dna double helix Search Results


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  • 99
    Millipore right handed double helical dna
    Right Handed Double Helical Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Double Helix deoxyribonucleic acid dna double helix
    A. Schematic diagram showing DnaI-mediated loading of the G. kaustophilus ring helicase, DnaC. Monomers of DnaI (green) upon binding to <t>ATP</t> assemble into a hexameric ring around single-stranded <t>DNA.</t> The N-terminal tier of the DnaI ring interacts with the C-terminal tier of the helicase (brown) recruiting and opening up the helicase ring. Single-stranded DNA passes into the central channel of the ring. Binding of the DNA to the internal surface of the central channel stimulates the helicase activity and induces dissociation of DnaI ( Tsai et al ., 2009 ). B. Loading of helicase-primase bifunctional proteins. A helicase-primase protein initially interacts with the single-stranded DNA via its primase domains inducing an opening of the helicase ring with the DNA passing through the gap into the central channel. Binding of the DNA in the central cavity induces ring closure and activates the helicase-primase protein. The T7 gp4 primase-helicase crystallized as a heptamer (the seven subunits are coloured differently in the side view of the structure shown) but the translocating species along single-stranded DNA is believed to be the hexamer ( Toth et al ., 2003 ).
    Deoxyribonucleic Acid Dna Double Helix, supplied by Double Helix, used in various techniques. Bioz Stars score: 85/100, based on 1140 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    A. Schematic diagram showing DnaI-mediated loading of the G. kaustophilus ring helicase, DnaC. Monomers of DnaI (green) upon binding to ATP assemble into a hexameric ring around single-stranded DNA. The N-terminal tier of the DnaI ring interacts with the C-terminal tier of the helicase (brown) recruiting and opening up the helicase ring. Single-stranded DNA passes into the central channel of the ring. Binding of the DNA to the internal surface of the central channel stimulates the helicase activity and induces dissociation of DnaI ( Tsai et al ., 2009 ). B. Loading of helicase-primase bifunctional proteins. A helicase-primase protein initially interacts with the single-stranded DNA via its primase domains inducing an opening of the helicase ring with the DNA passing through the gap into the central channel. Binding of the DNA in the central cavity induces ring closure and activates the helicase-primase protein. The T7 gp4 primase-helicase crystallized as a heptamer (the seven subunits are coloured differently in the side view of the structure shown) but the translocating species along single-stranded DNA is believed to be the hexamer ( Toth et al ., 2003 ).

    Journal: Molecular Microbiology

    Article Title: Loading mechanisms of ring helicases at replication origins

    doi: 10.1111/j.1365-2958.2012.08012.x

    Figure Lengend Snippet: A. Schematic diagram showing DnaI-mediated loading of the G. kaustophilus ring helicase, DnaC. Monomers of DnaI (green) upon binding to ATP assemble into a hexameric ring around single-stranded DNA. The N-terminal tier of the DnaI ring interacts with the C-terminal tier of the helicase (brown) recruiting and opening up the helicase ring. Single-stranded DNA passes into the central channel of the ring. Binding of the DNA to the internal surface of the central channel stimulates the helicase activity and induces dissociation of DnaI ( Tsai et al ., 2009 ). B. Loading of helicase-primase bifunctional proteins. A helicase-primase protein initially interacts with the single-stranded DNA via its primase domains inducing an opening of the helicase ring with the DNA passing through the gap into the central channel. Binding of the DNA in the central cavity induces ring closure and activates the helicase-primase protein. The T7 gp4 primase-helicase crystallized as a heptamer (the seven subunits are coloured differently in the side view of the structure shown) but the translocating species along single-stranded DNA is believed to be the hexamer ( Toth et al ., 2003 ).

    Article Snippet: Structural distortions imposed on the DNA double helix and a squeeze-pump ATP-driven action of the two head-to-head hexameric helicases pulling the DNA in opposite directions force melting of the double helix (reviewed in ).

