101
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Greenbaum JA, Pang B, Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res 2007; 17:947-53. [PMID: 17568010 PMCID: PMC1891353 DOI: 10.1101/gr.6073107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relational database, ORChID (OH Radical Cleavage Intensity Database), that contains extensive hydroxyl radical cleavage data produced from two DNA libraries. We have used the ORChID database to develop a set of algorithms that are capable of predicting the hydroxyl radical cleavage pattern of a DNA sequence of essentially any length, to high accuracy. We have used the prediction algorithm to produce a structural map of the 30 Mb of the ENCODE regions of the human genome.
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Affiliation(s)
- Jason A. Greenbaum
- Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
| | - Bo Pang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas D. Tullius
- Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
- Corresponding author.E-mail ; fax (617) 353-6466
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102
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Brogden A, Hopcroft N, Searcey M, Cardin C. Ligand Bridging of the DNA Holliday Junction: Molecular Recognition of a Stacked-X Four-Way Junction by a Small Molecule. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603760] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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103
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Brogden AL, Hopcroft NH, Searcey M, Cardin CJ. Ligand Bridging of the DNA Holliday Junction: Molecular Recognition of a Stacked-X Four-Way Junction by a Small Molecule. Angew Chem Int Ed Engl 2007; 46:3850-4. [PMID: 17477457 DOI: 10.1002/anie.200603760] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L Brogden
- School of Chemistry, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AD, UK
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104
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Sundaresan N, Suresh CH. A Base-Sugar−Phosphate Three-Layer ONIOM Model for Cation Binding: Relative Binding Affinities of Alkali Metal Ions for Phosphate Anion in DNA. J Chem Theory Comput 2007; 3:1172-82. [DOI: 10.1021/ct600245w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Neethu Sundaresan
- Chemical Sciences and Technology Division and Computational Modeling and Simulation Section, Regional Research Laboratory (Council of Scientific and Industrial Research), Trivandrum 695019, India
| | - Cherumuttathu H. Suresh
- Chemical Sciences and Technology Division and Computational Modeling and Simulation Section, Regional Research Laboratory (Council of Scientific and Industrial Research), Trivandrum 695019, India
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105
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Voth AR, Hays FA, Ho PS. Directing macromolecular conformation through halogen bonds. Proc Natl Acad Sci U S A 2007; 104:6188-93. [PMID: 17379665 PMCID: PMC1851028 DOI: 10.1073/pnas.0610531104] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Indexed: 11/18/2022] Open
Abstract
The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be approximately 2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- Andrea Regier Voth
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
| | - Franklin A. Hays
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
| | - P. Shing Ho
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7503
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106
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René B, Fermandjian S, Mauffret O. Does topoisomerase II specifically recognize and cleave hairpins, cruciforms and crossovers of DNA? Biochimie 2007; 89:508-15. [PMID: 17397986 DOI: 10.1016/j.biochi.2007.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 02/16/2007] [Indexed: 01/05/2023]
Abstract
DNA topoisomerase II is an enzyme that specializes in DNA disentanglement. It catalyzes the interconversion of DNA between different topological states. This event requires the passage of one duplex through another one via a transient double-strand break. Topoisomerase II is able to process any type of DNA, including structures such as DNA juxtapositions (crossovers), DNA hairpins or cruciforms, which are recognized with high specificity. In this review, we focused our attention on topoisomerase II recognizing DNA substrates that possess particular geometries. A strong cleavage site, as we identified in pBR322 DNA in the presence of ellipticine (site 22), appears to be characterized by a cruciform structure formed from two stable hairpins. The same sequence could also constitute a four-way junction structure stabilized by interactions involving ATC sequences. The latter have been shown to be able to promote Holliday junctions. We reviewed the recent literature that deals with the preferential recognition of crossovers by various topoisomerases. The single molecule relaxation experiments have demonstrated the differential abilities of the topoisomerases to recognize crossovers. It appears that enzymes, which distinguish the chirality of the crossovers, possess specialized domains dedicated to this function. We also stress that the formation of crossovers is dependent on the presence of adequate stabilizing sequences. Investigation of the impact of such structures on enzyme activity is important in order to both improve our knowledge of the mechanism of action of the topoisomerase II and to develop new inhibitors of this enzyme.
