1
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Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
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Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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2
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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3
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Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. J Comput Aided Mol Des 2020; 34:253-265. [PMID: 31950463 DOI: 10.1007/s10822-020-00288-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022]
Abstract
Bending of double-stranded (ds) DNA plays a crucial role in many important biological processes and is relevant for nanotechnological applications. Among all the elements that have been studied in relation to dsDNA bending, A-tracts stand out as one of the most controversial. The "ApA wedge" theory was disproved when a series of linear polynucleotides containing phased 5'-A4T4-3' or 5'-T4A4-3' runs were shown to be bent or straight, respectively, and crystallographic evidence revealed that A-tracts are unbent. Furthermore, some of the smallest dsDNA minicircles described to date (~ 100 bp in size) lack A-tracts and are subjected to varying levels of torsional stress. Representative DNA sequences from this experimental background were modeled in atomic detail and their dynamic behavior was simulated over hundreds of nanoseconds using the AMBER force field ParmBSC1. Subsequent analysis of the resulting trajectories allowed us to (i) unambiguously establish the location of the bends in all cases; (ii) identify the structural elements that are directly responsible for the macroscopically detected curvature; and (iii) reveal the importance not only of coherently summing the effects of the bending elements when they are in synchrony with the natural repeat of the helix (i.e. separated by an integral number of helical turns) but also when alternated with a half-integral separation of opposite effects. We conclude that the major determinant of the macroscopically observed bending is the proper grouping and phasing of the positive roll imposed by pyrimidine-purine (YR) steps and the negative or null roll characteristic of RY steps and A-tracts, respectively. This conclusion is in very good agreement with the structural parameters experimentally derived for much smaller DNA molecules either alone or as found in DNA-protein complexes. We expect that this work will pave the way for future studies on drug-induced DNA bending, DNA shape readout by transcription factors, structure of circular extrachromosomal DNA, and custom design of curved DNA origami scaffolds.
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4
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Hassan F, Lossie SL, Kasik EP, Channon AM, Ni S, Kennedy MA. A mouse model study of toxicity and biodistribution of a replication defective adenovirus serotype 5 virus with its genome engineered to contain a decoy hyper binding site to sequester and suppress oncogenic HMGA1 as a new cancer treatment therapy. PLoS One 2018; 13:e0192882. [PMID: 29462157 PMCID: PMC5819794 DOI: 10.1371/journal.pone.0192882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
The HGMA1 architectural transcription factor is highly overexpressed in many human cancers. Because HMGA1 is a hub for regulation of many oncogenes, its overexpression in cancer plays a central role in cancer progression and therefore HMGA1 is gaining increasing attention as a target for development of therapeutic approaches to suppress either its expression or action in cancer cells. We have developed the strategy of introducing decoy hyper binding sites for HMGA1 into the nucleus of cancer cells with the goal of competetively sequestering overexpressed HMGA1 and thus suppressing its oncogenic action. Towards achieving this goal, we have introduced an HMGA1 decoy hyper binding site composed of six copies of a high affinity HMGA1 binding site into the genome of the replication defective adenovirus serotype 5 genome and shown that the engineered virus effectively reduces the viability of human pancreatic and cancer cells. Here we report the first pre-clinical measures of toxicity and biodistribution of the engineered virus in C57BL/6J Black 6 mice. The immune response to exposure of the engineered virus was determined by assaying the serum levels of key cytokines, IL-6 and TNF-α. Toxicity due to exposure to the virus was determined by measuring the serum levels of the liver enzymes aspartate aminotransferase and alanine aminotransferase. Biodistribution was measured following direct injection into the pancreas or liver by quantifying viral loads in the pancreas, liver, spleen and brain.