    Techniques: Binding Assay, Activity Assay

    A. Self-loading of the SV40 LTag DNA helicase. Two monomers of LTag bind head to head to the SV40 core ori sequence via their OBDs (green). One hexamer assembles around the double-stranded DNA followed by the second hexamer in a cooperative manner. The J-OBD cap is sandwiched between the helicase rings and forms a network of interactions holding the dodecamer together. The double-stranded DNA is melted by the reverse ‘iris pumping’ action of the two helicases and the single strands loop out of the dodecamer from side channels at the periphery of the helicase rings. Six positively charged side channels that could potentially provide outlets for the unwound single strands can be seen in the crystal structure of the SV40 LTag helicase domains ( Li et al ., 2003 ) and two of them, in the pink and yellow monomers, are highlighted in two different side views (60° rotated around the vertical axis relative to each other) of the hexameric ring. B. Self-loading mechanism of the papilloma virus E1 DNA helicase. Two E1-ATP subunits bind cooperatively to the specific ori sequence via their DBDs (green) to form two head-to-head mini-filaments. Upon ATP hydrolysis a double hexamer forms. Each hexamer encircles opposite single strands and the DBDs form a cap sandwiched between the two helicase hexamers. The two hexamers translocate 3′–5′ in the opposite directions along their respective strands, as shown by the opposing vertical arrows, effectively pumping the double-stranded DNA towards the centre of the complex. Two ‘pumping mechanisms’ are possible. The two hexameric rings dissociate and keep on moving in opposite directions expanding the ensuing ‘bubble’ of the separated DNA duplex. Alternatively, the two hexameric rings as they cross each other adhere to each other via interactions of their helicase domains resulting in a double hexamer that keeps on pumping the double-stranded DNA towards the centre of the complex yielding a ‘rabbit ear structure’. The latter is supported by the crystal structure of the E1 helicase domains showing two hexameric rings associated with each other but not collinear as each encircles a different single strand ( Enemark and Joshua-Tor, 2006 ). C. Loading of the MCM2–7 eukaryotic DNA helicase. MCM2–7 is loaded onto double-stranded DNA as a dodecamer, by the ORC/Cdc6 complex. Double-stranded DNA passes to the interior of the MCM2–7 ring channel through an opening between the MCM2 and 5 subunits. Binding of the dodecamer to double-stranded DNA distorts the DNA and additional pumping of the DNA by the two hexamers towards the centre of the dodecamer causes melting of the duplex inside the central cavity. Binding of the GINS/Cdc45 complex (green) to the periphery of the rings stabilizes open active forms of the rings, excluding different single strands from the central channels thus conferring 3′–5′ directionality along anti-parallel strands. The two hexamers then dissociate from each other and translocate in opposite directions.

    Journal: Molecular Microbiology

    Article Title: Loading mechanisms of ring helicases at replication origins

    doi: 10.1111/j.1365-2958.2012.08012.x

    Figure Lengend Snippet: A. Self-loading of the SV40 LTag DNA helicase. Two monomers of LTag bind head to head to the SV40 core ori sequence via their OBDs (green). One hexamer assembles around the double-stranded DNA followed by the second hexamer in a cooperative manner. The J-OBD cap is sandwiched between the helicase rings and forms a network of interactions holding the dodecamer together. The double-stranded DNA is melted by the reverse ‘iris pumping’ action of the two helicases and the single strands loop out of the dodecamer from side channels at the periphery of the helicase rings. Six positively charged side channels that could potentially provide outlets for the unwound single strands can be seen in the crystal structure of the SV40 LTag helicase domains ( Li et al ., 2003 ) and two of them, in the pink and yellow monomers, are highlighted in two different side views (60° rotated around the vertical axis relative to each other) of the hexameric ring. B. Self-loading mechanism of the papilloma virus E1 DNA helicase. Two E1-ATP subunits bind cooperatively to the specific ori sequence via their DBDs (green) to form two head-to-head mini-filaments. Upon ATP hydrolysis a double hexamer forms. Each hexamer encircles opposite single strands and the DBDs form a cap sandwiched between the two helicase hexamers. The two hexamers translocate 3′–5′ in the opposite directions along their respective strands, as shown by the opposing vertical arrows, effectively pumping the double-stranded DNA towards the centre of the complex. Two ‘pumping mechanisms’ are possible. The two hexameric rings dissociate and keep on moving in opposite directions expanding the ensuing ‘bubble’ of the separated DNA duplex. Alternatively, the two hexameric rings as they cross each other adhere to each other via interactions of their helicase domains resulting in a double hexamer that keeps on pumping the double-stranded DNA towards the centre of the complex yielding a ‘rabbit ear structure’. The latter is supported by the crystal structure of the E1 helicase domains showing two hexameric rings associated with each other but not collinear as each encircles a different single strand ( Enemark and Joshua-Tor, 2006 ). C. Loading of the MCM2–7 eukaryotic DNA helicase. MCM2–7 is loaded onto double-stranded DNA as a dodecamer, by the ORC/Cdc6 complex. Double-stranded DNA passes to the interior of the MCM2–7 ring channel through an opening between the MCM2 and 5 subunits. Binding of the dodecamer to double-stranded DNA distorts the DNA and additional pumping of the DNA by the two hexamers towards the centre of the dodecamer causes melting of the duplex inside the central cavity. Binding of the GINS/Cdc45 complex (green) to the periphery of the rings stabilizes open active forms of the rings, excluding different single strands from the central channels thus conferring 3′–5′ directionality along anti-parallel strands. The two hexamers then dissociate from each other and translocate in opposite directions.