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Affiliation(s)
- Brigitte René
- Département de Biologie et Pharmacologie Structurales, UMR 8113 CNRS LBPA (ENS Cachan), Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France
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107
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Chenoweth DM, Poposki JA, Marques MA, Dervan PB. Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-kappaB binding inhibition. Bioorg Med Chem 2006; 15:759-70. [PMID: 17095230 PMCID: PMC3208330 DOI: 10.1016/j.bmc.2006.10.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 10/23/2006] [Accepted: 10/23/2006] [Indexed: 11/24/2022]
Abstract
A series of hairpin oligomers containing benzimidazole (Bi) and imidazopyridine (Ip) rings were synthesized and screened to target 5'-WGGGGW-3', a core sequence in the DNA-binding site of NF-kappaB, a prolific transcription factor important in biology and disease. Five Bi and Ip containing oligomers bound to the 5'-WGGGGW-3' site with high affinity. One of the oligomers (Im-Im-Im-Im-gamma-Py-Bi-Py-Bi-beta-Dp) was able to inhibit DNA binding by the transcription factor NF-kappaB.
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108
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Sadowska-Aleksiejew A, Rak J, Voityuk AA. Effects of intra base-pairs flexibility on hole transfer coupling in DNA. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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109
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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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110
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Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol 2006; 4:e180. [PMID: 16700628 PMCID: PMC1463026 DOI: 10.1371/journal.pbio.0040180] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Accepted: 03/29/2006] [Indexed: 02/05/2023] Open
Abstract
Mammalian genes are highly heterogeneous with respect to their nucleotide composition, but the functional consequences of this heterogeneity are not clear. In the previous studies, weak positive or negative correlations have been found between the silent-site guanine and cytosine (GC) content and expression of mammalian genes. However, previous studies disregarded differences in the genomic context of genes, which could potentially obscure any correlation between GC content and expression. In the present work, we directly compared the expression of GC-rich and GC-poor genes placed in the context of identical promoters and UTR sequences. We performed transient and stable transfections of mammalian cells with GC-rich and GC-poor versions of Hsp70, green fluorescent protein, and IL2 genes. The GC-rich genes were expressed several-fold to over a 100-fold more efficiently than their GC-poor counterparts. This effect was not due to different translation rates of GC-rich and GC-poor mRNA. On the contrary, the efficient expression of GC-rich genes resulted from their increased steady-state mRNA levels. mRNA degradation rates were not correlated with GC content, suggesting that efficient transcription or mRNA processing is responsible for the high expression of GC-rich genes. We conclude that silent-site GC content correlates with gene expression efficiency in mammalian cells. The effect of nucleotide composition on gene transcription is investigated for Hsp70, GFP, and IL-2, which all show increased expression to correlate with increased GC content at codon position 3.
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Affiliation(s)
- Grzegorz Kudla
- International Institute of Molecular and Cell Biology, Warsaw, Poland.
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111
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Abstract
The crystal structure of the four-stranded DNA Holliday junction has now been determined in the presence and absence of junction binding proteins, with the extended open-X form of the junction seen in all protein complexes, but the more compact stacked-X structure observed in free DNA. The structures of the stacked-X junction were crystallized because of an unexpected sequence dependence on the stability of this structure. Inverted repeat sequences that contain the general motif NCC or ANC favor formation of stacked-X junctions, with the junction cross-over occurring between the first two positions of the trinucleotides. This review focuses on the sequence dependent structure of the stacked-X junction and how it may play a role in structural recognition by a class of dimeric junction resolving enzymes that themselves show no direct sequence recognition.
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Affiliation(s)
- Patricia A. Khuu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA
| | - Andrea Regier Voth
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA
| | | | - P. Shing Ho
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331-7305, USA
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112
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Hays FA, Schirf V, Ho PS, Demeler B. Solution formation of Holliday junctions in inverted-repeat DNA sequences. Biochemistry 2006; 45:2467-71. [PMID: 16489738 PMCID: PMC2034439 DOI: 10.1021/bi052129x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of Holliday junctions has now been well characterized at the atomic level through single-crystal X-ray diffraction in symmetric (inverted-repeat) DNA sequences. At issue, however, is whether the formation of these four-stranded complexes in solution is truly sequence dependent in the manner proposed or is an artifact of the crystallization process and, therefore, has no relevance to the behavior of this central intermediate in homologous recombination and recombination-dependent cellular processes. Here, we apply analytical ultracentrifugation to demonstrate that the sequence d(CCGGTACCGG), which crystallizes in the stacked-X form of the junction, assembles into four-stranded junctions in solution in a manner that is dependent on the DNA and cation concentrations, with an equilibrium established between the junction and duplex forms at 100-200 microM DNA duplex. In contrast, the sequence d(CCGCTAGCGG), which has been crystallized as B-DNA, is seen to adopt only the double-helical form at all DNA and salt concentrations that were tested. Thus, the ACC trinucleotide core is now shown to be important for the formation of Holliday junctions in both crystals and in solution and can be estimated to contribute approximately -4 kcal/mol to stabilizing this recombination intermediate in inverted-repeat sequences.
