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Richter SN, Giaretta G, Comuzzi V, Leo E, Mitchenall LA, Fisher LM, Maxwell A, Palumbo M. Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases. Nucleic Acids Res 2007; 35:6075-85. [PMID: 17766248 PMCID: PMC2094056 DOI: 10.1093/nar/gkm653] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bacterial DNA gyrase and topoisomerase IV are selective targets of fluoroquinolones. Topoisomerase IV versus gyrase and Gram-positive versus Gram-negative behavior was studied based on the different recognition of DNA sequences by topoisomerase-quinolone complexes. A careful statistical analysis of preferred bases was performed on a large number (>400) of cleavage sites. We found discrete preferred sequences that were similar when using different enzymes (i.e. gyrase and topoisomerase IV) from the same bacterial source, but in part diverse when employing enzymes from different origins (i.e. Escherichia coli and Streptococcus pneumoniae). Subsequent analysis on the wild-type and mutated consensus sequences showed that: (i) Gn/Cn-rich sequences at and around the cleavage site are hot spots for quinolone-mediated strand breaks, especially for E. coli topoisomerases: we elucidated positions required for quinolone and enzyme recognition; (ii) for S. pneumoniae enzymes only, A and T at positions -2 and +6 are discriminating cleavage determinants; (iii) symmetry of the target sequence is a key trait to promote cleavage and (iv) the consensus sequence adopts a heteronomous A/B conformation, which may trigger DNA processing by the enzyme-drug complex.
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Affiliation(s)
- Sara N. Richter
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Giulia Giaretta
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Valentina Comuzzi
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Elisabetta Leo
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Lesley A. Mitchenall
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - L. Mark Fisher
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Manlio Palumbo
- Department of Pharmaceutical Sciences, Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35131 Padova, Italy, Molecular Genetics Group, Molecular and Metabolic Signalling Centre, Division of Basic Medical Sciences, St. George's, University of London, London SW17 0RE and Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
- *To whom correspondence should be addressed. +39049 827 5699+39049 827 5366
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Stefl R, Trantírek L, Vorlícková M, Koca J, Sklenár V, Kypr J. A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC). J Mol Biol 2001; 307:513-24. [PMID: 11254379 DOI: 10.1006/jmbi.2001.4484] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used CD spectroscopy, NMR spectroscopy and unrestrained molecular dynamics to study conformational properties of a DNA duplex formed by the self-complementary octamer d(GGGGCCCC). Its unusual CD spectrum contains features indicating A-like stacking of half of the bases, whereas the other half stack in a B-like fashion. Unrestrained molecular dynamics simulations converged to a stable B-like double-helix of d(GGGGCCCC). However, the double-helix contained a central hole whose size was half of that occurring in structure A. In the canonical structure B, the hole does not exist at all because the base-pairs cross the double-helix centre. The cytosine bases were stacked in the duplex of d(GGGGCCCC) as in structure B, while stacking of the guanine bases displayed features characteristic for structure A. NMR spectroscopy revealed that the A-like guanine-guanine stacking was accompanied by an increased tendency of the deoxyribose rings attached to the guanine bases to be puckered in an A-like fashion. Otherwise, the duplex of d(GGGGCCCC) showed no clash, no bend and no other significant deviation from structure B. The present analysis demonstrates a remarkable propensity of the guanine runs to stack in an A-like fashion even within the B-DNA framework. This property explains why the oligo(dG). oligo(dC) tracts switch into structure A so easily. Secondly, this property may influence replication, because structure A is replicated more faithfully than structure B. Thirdly, the oligo(dG) runs might have played an important role in early evolution, when DNA took on functions that originally evolved on RNA. Fourthly, the present study extends the vocabulary of DNA secondary structures by the heteronomous duplex of d(GGGGCCCC) in which the B-like strand of oligo(dC) is bound to the A-like strand of oligo(dG).
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Affiliation(s)
- R Stefl
- Institute of Biophysics of the Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
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Abstract
We calculated nucleotide distribution curves along the DNA molecules of the human chromosomes 21 and 22, their correlations in more than 10,000 equidistant positions, and subjected the correlations to cluster analysis. The cluster analysis demonstrated that both DNA molecules were composed of two types of segments exhibiting qualitatively different correlations. The segments differed most in the correlation of the distribution curves of cytosine and guanine, which was very high in type I segments but weak in type II segments. The type I and II segments also significantly differed in the correlations of the distribution curves of adenine with thymine. In addition, adenine strongly anticorrelated with cytosine but this anticorrelation was uniform along both chromosomes and, therefore, it did not contribute to the distinction of the two types of segments. The segments were up to 100 kbp long but they had nothing in common with isochores. Building blocks of the mosaic structure of the DNA molecules of the human chromosomes 21 and 22 are very similar but different in several interesting aspects from those of E. coli.
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Affiliation(s)
- D Häring
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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Abstract
The human genome is described in the literature as being composed of the isochores, i.e., long (hundreds of kilobases) segments with a homogeneous (G + C) content. We calculated the (G + C) content variations along the DNA molecules of the human chromosomes 21 and 22 and found the variations to be higher everywhere compared to the randomized sequences. Hence the (G + C) content is certainly not homogeneous on the isochore scale in the two human chromosomes. In addition, we found no significant difference between the two human molecules and the genome of E. coli regarding the (G + C) content variations. Hence no isochores are either present in the DNA molecules of the human chromosomes 21 and 22, or the isochores are also present in the genome of Escherichia coli. In any case, the present communication demonstrates that the isochores should be defined in unambiguous molecular terms if they are to be used for an up-to-date genome structure characterization.
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Affiliation(s)
- D Häring
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, CZ-61265, Czech Republic
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