    Article Snippet: Structural distortions imposed on the DNA double helix and a squeeze-pump ATP-driven action of the two head-to-head hexameric helicases pulling the DNA in opposite directions force melting of the double helix (reviewed in ).

    Techniques: Sequencing, Binding Assay

    A. The domain organization of DnaA. Structures of the N-terminal helicase-interacting domain (domain I) are shown in cyan, domain III comprising the AAA+ subdomain IIIA that binds ATP and the lid subdomain IIIB in yellow, and the C-terminal domain IV that interacts with double-stranded DNA in pink. The flexible linker domain II is missing while the ATP and Mg 2+ (grey ball) are shown in the active site of the AAA+ domain III. B. DnaA oligomerization. Two monomers of domain III are shown in yellow and grey with their arginines from Box VII and sensor II coloured in blue (yellow subunit) and red (grey subunit). The sensor II (red) of the grey monomer interacts in cis with the ATP (cyan) bound in its active site whereas the Box VII (blue) of the yellow monomer interacts in trans with the same ATP, as shown by the arrow. The ATP bound in the active site of the yellow monomer is shown with the relevant sensor II arginine defining the ATP-end of a filament, while the position of the Box VII of the grey monomer defines the R-end of the filament. C. The DnaA-ssDNA filament. A mini filament comprising four DnaA subunits bound to single-stranded DNA (red) and ATP (blue). The contiguous network of the α3/α4 and α5/α6 helices (domains III + IV) forming the single-stranded DNA binding surface lining the inside of the filament is highlighted in black ( Duderstadt et al ., 2011 ).

    Journal: Molecular Microbiology

    Article Title: Loading mechanisms of ring helicases at replication origins

    doi: 10.1111/j.1365-2958.2012.08012.x

    Figure Lengend Snippet: A. The domain organization of DnaA. Structures of the N-terminal helicase-interacting domain (domain I) are shown in cyan, domain III comprising the AAA+ subdomain IIIA that binds ATP and the lid subdomain IIIB in yellow, and the C-terminal domain IV that interacts with double-stranded DNA in pink. The flexible linker domain II is missing while the ATP and Mg 2+ (grey ball) are shown in the active site of the AAA+ domain III. B. DnaA oligomerization. Two monomers of domain III are shown in yellow and grey with their arginines from Box VII and sensor II coloured in blue (yellow subunit) and red (grey subunit). The sensor II (red) of the grey monomer interacts in cis with the ATP (cyan) bound in its active site whereas the Box VII (blue) of the yellow monomer interacts in trans with the same ATP, as shown by the arrow. The ATP bound in the active site of the yellow monomer is shown with the relevant sensor II arginine defining the ATP-end of a filament, while the position of the Box VII of the grey monomer defines the R-end of the filament. C. The DnaA-ssDNA filament. A mini filament comprising four DnaA subunits bound to single-stranded DNA (red) and ATP (blue). The contiguous network of the α3/α4 and α5/α6 helices (domains III + IV) forming the single-stranded DNA binding surface lining the inside of the filament is highlighted in black ( Duderstadt et al ., 2011 ).

    Article Snippet: Structural distortions imposed on the DNA double helix and a squeeze-pump ATP-driven action of the two head-to-head hexameric helicases pulling the DNA in opposite directions force melting of the double helix (reviewed in ).

    Techniques: Binding Assay

    A. Helicase loader-mediated loading in A. aeolicus . A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system ( Duderstadt et al ., 2011 ). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases ( Bailey et al ., 2007 ). B. Organization of the E. coli oriC . The relative positions of DnaA binding sites (R, I and τ sites), NAP ( N ucleoid A ssociated P roteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA. C. DnaA-mediated helicase loading in E. coli . A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC ( Ozaki and Katayama, 2012 ). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.