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Affiliation(s)
| | | | - P. Shing Ho
- * To whom correspondence should be addressed. P.S.H.: telephone, (541) 737-2769; fax, (541) 737-0481; e-mail, . B.D.: telephone, (210) 567-6592; fax, (210) 567-6595; e-mail,
| | - Borries Demeler
- * To whom correspondence should be addressed. P.S.H.: telephone, (541) 737-2769; fax, (541) 737-0481; e-mail, . B.D.: telephone, (210) 567-6592; fax, (210) 567-6595; e-mail,
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113
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Dixit SB, Beveridge DL. Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction. Bioinformatics 2006; 22:1007-9. [PMID: 16489208 DOI: 10.1093/bioinformatics/btl059] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included. AVAILABILITY http://humphry.chem.wesleyan.edu:8080/MDDNA. SUPPLEMENTARY INFORMATION Supplementary data including color figures are available at Bioinformatics online.
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Affiliation(s)
- Surjit B Dixit
- Department of Chemistry and Molecular Biophysics Program Hall-Atwater Laboratories, Wesleyan University, Middletown, CT 06459, USA.
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114
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Hihath J, Xu B, Zhang P, Tao N. Study of single-nucleotide polymorphisms by means of electrical conductance measurements. Proc Natl Acad Sci U S A 2005; 102:16979-83. [PMID: 16284253 PMCID: PMC1287980 DOI: 10.1073/pnas.0505175102] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the complexities of DNA has been a hallmark of science for over a half century, and one of the important topics in DNA research is recognizing the occurrence of mutations in the base-stack. In this article, we present a study of SNPs by direct-contact electrical measurements to a single DNA duplex. We have used short, 11- and 12-bp dsDNA to investigate the change in conductance that occurs if a single base pair, a single base, or two separate bases in the stack are modified. All measurements are carried out in aqueous solution with the DNA chemically bound to the electrodes. These measurements demonstrate that the presence of a single base pair mismatch can be identified by the conductance of the molecule and can cause a change in the conductance of dsDNA by as much as an order of magnitude, depending on the specific details of the double helix and the single nucleotide polymorphism.
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Affiliation(s)
- Joshua Hihath
- Department of Electrical Engineering, Center for Solid State Electronics Research, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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115
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Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J 2005; 89:3721-40. [PMID: 16169978 PMCID: PMC1366942 DOI: 10.1529/biophysj.105.067397] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide basepair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, use the results to examine issues with regard to convergence and dynamical stability of MD on DNA, and determine the significance of sequence context effects on all unique dinucleotide steps. This information is essential to understand sequence effects on DNA structure and has implications on diverse problems in the structural biology of DNA. Calculations were carried out on the 136 cases embedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All simulations were carried out using a well-defined state-of-the-art MD protocol, the AMBER suite of programs, and the parm94 force field. In a previous article (Beveridge et al. 2004. Biophysical Journal. 87:3799-3813), the research design, details of the simulation protocol, and informatics issues were described. Preliminary results from 15 ns MD trajectories were presented for the d(CpG) step in all 10 unique sequence contexts. The results indicated the sequence context effects to be small for this step, but revealed that MD on DNA at this length of trajectory is subject to surprisingly persistent cooperative transitions of the sugar-phosphate backbone torsion angles alpha and gamma. In this article, we report detailed analysis of the entire trajectory database and occurrence of various conformational substates and its impact on studies of context effects. The analysis reveals a possible direct correspondence between the sequence-dependent dynamical tendencies of DNA structure and the tendency to undergo transitions that "trap" them in nonstandard conformational substates. The difference in mean of the observed basepair step helicoidal parameter distribution with different flanking sequence sometimes differs by as much as one standard deviation, indicating that the extent of sequence effects could be significant. The observations reveal that the impact of a flexible dinucleotide such as CpG could extend beyond the immediate basepair neighbors. The results in general provide new insight into MD on DNA and the sequence-dependent dynamical structural characteristics of DNA.
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Affiliation(s)
- Surjit B Dixit
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
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