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Alexandrov LB, Bishop AR, Rasmussen KØ, Alexandrov BS. The role of structural parameters in DNA cyclization. BMC Bioinformatics 2016; 17:68. [PMID: 26846597 PMCID: PMC4743258 DOI: 10.1186/s12859-016-0897-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization. RESULTS We calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data. CONCLUSIONS Our data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. .,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Alan R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Boian S Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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Blakaj DM, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, Burk RD, Brenowitz M. Evolutionary and biophysical relationships among the papillomavirus E2 proteins. Front Biosci (Landmark Ed) 2009; 14:900-17. [PMID: 19273107 DOI: 10.2741/3285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed.
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Affiliation(s)
- Dukagjin M Blakaj
- Department of Biochemistry, Albert Einstein College of Medicine,1300 Morris Park Avenue, Bronx NY 10461, USA
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Lee I, Berdis A. Fluorescent analysis of translesion DNA synthesis by using a novel, non-natural nucleotide analogue. Chembiochem 2007; 7:1990-7. [PMID: 17091513 DOI: 10.1002/cbic.200600128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of nucleotide incorporation opposite an abasic site, a commonly formed DNA lesion, by using two fluorescent nucleotide analogues, 2-aminopurine deoxyribose triphosphate (2-APTP) and 5-phenylindole deoxyribose triphosphate (5-PhITP). In both cases, the kinetics of incorporation were compared by using a 32P-radiolabel extension assay versus a fluorescence-quenching assay. Although 2-APTP is efficiently incorporated opposite a templating nucleobase (thymine), the kinetics for incorporation opposite an abasic site are significantly slower. The lower catalytic efficiency hinders its use as a probe to study translesion DNA synthesis. In contrast, the rate constant for the incorporation of 5-PhITP opposite the DNA lesion is 100-fold faster than that for 2-APTP. Nearly identical kinetic parameters are obtained from fluorescence quenching or the 32P-radiolabel assay. Surprisingly, distinct differences in the kinetics of 5-PhITP incorporation opposite the DNA lesion are detected when using either bacteriophage T4 DNA polymerase or the Escherichia coli Klenow fragment. These differences suggest that the dynamics of nucleotide incorporation opposite an abasic site are polymerase-dependent. Collectively, these data indicate that 5-PhITP can be used to perform real-time analyses of translesion DNA synthesis as well as to functionally probe differences in polymerase function.
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Affiliation(s)
- Irene Lee
- Case Western Reserve University, 2109 Adelbert Road, Cleveland, OH 44106, USA
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Blakaj DM, Kattamuri C, Khrapunov S, Hegde RS, Brenowitz M. Indirect readout of DNA sequence by papillomavirus E2 proteins depends upon net cation uptake. J Mol Biol 2006; 358:224-40. [PMID: 16513133 DOI: 10.1016/j.jmb.2006.01.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 01/08/2006] [Accepted: 01/27/2006] [Indexed: 10/25/2022]
Abstract
The papillomavirus E2 proteins bind with high affinity to palindromic DNA sequences consisting of two highly conserved four base-pair sequences flanking a variable "spacer" of identical length (ACCG NNNN CGGT). While intimate contacts are observed between the bound proteins and conserved DNA in the available co-crystal structures, no contact is seen between the proteins and the spacer DNA. The ability of human papillomavirus strain 16 (HPV-16) E2 and bovine papillomavirus strain 1 (BPV-1) E2 to discriminate among binding sites with different spacer sequences is dependent on their sensitivity to the unique conformational and/or dynamic properties of the spacer DNA in a process termed "indirect readout". Differential sequence-specific K(+) uptake in low ionic strength solutions lacking Mg(2+) is observed upon E2 protein binding to sites containing the AATT, TTAA or ACGT spacer sequences. In contrast, the cation displacement typical of protein-DNA complex formation is observed at high K(+) concentrations or in the presence of Mg(2+). These results are interpreted to reflect the sequence-specific stabilization of bent DNA conformations by cations localized within the narrowed minor grooves of the protein-bound DNA and the intrinsic structure and flexibility of the DNA target. Mg(2+) differentially affects the binding of the HPV-16 E2 DNA binding domain (HPV16-E2/D) and the BPV-1 E2 DNA binding domain (BPV1-E2/D) to sites bearing different spacer sequences. This study suggests that monovalent and divalent cations contribute to the discrimination of DNA structure and flexibility that could in turn contribute to the specificity with which HPV16-E2/D and BPV1-E2/D mediate DNA replication and gene transcription.
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Affiliation(s)
- Dukagjin M Blakaj
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Seibert E, Chin AS, Pfleiderer W, Hawkins ME, Laws WR, Osman R, Ross JBA. pH-Dependent Spectroscopy and Electronic Structure of the Guanine Analogue 6,8-Dimethylisoxanthopterin. J Phys Chem A 2002. [DOI: 10.1021/jp026904j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eleanore Seibert
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - Alexander S. Chin
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - Wolfgang Pfleiderer
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - Mary E. Hawkins
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - William R. Laws
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - Roman Osman
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
| | - J. B. Alexander Ross
- Departments of Pharmacology and Biological Chemistry and Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, Facultät für Chemie, Universität Konstanz, Konstanz, Germany, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, and Department of Chemistry, University of Montana, Missoula, Montana 59812
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