    Journal: Molecular Microbiology

    Article Title: Loading mechanisms of ring helicases at replication origins

    doi: 10.1111/j.1365-2958.2012.08012.x

    Figure Lengend Snippet: A. Helicase loader-mediated loading in A. aeolicus . A schematic diagram showing directional helicase loader-mediated and DnaA-mediated loading mechanisms on the 5′ and 3′ strands, respectively, based upon the A. aeolicus system ( Duderstadt et al ., 2011 ). The DnaA filament is shown to wrap double-stranded DNA around the outside with flexible helicase-interacting domains (domain I) projecting out from the filament. The filament extends into the 5′ strand of the melted DUE but in this case with the ssDNA in the interior of the filament. The helicase loader (green) forms a continuous heterofilament with the ATP-end of the DnaA-ssDNA filament, by docking the arginine from its Box VII into the ATP binding site of the DnaA, and delivers the helicase (brown) in the correct orientation onto the 5′ strand. The interactions of the flexible N-terminal DnaA domains with the helicase deliver it onto the 3′ strand in the opposite direction. A side-view of the Bacillus stearothermophilus DnaB helicase is shown with the characteristic two-tier (N-terminal and C-terminal tiers) ring structure of bacterial helicases ( Bailey et al ., 2007 ). B. Organization of the E. coli oriC . The relative positions of DnaA binding sites (R, I and τ sites), NAP ( N ucleoid A ssociated P roteins) binding sites for IHF and FIS and the DUE are indicated. Binding of IHF between the R1 and R5 sites sharply bends the DNA, as indicated in the inset showing the crystal structure of IHF binding and bending double-stranded DNA. C. DnaA-mediated helicase loading in E. coli . A schematic model showing how two ring helicases are directionally loaded onto the E. coli oriC ( Ozaki and Katayama, 2012 ). The DUE is cooperatively melted via binding of DnaA and IHF and the first helicase is loaded onto the bottom (A-rich) strand directionally. Subsequent translocation forward (in the 5′–3′ direction) melts a larger segment of the duplex allowing loading of the second helicase in the top (T-rich) strand and in the opposite direction. In both cases loading is mediated by the flexible N-terminal helicase-interacting domains of DnaA projecting out of the filament. For the sake of simplicity no helicase loader is depicted but it may participate indirectly in the process by binding onto the C-terminal tier of the helicase ring forcing opening of the ring for loading to proceed.

    Article Snippet: Structural distortions imposed on the DNA double helix and a squeeze-pump ATP-driven action of the two head-to-head hexameric helicases pulling the DNA in opposite directions force melting of the double helix (reviewed in ).

    Techniques: Binding Assay, Immunohistofluorescence, Translocation Assay

    Interaction of BCDX2 complex with single-stranded regions in duplex DNA. ( A – C ) Electron microscopic visualization of complexes formed between BCDX2 and tailed duplex DNA ( A ) or gapped circular duplex DNA ( B ). The bound single-stranded regions are indicated by white arrows. ( C ) Control indicating the failure of BCDX2 to bind linear duplex DNA. ( D ) Juxtaposition of BCDX2 complex and RAD51 on gapped circular DNA. The DNA was preincubated with BCDX2 complex (90 nM) for 5 min and then supplemented with RAD51 (0.3 μM). After 5 min at 37°C, the products were visualized by electron microscopy. The white arrow indicates a RAD51 filament, and the black arrow indicates the BCDX2–DNA complexes.

    Journal: Genes & Development

    Article Title: Identification and purification of two distinct complexes containing the five RAD51 paralogs

    doi: 10.1101/gad.947001

    Figure Lengend Snippet: Interaction of BCDX2 complex with single-stranded regions in duplex DNA. ( A – C ) Electron microscopic visualization of complexes formed between BCDX2 and tailed duplex DNA ( A ) or gapped circular duplex DNA ( B ). The bound single-stranded regions are indicated by white arrows. ( C ) Control indicating the failure of BCDX2 to bind linear duplex DNA. ( D ) Juxtaposition of BCDX2 complex and RAD51 on gapped circular DNA. The DNA was preincubated with BCDX2 complex (90 nM) for 5 min and then supplemented with RAD51 (0.3 μM). After 5 min at 37°C, the products were visualized by electron microscopy. The white arrow indicates a RAD51 filament, and the black arrow indicates the BCDX2–DNA complexes.

    Article Snippet: [ ] Petukhova G, Van Komen S, Vergano S, Klein H, Sung P. Yeast Rad54 promotes Rad51-dependent homologous DNA pairing via ATP hydrolysis-driven change in DNA double helix conformation.

