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  1. Article: Changing disciplinary borders into frontiers of progress.

    Falaschi, Arturo

    HFSP journal

    2008  Volume 1, Issue 1, Page(s) 1–3

    Language English
    Publishing date 2008-01-25
    Publishing country France
    Document type Journal Article
    ZDB-ID 2277026-4
    ISSN 1955-205X ; 1955-2068
    ISSN (online) 1955-205X
    ISSN 1955-2068
    DOI 10.2976/1.2422707/10.2976/1
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  2. Article: The HFSP Journal one year on: moving forward with a new feature.

    Falaschi, Arturo

    HFSP journal

    2008  Volume 2, Issue 3, Page(s) 123

    Language English
    Publishing date 2008-05-12
    Publishing country France
    Document type Journal Article
    ZDB-ID 2277026-4
    ISSN 1955-205X ; 1955-2068
    ISSN (online) 1955-205X
    ISSN 1955-2068
    DOI 10.1080/19552068.2008.9635743
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  3. Article ; Online: Binding of DNA topoisomerases I and II to replication origins.

    Falaschi, Arturo

    Methods in molecular biology (Clifton, N.J.)

    2009  Volume 582, Page(s) 131–143

    Abstract: The interaction of DNA topology modifying enzymes with eukaryotic DNA replication origins can be detected with nucleotide precision exploiting the action of enzyme poisons specific for type I or type II DNA topoisomerases. Using the topoisomerase I ... ...

    Abstract The interaction of DNA topology modifying enzymes with eukaryotic DNA replication origins can be detected with nucleotide precision exploiting the action of enzyme poisons specific for type I or type II DNA topoisomerases. Using the topoisomerase I poison camptothecin and the topoisomerase II poison VP16, the precise sites of interaction of these enzymes around the lamin B2 origin have been identified at different points in the cell cycle. The procedure can be applied to any origin for which the sequence has been identified within approximately 1 kb.
    MeSH term(s) Animals ; Antineoplastic Agents, Phytogenic/metabolism ; Base Sequence ; Biological Assay/methods ; Camptothecin/metabolism ; Cell Cycle/physiology ; DNA Topoisomerases, Type I/metabolism ; DNA Topoisomerases, Type II/metabolism ; Enzyme Inhibitors/metabolism ; Etoposide/metabolism ; HeLa Cells ; Humans ; Lamin Type B/genetics ; Molecular Sequence Data ; Protein Binding ; Replication Origin ; Topoisomerase I Inhibitors ; Topoisomerase II Inhibitors
    Chemical Substances Antineoplastic Agents, Phytogenic ; Enzyme Inhibitors ; Lamin Type B ; Topoisomerase I Inhibitors ; Topoisomerase II Inhibitors ; Etoposide (6PLQ3CP4P3) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; DNA Topoisomerases, Type II (EC 5.99.1.3) ; Camptothecin (XT3Z54Z28A)
    Language English
    Publishing date 2009-09-09
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-60761-340-4_11
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  4. Article: Similia similibus: pairing of homologous chromosomes driven by the physicochemical properties of DNA.

    Falaschi, Arturo

    HFSP journal

    2008  Volume 2, Issue 5, Page(s) 257–261

    Abstract: Genetic recombination in eukaryotes requires the pairing of homologous chromosomes to allow precise molecular exchanges between chromosome pairs at intertwined structures called Holliday junctions, the formation of which requires the action of the RecA ... ...

    Abstract Genetic recombination in eukaryotes requires the pairing of homologous chromosomes to allow precise molecular exchanges between chromosome pairs at intertwined structures called Holliday junctions, the formation of which requires the action of the RecA protein. The mechanism behind the precise pairing of structures as long as chromosomes remains mysterious. In yeast, during the initial phases of meiosis, chromosomes are paired at approximately 65 kilobase intervals via paranemic interactions that do not involve strand breakage nor the intervention of analogs of the RecA protein. It has been proposed that these paranemic interactions could occur between G-rich chromosomal regions, but putting in register stretches of homologous sequences hundreds of kb long remains challenging. Recent developments on the theory of the physicochemical properties of DNA in aqueous solutions, in presence of di- or multivalent counterions, leads to the prediction that molecules with the same sequence tend to pair spontaneously by paranemic interactions depending on the electrostatic properties of DNA. Experimental support for this prediction has now been provided in vitro with naked DNA. This newly discovered property of DNA duplexes may thus provide a clue to solve the puzzle of the premeiotic pairing.
    Language English
    Publishing date 2008-09-15
    Publishing country France
    Document type Journal Article
    ZDB-ID 2277026-4
    ISSN 1955-205X ; 1955-2068
    ISSN (online) 1955-205X
    ISSN 1955-2068
    DOI 10.2976/1.2980374
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  5. Article ; Online: Frontiers in life science.

