dna-bound proteins Search Results


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  • 96
    Thermo Fisher single stranded dna
    Single Stranded Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 955 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore dna bound protein
    Dna Bound Protein, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dna bound proteins
    Dna Bound Proteins, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore protein bound dna
    Protein Bound Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Double Helix dna bound proteins
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Bound Proteins, supplied by Double Helix, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies dna bound proteins
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Bound Proteins, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Schiff Nutrition International dna bound protein
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Bound Protein, supplied by Schiff Nutrition International, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Cell Signaling Technology Inc dna bound runx proteins
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Bound Runx Proteins, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Millipore double stranded calf thymus dna
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Double Stranded Calf Thymus Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 94/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Millipore ssdna column
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Ssdna Column, supplied by Millipore, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Merck KGaA dna blocked protein g agarose
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Blocked Protein G Agarose, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Millipore protein a salmon sperm dna beads
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Protein A Salmon Sperm Dna Beads, supplied by Millipore, used in various techniques. Bioz Stars score: 96/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dna blocked protein g agarose
    <t>TRF-DNA</t> complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.
    Dna Blocked Protein G Agarose, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    GE Healthcare membrane bound cyclin d2 protein
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Membrane Bound Cyclin D2 Protein, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore protein a agarose salmon sperm dna
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Protein A Agarose Salmon Sperm Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 634 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Double Helix dna double helix
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Dna Double Helix, supplied by Double Helix, used in various techniques. Bioz Stars score: 96/100, based on 10290 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Double Helix atp bound msh2 msh6 signals dna repair
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Atp Bound Msh2 Msh6 Signals Dna Repair, supplied by Double Helix, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    GE Healthcare nap5 sephadex g25 dna grade column
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Nap5 Sephadex G25 Dna Grade Column, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher topoisomerase i bound vector
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Topoisomerase I Bound Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher protein a agarose beads
    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for <t>cyclin</t> D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin <t>D2</t> protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.
    Protein A Agarose Beads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3408 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    TRF-DNA complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.

    Journal: PLoS ONE

    Article Title: Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA

    doi: 10.1371/journal.pone.0089460

    Figure Lengend Snippet: TRF-DNA complex structure and comparison of the TRF1/TRF2 DBD domains. (A) A schematic representation of the system used for the calculation of the binding free energy profiles. The DNA dodecamer ( 5′-GGTTAGGGTTAG-3′ ) is aligned with the z axis, and the xy-distance between the centers of mass of TRF and DNA serves as a convenient reaction coordinate describing the binding process (for a precise definition of the reaction coordinate, see Methods and Fig. S1 ). The C-terminal recognition helix interacting with the DNA major groove is shown in green and the N-terminal linker binding within the minor groove is in purple. (B) Distribution of different types of amino acid residues in the TRF2 structure: hydrophobic residues are depicted in white, hydrophilic in green, basic in blue and acidic in red. (C) Differences in amino acid sequence between TRF1 and TRF2 mapped onto the TRF2 structure in a color coded manner: identical amino acids are marked in blue, green denotes conservative substitutions (little change) and red non-conservative substitutions (significant change). (D) Alignment of TRF1 and TRF2 sequences. Color-coding is consistent with panel C. The purple and green highlights denote the N-terminal linker and the C-terminal helix, respectively.

    Article Snippet: We also propose a simple model of the TRF/DNA binding equilibrium in which DNA-bound proteins bind to the double helix either tightly, via the C-terminal helix involved in sequence-specific interactions in the major groove, or loosely, through the N-terminal linker maintaining a non-specific contact with the minor groove or the DNA backbone.

    Techniques: Binding Assay, Sequencing

    Hydrogen bond profiles for individual TRF residues. The probability of hydrogen bond formation between individual protein residues and DNA as a function of the distance from the DNA axis. Only the residues for which the probability exceeds 0.2 are presented. The protein structure is subdivided into three separate regions: the N-terminal linker (top), the middle region (middle) and the C-terminal helix (bottom).

    Journal: PLoS ONE

    Article Title: Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA

    doi: 10.1371/journal.pone.0089460

    Figure Lengend Snippet: Hydrogen bond profiles for individual TRF residues. The probability of hydrogen bond formation between individual protein residues and DNA as a function of the distance from the DNA axis. Only the residues for which the probability exceeds 0.2 are presented. The protein structure is subdivided into three separate regions: the N-terminal linker (top), the middle region (middle) and the C-terminal helix (bottom).

    Article Snippet: We also propose a simple model of the TRF/DNA binding equilibrium in which DNA-bound proteins bind to the double helix either tightly, via the C-terminal helix involved in sequence-specific interactions in the major groove, or loosely, through the N-terminal linker maintaining a non-specific contact with the minor groove or the DNA backbone.