    Techniques: Electron Microscopy

    Alignment of sequences of Endo III from E. coli ( Eco-Endo III ) and G. stearothermophilus ( Bst-Endo III ). Motifs responsible for DNA distortion are boxed green . The catalytic Lys and Asp residues are underlined . Cys residues forming the FeS cluster are

    Journal: The Journal of Biological Chemistry

    Article Title: Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III *

    doi: 10.1074/jbc.M114.621128

    Figure Lengend Snippet: Alignment of sequences of Endo III from E. coli ( Eco-Endo III ) and G. stearothermophilus ( Bst-Endo III ). Motifs responsible for DNA distortion are boxed green . The catalytic Lys and Asp residues are underlined . Cys residues forming the FeS cluster are

    Article Snippet: The decrease in the aPu fluorescence intensity is suggestive of the transition of the aPu base into a more hydrophobic environment, most reasonably explained by an insertion of amino acid side chains of Endo III (such as Gln41 ) into the vacant space present in the DNA double helix due to the abasic void.

    Techniques:

    Structural superposition of the non-covalent complexes of hOGG1 ( reddish , Protein Data Bank code 1FN7 )) and G. stearothermophilus Endo III ( greenish , Protein Data Bank code 1P59 )) with F-site contained DNA. A, the arginines interacted with phosphate

    Journal: The Journal of Biological Chemistry

    Article Title: Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III *

    doi: 10.1074/jbc.M114.621128

    Figure Lengend Snippet: Structural superposition of the non-covalent complexes of hOGG1 ( reddish , Protein Data Bank code 1FN7 )) and G. stearothermophilus Endo III ( greenish , Protein Data Bank code 1P59 )) with F-site contained DNA. A, the arginines interacted with phosphate

    Article Snippet: The decrease in the aPu fluorescence intensity is suggestive of the transition of the aPu base into a more hydrophobic environment, most reasonably explained by an insertion of amino acid side chains of Endo III (such as Gln41 ) into the vacant space present in the DNA double helix due to the abasic void.

    Techniques:

    The structures of Endo III from G. stearothermophilus complexed with DNA containing an F abasic site analog (Protein Data Bank code 1P59 ). The F nucleotide everted into the active site of enzyme and the catalytic amino acids Lys 121 and Asp 139 are labeled.

    Journal: The Journal of Biological Chemistry

    Article Title: Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III *

    doi: 10.1074/jbc.M114.621128

    Figure Lengend Snippet: The structures of Endo III from G. stearothermophilus complexed with DNA containing an F abasic site analog (Protein Data Bank code 1P59 ). The F nucleotide everted into the active site of enzyme and the catalytic amino acids Lys 121 and Asp 139 are labeled.

    Article Snippet: The decrease in the aPu fluorescence intensity is suggestive of the transition of the aPu base into a more hydrophobic environment, most reasonably explained by an insertion of amino acid side chains of Endo III (such as Gln41 ) into the vacant space present in the DNA double helix due to the abasic void.

    Techniques: Labeling

    Schematic mechanism of structural rearrangements during interaction of Endo III with DNA.

    Journal: The Journal of Biological Chemistry

    Article Title: Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III *

    doi: 10.1074/jbc.M114.621128

    Figure Lengend Snippet: Schematic mechanism of structural rearrangements during interaction of Endo III with DNA.

    Article Snippet: The decrease in the aPu fluorescence intensity is suggestive of the transition of the aPu base into a more hydrophobic environment, most reasonably explained by an insertion of amino acid side chains of Endo III (such as Gln41 ) into the vacant space present in the DNA double helix due to the abasic void.

    Techniques:

    Modified DNA base surrogates and a cartoon representing the control DNA duplex 1 as well as the insertions of natural DNA bases (duplex 2 and duplex 3), spacer units (duplex 4) and the four NDI and DAN modified units (duplexes 5-8). Figure reprinted from

    Journal: Chemical communications (Cambridge, England)

    Article Title: Exploiting the Interactions of Aromatic Units for Folding and Assembly in Aqueous Environments

    doi: 10.1039/c6cc01861k

    Figure Lengend Snippet: Modified DNA base surrogates and a cartoon representing the control DNA duplex 1 as well as the insertions of natural DNA bases (duplex 2 and duplex 3), spacer units (duplex 4) and the four NDI and DAN modified units (duplexes 5-8). Figure reprinted from

    Article Snippet: A 1:1 duplex formation was confirmed by the PAGE gel experiments in analogy to DNA double helix formation, as a fast-moving oligo-DAN-oligo-NDI duplex was observed as the only band when a 1:1 mixture of the oligo-DAN and oligo-NDI units were mixed.