    Cookson, Rod / Ferrier, Valerie / Falaschi, Arturo

    HFSP journal

    2010  Volume 4, Issue 3-4, Page(s) 93

    Language English
    Publishing date 2010-06-03
    Publishing country France
    Document type Journal Article
    ZDB-ID 2277026-4
    ISSN 1955-205X ; 1955-2068
    ISSN (online) 1955-205X
    ISSN 1955-2068
    DOI 10.1080/19552068.2010.9635845
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Molecular mechanics and DNA replication regulation.

    Falaschi, Arturo / Abdurashidova, Gulnara

    HFSP journal

    2007  Volume 1, Issue 4, Page(s) 215–219

    Abstract: Magnetic and optical tweezers are providing novel insights on the structure, energetics, and functional dynamics of biological macromolecules. The modulation of DNA topology has provided very appropriate opportunities to study with these technologies the ...

    Abstract Magnetic and optical tweezers are providing novel insights on the structure, energetics, and functional dynamics of biological macromolecules. The modulation of DNA topology has provided very appropriate opportunities to study with these technologies the energetic and mechanistic features of the action of DNA topoisomerases, the enzymes that maintain the physiological level of negative superhelicity in the genome. Modulation of the superhelical state of the DNA replication origins is essential for the initiation of DNA synthesis in prokaryotes and eukaryotes. The results obtained recently from independent studies of two different groups combine to give new insights on the topological aspects of this process. With magnetic tweezers it was shown that the inhibition of human topoisomerase I by camptothecin freezes the drug-enzyme-DNA complex and specifically forbids the relaxation of positive supercoils; a study of the in vivo role of topoisomerase I on the activation of a human origin showed that this process is forbidden when the enzyme is frozen on the origin DNA by camptothecin. The inhibition of the relaxation of positive supercoils, probably introduced by the proteins performing origin activation, is therefore lethal for this process. Thus, the use of advanced physical technologies provides insights on an essential biological process.
    Language English
    Publishing date 2007-11-16
    Publishing country France
    Document type Journal Article
    ZDB-ID 2277026-4
    ISSN 1955-205X ; 1955-2068
    ISSN (online) 1955-205X
    ISSN 1955-2068
    DOI 10.2976/1.2812798
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  7. Article ; Online: DNA replication, development and cancer: a homeotic connection?

    Falaschi, Arturo / Abdurashidova, Gulnara / Biamonti, Giuseppe

    Critical reviews in biochemistry and molecular biology

    2010  Volume 45, Issue 1, Page(s) 14–22

    Abstract: The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in ... ...

    Abstract The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in multi-molecular associations that assure their target and function specificity. Homeotic proteins are known to play a role in the positive or negative regulation of cell proliferation. Furthermore, many homeotic proteins are actually proto-oncogenes, since different translocations involving their genes cause tumors, particularly in the hematopoietic system. A one-hybrid screen to detect proteins with affinity for the lamin B2 replication origin identified three homeotic proteins, namely HoxA13, HoxC10 and HoxC13. Recent data demonstrate that the HoxC13 oncoprotein specifically associates with replication foci and binds in vitro and in vivo to several human DNA replication origins. Moreover, Hox proteins interact with geminin, a regulator of cell cycle progression, and control the interaction of this protein with the DNA replication licensing factor Ctd1. Thus, the homeotic proteins, by participating directly in the function of DNA replication origins, may provide a direct link between the accurate regulation of DNA replication required by the morphogenetic program and the deregulation of this process typical of cancer.
    MeSH term(s) Animals ; Cell Proliferation ; DNA Replication ; Gene Expression Regulation, Developmental ; Genome, Human ; Homeodomain Proteins/physiology ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Replication Origin ; Substrate Specificity
    Chemical Substances Homeodomain Proteins
    Language English
    Publishing date 2010-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1000977-2
    ISSN 1549-7798 ; 1381-3455 ; 1040-9238
    ISSN (online) 1549-7798
    ISSN 1381-3455 ; 1040-9238
    DOI 10.3109/10409230903365608
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1024: Show issues Location:
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  8. Article: Identification of start sites of bi-directional DNA synthesis at eukaryotic DNA replication origins.

    Vindigni, Alessandro / Abdurashidova, Gulnara / Falaschi, Arturo

    Methods in molecular biology (Clifton, N.J.)

    2004  Volume 240, Page(s) 105–122

    MeSH term(s) DNA Replication/genetics ; Eukaryotic Cells ; HeLa Cells ; Humans
    Language English
    Publishing date 2004-01-01
    Publishing country United States
    Document type Journal Article
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1385/1-59259-434-4:105
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  9. Article ; Online: Stimulation of the DNA unwinding activity of human DNA helicase II/Ku by phosphorylation.