    Techniques:

    Direct and water-mediated hydrogen bonds between the TRF proteins and DNA bases. The pattern of direct and water-mediated hydrogen bonds between the TRF proteins and DNA bases. Only interactions between amino acid residues and nucleic bases are considered, as these base-specific contacts are potentially critical for sequence recognition. Filled circles at individual bases are scaled to reflect the probability that two residues are connected through a direct (orange) or water-mediated (cyan) hydrogen bond (for numeric probability values and hydrogen bond lifetimes, see Table S1 in File S1 and Table S5 in File S1 ). All contacts that are made with probability 0.05 are included. Grey percentage bars show the probability for a given base to be involved, at any given time, in either direct or water-mediated hydrogen bonds with the protein.

    Journal: PLoS ONE

    Article Title: Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA

    doi: 10.1371/journal.pone.0089460

    Figure Lengend Snippet: Direct and water-mediated hydrogen bonds between the TRF proteins and DNA bases. The pattern of direct and water-mediated hydrogen bonds between the TRF proteins and DNA bases. Only interactions between amino acid residues and nucleic bases are considered, as these base-specific contacts are potentially critical for sequence recognition. Filled circles at individual bases are scaled to reflect the probability that two residues are connected through a direct (orange) or water-mediated (cyan) hydrogen bond (for numeric probability values and hydrogen bond lifetimes, see Table S1 in File S1 and Table S5 in File S1 ). All contacts that are made with probability 0.05 are included. Grey percentage bars show the probability for a given base to be involved, at any given time, in either direct or water-mediated hydrogen bonds with the protein.

    Article Snippet: We also propose a simple model of the TRF/DNA binding equilibrium in which DNA-bound proteins bind to the double helix either tightly, via the C-terminal helix involved in sequence-specific interactions in the major groove, or loosely, through the N-terminal linker maintaining a non-specific contact with the minor groove or the DNA backbone.

    Techniques: Sequencing

    ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for cyclin D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin D2 protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.

    Journal: Molecular and Cellular Biology

    Article Title: Increased Expression of Cyclin D2 during Multiple States of Growth Arrest in Primary and Established Cells

    doi:

    Figure Lengend Snippet: ). Initially subconfluent NIH 3T3 murine fibroblasts were harvested at the days shown and analyzed for cyclin D2 expression by RT-PCR (B) and by Western immunoblotting using a monoclonal antibody against cyclin D2 protein (C). Amplification of cyclin D2 mRNA from NIH 3T3 cells consistently required five to six fewer PCR cycles than for similar detection of the transcript from HDFs. Assuming 80% efficiency for the PCR, this represents a 25- to 50-fold difference in abundance. (D) For Western blots, approximately 80 μg of total protein was loaded per lane, and equivalent protein loading of lanes was confirmed by Coomassie blue staining of gels.

    Article Snippet: The membrane-bound cyclin D2 protein was detected by enhanced chemiluminescence as instructed by the manufacturer (Amersham).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Western Blot, Amplification, Polymerase Chain Reaction, Staining

    Ectopic overexpression of cyclin D2 inhibits S-phase progression. Serum-synchronized HDFs microinjected with CMV-cyclin D2 (A) and CMV-cyclin E expression constructs (C) and analyzed for BrdU incorporation (B and D, respectively). The microinjected cells were detected by staining for cyclin D2 protein (A) or nonspecific IgG (C). Arrowheads in panels B and D indicate cells injected with cyclin D2 and cyclin E expression constructs, respectively. (E) Effect on DNA synthesis (as determined by BrdU incorporation) in HDFs microinjected with the control plasmid (RcCMV) or with a CMV construct expressing cyclin B1, D1, D2, or E. Each microinjection experiment was performed at least three times with approximately 100 cells injected in total for each experiment. (F) Inhibition of entry into the S phase of the cell cycle by transient transfection of expression constructs encoding p16, cyclin D2, and anti-sense cyclin D2. Results are plotted relative to RcCMV vector controls for cells positive for CD20 surface marker staining. Bars represent the averages and standard deviations of three independent transfections.