    Techniques: Modification

    Completion of DNA lagging strand maturation and BER through pol β bypass of a cdA lesion

    Journal: DNA repair

    Article Title: Bypass of a 5′,8-cyclopurine-2′-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks

    doi: 10.1016/j.dnarep.2015.06.004

    Figure Lengend Snippet: Completion of DNA lagging strand maturation and BER through pol β bypass of a cdA lesion

    Article Snippet: This further suggests that a 5′ S -cdA on the template distorted the DNA double-helix structure.

    Techniques:

    Pol β plays an important role in bypassing a cdA lesion during DNA replication and BER

    Journal: DNA repair

    Article Title: Bypass of a 5′,8-cyclopurine-2′-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks

    doi: 10.1016/j.dnarep.2015.06.004

    Figure Lengend Snippet: Pol β plays an important role in bypassing a cdA lesion during DNA replication and BER

    Article Snippet: This further suggests that a 5′ S -cdA on the template distorted the DNA double-helix structure.

    Techniques:

    Pol β DNA synthesis with a template cdA lesion during DNA replication and BER

    Journal: DNA repair

    Article Title: Bypass of a 5′,8-cyclopurine-2′-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks

    doi: 10.1016/j.dnarep.2015.06.004

    Figure Lengend Snippet: Pol β DNA synthesis with a template cdA lesion during DNA replication and BER

    Article Snippet: This further suggests that a 5′ S -cdA on the template distorted the DNA double-helix structure.

    Techniques: DNA Synthesis

    Pol β nucleotide insertions in bypassing a cdA lesion during DNA replication and BER

    Journal: DNA repair

    Article Title: Bypass of a 5′,8-cyclopurine-2′-deoxynucleoside by DNA polymerase β during DNA replication and base excision repair leads to nucleotide misinsertions and DNA strand breaks

    doi: 10.1016/j.dnarep.2015.06.004

    Figure Lengend Snippet: Pol β nucleotide insertions in bypassing a cdA lesion during DNA replication and BER

    Article Snippet: This further suggests that a 5′ S -cdA on the template distorted the DNA double-helix structure.

    Techniques:

    Representative snapshots of a CNR (100,100) inserting into the SWCNT (25, 25) to form a helical configuration. The length of the CNR is 14.76 Å. (a) Sketch of DNA chains which has a double spiral configuration. (b) Concentration distribution profiles of the CNR and SWCNT in the systems in the X-direction.

    Journal: Scientific Reports

    Article Title: How Does Carbon Nanoring Deform to Spiral Induced by Carbon Nanotube?

    doi: 10.1038/srep03865

    Figure Lengend Snippet: Representative snapshots of a CNR (100,100) inserting into the SWCNT (25, 25) to form a helical configuration. The length of the CNR is 14.76 Å. (a) Sketch of DNA chains which has a double spiral configuration. (b) Concentration distribution profiles of the CNR and SWCNT in the systems in the X-direction.

    Article Snippet: The CNR can spontaneously insert into the inner cavity of the SWCNT to form a DNA-like double-helix.

    Techniques: Concentration Assay

    Combined interaction of diphenyl-N-(trichloroacetyl)-amidophosphate (HL) and C 60 fullerene with DNA (HL+C 60 or C 60 +HL versions): a , b binding with minor and major grooves, c , d intercalation into minor and major grooves. The used DNA structures of the PDB database: a , b —2M2C, c —1XRW, and d —2MIW

    Journal: Nanoscale Research Letters

    Article Title: C60 Fullerene Effects on Diphenyl-N-(trichloroacetyl)-amidophosphate Interaction with DNA In Silico and Its Cytotoxic Activity Against Human Leukemic Cell Line In Vitro

    doi: 10.1186/s11671-018-2490-9

    Figure Lengend Snippet: Combined interaction of diphenyl-N-(trichloroacetyl)-amidophosphate (HL) and C 60 fullerene with DNA (HL+C 60 or C 60 +HL versions): a , b binding with minor and major grooves, c , d intercalation into minor and major grooves. The used DNA structures of the PDB database: a , b —2M2C, c —1XRW, and d —2MIW

    Article Snippet: The double-helix DNA molecule was used as a template from PDB (Protein Data Bank) base.

    Techniques: Binding Assay