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Affiliation(s)
- Faizule Hassan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
| | - Sarah L. Lossie
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
| | - Ellen P. Kasik
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
| | - Audrey M. Channon
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio United States of America
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5
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Imeddourene AB, Xu X, Zargarian L, Oguey C, Foloppe N, Mauffret O, Hartmann B. The intrinsic mechanics of B-DNA in solution characterized by NMR. Nucleic Acids Res 2016; 44:3432-47. [PMID: 26883628 PMCID: PMC4838374 DOI: 10.1093/nar/gkw084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/01/2016] [Indexed: 12/19/2022] Open
Abstract
Experimental characterization of the structural couplings in free B-DNA in solution has been elusive, because of subtle effects that are challenging to tackle. Here, the exploitation of the NMR measurements collected on four dodecamers containing a substantial set of dinucleotide sequences provides new, consistent correlations revealing the DNA intrinsic mechanics. The difference between two successive residual dipolar couplings (ΔRDCs) involving C6/8-H6/8, C3′-H3′ and C4′-H4′ vectors are correlated to the 31P chemical shifts (δP), which reflect the populations of the BI and BII backbone states. The δPs are also correlated to the internucleotide distances (Dinter) involving H6/8, H2′ and H2″ protons. Calculations of NMR quantities on high resolution X-ray structures and controlled models of DNA enable to interpret these couplings: the studied ΔRDCs depend mostly on roll, while Dinter are mainly sensitive to twist or slide. Overall, these relations demonstrate how δP measurements inform on key inter base parameters, in addition to probe the BI↔BII backbone equilibrium, and shed new light into coordinated motions of phosphate groups and bases in free B-DNA in solution. Inspection of the 5′ and 3′ ends of the dodecamers also supplies new information on the fraying events, otherwise neglected.
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Affiliation(s)
- Akli Ben Imeddourene
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France Université Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
| | - Xiaoqian Xu
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France Department of Life Sciences, East China Normal University, 200062 Shanghai, People's Republic of China
| | - Loussiné Zargarian
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Christophe Oguey
- Laboratoire de Physique Théorique et Modélisation, UMR 8089, CNRS, Université de Cergy-Pontoise, Cergy-Pontoise, France
| | | | - Olivier Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Brigitte Hartmann
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
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6
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Weidenbach S, Hou C, Chen JM, Tsodikov OV, Rohr J. Dimerization and DNA recognition rules of mithramycin and its analogues. J Inorg Biochem 2015; 156:40-7. [PMID: 26760230 DOI: 10.1016/j.jinorgbio.2015.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/10/2015] [Accepted: 12/16/2015] [Indexed: 12/25/2022]
Abstract
The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me(2+))-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM binds G/C-rich DNA, the exact DNA recognition rules that would allow one to map MTM binding sites remain incompletely understood. Towards this goal, we quantitatively investigated dimerization of MTM and several of its analogues, MTM SDK (for Short side chain, DiKeto), MTM SA-Trp (for Short side chain and Acid), MTM SA-Ala, and a biosynthetic precursor premithramycin B (PreMTM B), and measured the binding affinities of these molecules to DNA oligomers of different sequences and structural forms at physiological salt concentrations. We show that MTM and its analogues form stable dimers even in the absence of DNA. All molecules, except for PreMTM B, can bind DNA with the following rank order of affinities (strong to weak): MTM=MTM SDK>MTM SA-Trp>MTM SA-Ala. An X(G/C)(G/C)X motif, where X is any base, is necessary and sufficient for MTM binding to DNA, without a strong dependence on DNA conformation. These recognition rules will aid in mapping MTM sites across different promoters towards development of MTM analogues as useful anticancer agents.
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Affiliation(s)
- Stevi Weidenbach
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Jhong-Min Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
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7
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Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie S, Gao YQ. DNA Structural Correlation in Short and Long Ranges. J Phys Chem B 2015; 119:13980-90. [PMID: 26439165 DOI: 10.1021/acs.jpcb.5b06217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent single-molecule measurements have revealed the DNA allostery in protein/DNA binding. MD simulations showed that this allosteric effect is associated with the deformation properties of DNA. In this study, we used MD simulations to further investigate the mechanism of DNA structural correlation, its dependence on DNA sequence, and the chemical modification of the bases. Besides a random sequence, poly d(AT) and poly d(GC) are also used as simpler model systems, which show the different bending and twisting flexibilities. The base-stacking interactions and the methyl group on the 5-carbon site of thymine causes local structures and flexibility to be very different for the two model systems, which further lead to obviously different tendencies of the conformational deformations, including the long-range allosteric effects.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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8
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Campagne S, Gervais V, Milon A. Nuclear magnetic resonance analysis of protein-DNA interactions. J R Soc Interface 2011; 8:1065-78. [PMID: 21389020 DOI: 10.1098/rsif.2010.0543] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent methodological and instrumental advances in solution-state nuclear magnetic resonance have opened up the way to investigating challenging problems in structural biology such as large macromolecular complexes. This review focuses on the experimental strategies currently employed to solve structures of protein-DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.