    Journal: Molecular and Cellular Biology

    Article Title: Increased Expression of Cyclin D2 during Multiple States of Growth Arrest in Primary and Established Cells

    doi:

    Figure Lengend Snippet: Ectopic overexpression of cyclin D2 inhibits S-phase progression. Serum-synchronized HDFs microinjected with CMV-cyclin D2 (A) and CMV-cyclin E expression constructs (C) and analyzed for BrdU incorporation (B and D, respectively). The microinjected cells were detected by staining for cyclin D2 protein (A) or nonspecific IgG (C). Arrowheads in panels B and D indicate cells injected with cyclin D2 and cyclin E expression constructs, respectively. (E) Effect on DNA synthesis (as determined by BrdU incorporation) in HDFs microinjected with the control plasmid (RcCMV) or with a CMV construct expressing cyclin B1, D1, D2, or E. Each microinjection experiment was performed at least three times with approximately 100 cells injected in total for each experiment. (F) Inhibition of entry into the S phase of the cell cycle by transient transfection of expression constructs encoding p16, cyclin D2, and anti-sense cyclin D2. Results are plotted relative to RcCMV vector controls for cells positive for CD20 surface marker staining. Bars represent the averages and standard deviations of three independent transfections.

    Article Snippet: The membrane-bound cyclin D2 protein was detected by enhanced chemiluminescence as instructed by the manufacturer (Amersham).

    Techniques: Over Expression, Expressing, Construct, BrdU Incorporation Assay, Staining, Injection, DNA Synthesis, Plasmid Preparation, Inhibition, Transfection, Marker

    Localization of cyclin D2 protein in growth-arrested and proliferating fibroblasts by indirect immunofluorescence. Fibroblasts plated on glass coverslips were fixed and stained for cyclin D2 protein, BrdU, or nonspecific rabbit IgG. (A) Localization of cyclin D2 in serum-deprived NIH 3T3 fibroblasts. (B) Cyclin D2 in contact-inhibited (day 6) NIH 3T3 fibroblasts. (C) Cyclin D2 in NIH 3T3 cells at the G 1 /S boundary. (D) Cells shown in panel C stained for BrdU. Quiescent NIH 3T3 cells were stimulated for 14 h with serum prior to fixing and staining for cyclin D2 protein and BrdU. Arrowheads in panel D indicate cells that stained positively for nuclear cyclin D2 protein but had not progressed into S phase, as determined by lack of BrdU staining. (E) NIH 3T3 cells in G 2 /M phase stained for cyclin D2 protein and photographed with long exposure times. (F) Cells from panel E stained for BrdU. Quiescent NIH 3T3 cells were stimulated for 20 to 22 h with serum and BrdU and were fixed and stained for cyclin D2 protein and BrdU. (G) Hs68 HDFs microinjected with cyclin D2 expression constructs and nonspecific antibodies. The cells shown are stained for nonspecific rabbit IgGs. (H) HDFs from panel G stained for ectopic overexpression of cyclin D2 protein. Arrowheads in panel H show microinjected cells staining brightly for cyclin D2 protein that localized to either the nucleus or the cytoplasm.

    Journal: Molecular and Cellular Biology

    Article Title: Increased Expression of Cyclin D2 during Multiple States of Growth Arrest in Primary and Established Cells

    doi:

    Figure Lengend Snippet: Localization of cyclin D2 protein in growth-arrested and proliferating fibroblasts by indirect immunofluorescence. Fibroblasts plated on glass coverslips were fixed and stained for cyclin D2 protein, BrdU, or nonspecific rabbit IgG. (A) Localization of cyclin D2 in serum-deprived NIH 3T3 fibroblasts. (B) Cyclin D2 in contact-inhibited (day 6) NIH 3T3 fibroblasts. (C) Cyclin D2 in NIH 3T3 cells at the G 1 /S boundary. (D) Cells shown in panel C stained for BrdU. Quiescent NIH 3T3 cells were stimulated for 14 h with serum prior to fixing and staining for cyclin D2 protein and BrdU. Arrowheads in panel D indicate cells that stained positively for nuclear cyclin D2 protein but had not progressed into S phase, as determined by lack of BrdU staining. (E) NIH 3T3 cells in G 2 /M phase stained for cyclin D2 protein and photographed with long exposure times. (F) Cells from panel E stained for BrdU. Quiescent NIH 3T3 cells were stimulated for 20 to 22 h with serum and BrdU and were fixed and stained for cyclin D2 protein and BrdU. (G) Hs68 HDFs microinjected with cyclin D2 expression constructs and nonspecific antibodies. The cells shown are stained for nonspecific rabbit IgGs. (H) HDFs from panel G stained for ectopic overexpression of cyclin D2 protein. Arrowheads in panel H show microinjected cells staining brightly for cyclin D2 protein that localized to either the nucleus or the cytoplasm.

    Article Snippet: The membrane-bound cyclin D2 protein was detected by enhanced chemiluminescence as instructed by the manufacturer (Amersham).

    Techniques: Immunofluorescence, Staining, BrdU Staining, Expressing, Construct, Over Expression