    Ochem, Alexander E / Rechreche, Hocine / Skopac, Doris / Falaschi, Arturo

    Archives of biochemistry and biophysics

    2008  Volume 470, Issue 1, Page(s) 1–7

    Abstract: The Ku autoantigen is a heterodimeric protein of 70- and 83-kDa subunits, endowed with duplex DNA end-binding capacity and DNA helicase activity (Human DNA Helicase II, HDH II). HDH II/Ku is well established as the DNA binding component, the regulatory ... ...

    Abstract The Ku autoantigen is a heterodimeric protein of 70- and 83-kDa subunits, endowed with duplex DNA end-binding capacity and DNA helicase activity (Human DNA Helicase II, HDH II). HDH II/Ku is well established as the DNA binding component, the regulatory subunit as well as a substrate for the DNA-dependent protein kinase DNA-PK, a complex involved in the repair of DNA double-strand breaks and in V(D)J recombination in eukaryotes. The effects of phosphorylation by this kinase on the helicase activity of Escherichia coli-produced HDH II/Ku were studied. The rate of DNA unwinding by recombinant HDH II/Ku heterodimer is stimulated at least fivefold upon phosphorylation by DNA-PK(cs). This stimulation is due to the effective transfer of phosphate residues to the helicase rather than the mere presence of the complex. In vitro dephosphorylation of HeLa cellular HDH II/Ku caused a significant decrease in the DNA helicase activity of this enzyme.
    MeSH term(s) DNA/chemistry ; DNA/metabolism ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; Enzyme Activation ; HeLa Cells ; Humans ; Nucleic Acid Conformation ; Phosphorylation
    Chemical Substances DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2008-02-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2007.11.005
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    Uc I Zs.237: Show issues Location:
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  10. Article ; Online: Enhancement of gene targeting in human cells by intranuclear permeation of the Saccharomyces cerevisiae Rad52 protein.

    Kalvala, Arjun / Rainaldi, Giuseppe / Di Primio, Cristina / Liverani, Vania / Falaschi, Arturo / Galli, Alvaro

    Nucleic acids research

    2010  Volume 38, Issue 14, Page(s) e149

    Abstract: The introduction of exogenous DNA in human somatic cells results in a frequency of random integration at least 100-fold higher than gene targeting (GT), posing a seemingly insurmountable limitation for gene therapy applications. We previously reported ... ...

    Abstract The introduction of exogenous DNA in human somatic cells results in a frequency of random integration at least 100-fold higher than gene targeting (GT), posing a seemingly insurmountable limitation for gene therapy applications. We previously reported that, in human cells, the stable over-expression of the Saccharomyces cerevisiae Rad52 gene (yRAD52), which plays the major role in yeast homologous recombination (HR), caused an up to 37-fold increase in the frequency of GT, indicating that yRAD52 interacts with the double-strand break repair pathway(s) of human cells favoring homologous integration. In the present study, we tested the effect of the yRad52 protein by delivering it directly to the human cells. To this purpose, we fused the yRAD52 cDNA to the arginine-rich domain of the TAT protein of HIV (tat11) that is known to permeate the cell membranes. We observed that a recombinant yRad52tat11 fusion protein produced in Escherichia coli, which maintains its ability to bind single-stranded DNA (ssDNA), enters the cells and the nuclei, where it is able to increase both intrachromosomal recombination and GT up to 63- and 50-fold, respectively. Moreover, the non-homologous plasmid DNA integration decreased by 4-fold. yRAD52tat11 proteins carrying point mutations in the ssDNA binding domain caused a lower or nil increase in recombination proficiency. Thus, the yRad52tat11 could be instrumental to increase GT in human cells and a 'protein delivery approach' offers a new tool for developing novel strategies for genome modification and gene therapy applications.
    MeSH term(s) Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; DNA, Single-Stranded/metabolism ; Gene Targeting/methods ; HeLa Cells ; Humans ; Mutation ; Rad52 DNA Repair and Recombination Protein/genetics ; Rad52 DNA Repair and Recombination Protein/metabolism ; Recombinant Fusion Proteins/analysis ; Recombinant Fusion Proteins/biosynthesis ; Recombination, Genetic ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; tat Gene Products, Human Immunodeficiency Virus/genetics
    Chemical Substances DNA, Single-Stranded ; RAD52 protein, S cerevisiae ; Rad52 DNA Repair and Recombination Protein ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; tat Gene Products, Human Immunodeficiency Virus
    Language English
    Publishing date 2010-06-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkq486
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