer d(CGCAAATTTGCG)(2). The results suggest that the intrusion of Na(+) ion into the minor groove is a rare event and the structure of this dodecamer is not very sensitive to the location of the sodium ions. The prolonged MD simulation successfully leads to the formation of sequence dependent hydration patterns in the minor groove, often called spine of hydration near the A-rich region and ribbon of hydration near the GC regions. Such sequence dependent differences in the hydration patterns have been seen earlier in the high resolution crystal structure of the Drew-Dickerson sequence, but not reported for the medium resolution structures (2.0 approximately 3.0 A). Several water molecules are also seen in the major groove of the MD simulated structure, though they are not highly ordered over the extended MD. The characteristic narrowing of the minor groove in the A-tract region is seen to precede the formation of the spine of hydration. Finally, the occurrence of cross-strand C2-H2.O2 hydrogen bonds in the minor groove of A-tract sequences is confirmed. These are found to occur even before the narrowing of the minor groove, indicating that such interactions are an intrinsic feature of A-tract sequences.
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Affiliation(s)
- A Madhumalar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Amantia D, Price C, Shipman MA, Elsegood MRJ, Clegg W, Houlton A. Minor groove site coordination of adenine by platinum group metal ions: effects on basicity, base pairing, and electronic structure. Inorg Chem 2003; 42:3047-56. [PMID: 12716200 DOI: 10.1021/ic020657g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dithioether- or diamine-tethered adenine derivatives react with Pt(II), Pd(II), and Rh(III) ions to give N3-coordinated complexes of the types [MCl(SSN)](+) (M = Pt or Pd), [RhCl(3)(SSN)], or [RhCl(3)(NNN)] (where SSN = 1-(N9-adenine)-3,6-dithia-heptane or 1-(N9-adenine)-4,7-dithia-octane; NNN = ethylenediamine-N,9-ethyladenine). Single-crystal X-ray analysis confirms the nature of the metal-nucleobase interaction and highlights a conserved intermolecular hydrogen-bonding motif for all the complexes, irrespective of the metal-ion geometry. Coordination significantly reduces the basicity of the adeninyl group, as indicated by a pK(a) value of -0.16 for [PtCl(N3-1-(N9-adenine)-3,6-dithia-heptane)]BF(4), compared to a pK(a) value of 4.2 for 9-ethyladenine. The site of proton binding, N1 or N7, could not be unambiguously assigned from the (1)H NMR data, because of the similar effect on the chemical shifts of the H2 and H8 protons. Density functional calculations at the BP-LACVP level suggest N1 as the site of protonation for this type of complex. This is in contrast to the N7-protonation reported for [Pt(dien)(N3-6,6',9-trimethyladenine)](2+), as reported elsewhere (Meiser et al., Chem.-Eur. J. 1997, 3, 388). However, further electronic structure calculations in the gas phase reveal that the preferred site for protonation for N3-bound complexes is conformationally dependent. N3 coordination was also found to reduce the extent of base pairing between adenine and thymine in dimethylsulfoxide for the self-complementary complex [PtCl(L3)](+) (L3 = 1-(N9-adenine)-3,6-dithia-9-(N1-thymine)nonane), compared to that for the uncomplexed ligand.
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Affiliation(s)
- David Amantia
- School of Natural Sciences: Chemistry, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, U.K
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48
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Abstract
The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model).
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Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta 30332, USA.
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Ahmad R, Arakawa H, Tajmir-Riahi HA. A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings. Biophys J 2003; 84:2460-6. [PMID: 12668453 PMCID: PMC1302811 DOI: 10.1016/s0006-3495(03)75050-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although structural differences for the Mg-DNA and Ca-DNA complexes are provided in the solid state, such comparative study in aqueous solution has been less investigated. The aim of this study was to examine the bindings of Mg and Ca cations with calf thymus DNA in aqueous solution at physiological pH, using constant concentration of DNA (1.25 or 12.5 mM) and various concentrations of metal ions (2 microM-650 microM). Capillary electrophoresis, UV-visible, and Fourier transform infrared spectroscopic methods were used to determine the cation-binding modes, the binding constants, and DNA structural variations in aqueous solution. Direct Ca-PO(2) binding was evident by major spectral changes (shifting and splitting) of the backbone PO(2) asymmetric stretching at 1222 cm(-1) with K = 4.80 x 10(5) M(-1), whereas an indirect Mg-phosphate interaction occurred (due to the lack of shifting and splitting of the phosphate band at 1222 cm(-1)) with K = 5.6 x 10(4) M(-1). The metal-base bindings were directly for the Mg with K = 3.20 x 10(5) M(-1) and indirectly for the Ca cation with K = 3.0 x 10(4) M(-1). Both major and minor groove bindings were observed with no alteration of the B-DNA conformation.
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Affiliation(s)
- R Ahmad
- Department of Chemistry-Biology, University of Québec at Trois-Riviéres, Trois-Riviéres, Québec G9A 5H7, Canada
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Wong A, Wu G. Characterization of the Pentacoordinate Sodium Cations in Hydrated Nucleoside 5‘-Phosphates by Solid-State 23Na NMR and Quantum Mechanical Calculations. J Phys Chem A 2003. [DOI: 10.1021/jp021937k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alan Wong
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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