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Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

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Nucleic Acids Research

Oxford University Press

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      Abstract

      The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes.

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      • Record: found
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      • Article: not found

      T-Coffee: A novel method for fast and accurate multiple sequence alignment.

      We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests. Copyright 2000 Academic Press.
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        • Record: found
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        • Article: not found

        Histone acetylation and transcriptional regulatory mechanisms.

         K Struhl (1998)
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          • Record: found
          • Abstract: not found
          • Article: not found

          Colloquium: The physics of charge inversion in chemical and biological systems

            Bookmark

            Author and article information

            Affiliations
            Department of Biology, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, People's Republic of China
            Author notes
            *To whom correspondence should be addressed +86-852-2358-7343+86-852-2358-1559 botin@ 123456ust.hk
            Journal
            Nucleic Acids Res
            Nucleic Acids Res
            nar
            Nucleic Acids Research
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            April 2007
            4 April 2007
            4 April 2007
            : 35
            : 8
            : 2573-2583
            17412706 1885672 10.1093/nar/gkm165
            © 2007 The Author(s)

            This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

            Categories
            Molecular Biology

            Genetics

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