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Affiliation(s)
- S Campagne
- Université de Toulouse, UPS, Department of Structural Biology and Biophysics, F-31077 Toulouse, France
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9
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Lankas F, Spacková N, Moakher M, Enkhbayar P, Sponer J. A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Res 2010; 38:3414-22. [PMID: 20123729 PMCID: PMC2879501 DOI: 10.1093/nar/gkq001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 12/11/2009] [Accepted: 01/03/2010] [Indexed: 12/17/2022] Open
Abstract
A method is proposed to measure global bending in DNA and RNA structures. It relies on a properly defined averaging of base-fixed coordinate frames, computes mean frames of suitably chosen groups of bases and uses these mean frames to evaluate bending. The method is applied to DNA A-tracts, known to induce considerable bend to the double helix. We performed atomistic molecular dynamics simulations of sequences containing the A(4)T(4) and T(4)A(4) tracts, in a single copy and in two copies phased with the helical repeat. Various temperature and salt conditions were investigated. Our simulations indicate bending by roughly 10 degrees per A(4)T(4) tract into the minor groove, and an essentially straight structure containing T(4)A(4), in agreement with electrophoretic mobility data. In contrast, we show that the published NMR structures of analogous sequences containing A(4)T(4) and T(4)A(4) tracts are significantly bent into the minor groove for both sequences, although bending is less pronounced for the T(4)A(4) containing sequence. The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers.
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Affiliation(s)
- F Lankas
- Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic.
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10
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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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11
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Savelyev A, Papoian GA. Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA. Biophys J 2009; 96:4044-52. [PMID: 19450476 PMCID: PMC2712212 DOI: 10.1016/j.bpj.2009.02.067] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 02/09/2009] [Accepted: 02/24/2009] [Indexed: 10/20/2022] Open
Abstract
Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials. We demonstrate that such compactification allows us to reproduce many-body effects, generated by one-step renormalization, at low computational cost. In addition, compact Hamiltonians greatly increase the likelihood of finding unique solutions for the coarse-grained force-field parameter values. By successfully applying our molecular renormalization group coarse-graining technique to double-stranded DNA, we solved, for the first time, a long-standing problem in coarse-graining polymer systems, namely, how to accurately capture the correlations among various polymeric degrees of freedom. Excellent agreement is found among atomistic and coarse-grained distribution functions for various structural observables, including those not included in the Hamiltonian. We also suggest higher-order generalization of this method, which may allow capturing more subtle correlations in biopolymer dynamics.
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Affiliation(s)
| | - Garegin A. Papoian
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
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12
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Alvarez-Salgado F, Desvaux H, Boulard Y. NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1081-9. [PMID: 16972306 DOI: 10.1002/mrc.1902] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D(a) and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond.
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Affiliation(s)
- Francisco Alvarez-Salgado
- Laboratoire du Contrôle du Cycle Cellulaire, DSV/DBJC, Service de Biochimie et de Génétique Moléculaire, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
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13
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Savelyev A, Papoian GA. Electrostatic, Steric, and Hydration Interactions Favor Na+ Condensation around DNA Compared with K+. J Am Chem Soc 2006; 128:14506-18. [PMID: 17090034 DOI: 10.1021/ja0629460] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.
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Affiliation(s)
- Alexey Savelyev
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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14
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Wu B, Petersen M, Girard F, Tessari M, Wijmenga SS. Prediction of molecular alignment of nucleic acids in aligned media. JOURNAL OF BIOMOLECULAR NMR 2006; 35:103-15. [PMID: 16718586 DOI: 10.1007/s10858-006-9004-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 03/04/2006] [Accepted: 03/14/2006] [Indexed: 05/09/2023]
Abstract
We demonstrate--using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined--that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye-Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye-Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye-Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it's functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request.
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Affiliation(s)
- Bin Wu
- Laboratory of Physical Chemistry-Biophysical Chemistry, Institute of Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6225ED, Nijmegen, The Netherlands
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