DNA articles within Nature

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  • Article |

    We study the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins, showing how cohesin initially responds to replication and providing a molecular model for the establishment of sister chromatid cohesion.

    • Yasuto Murayama
    • , Shizuko Endo
    •  & Hiroyuki Araki

  • Article |

    X-ray crystallography and cryo-electron microscopy analyses of Lettuce—a DNA mimic of GFP—bound to various fluorophores reveal previously unknown structures of DNA that rival analogous RNAs in complexity.

    • Luiz F. M. Passalacqua
    • , Michael T. Banco
    •  & Adrian R. Ferré-D’Amaré

  • Article
    | Open Access

    Cryo-electron microscopy analysis of the Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA provides insights into the mechanism of TnpB function and the evolution of CRISPR–Cas12 effectors.

    • Ryoya Nakagawa
    • , Hisato Hirano
    •  & Osamu Nureki

  • Article
    | Open Access

    Structural studies of the CRISPR-associated transposon comprising Cas12k, TnsC, TnsB and TniQ from Scytonema hofmannii using cryo-electron microscopy reveal insights into the architecture and mechanism of RNA-guided DNA transposition.

    • Jung-Un Park
    • , Amy Wei-Lun Tsai
    •  & Elizabeth H. Kellogg

  • Article
    | Open Access

    The Polα–primase-associated CST complex organizes telomeric C-strand DNA synthesis, and, in combination with telomerase, it carries out complete replication of the single-stranded DNA overhang found at human telomeres.

    • Arthur J. Zaug
    • , Karen J. Goodrich
    •  & Thomas R. Cech

  • Article |

    The molecular determinants for primer synthesis are identified within the catalytic domain of primase-polymerase enzymes, elucidating the mechanisms underlying initiation of primer synthesis.

    • Arthur W. H. Li
    • , Katerina Zabrady
    •  & Aidan J. Doherty

  • Article |

    A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

    • Aakash Basu
    • , Dmitriy G. Bobrovnikov
    •  & Taekjip Ha

  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall

  • Article |

    The jumbo phage ΦKZ constructs a proteinaceous nucleus-like compartment around its genome that protects phage DNA from degradation by DNA-targeting immune effectors of the host, including CRISPR–Cas and restriction enzymes.

    • Senén D. Mendoza
    • , Eliza S. Nieweglowska
    •  & Joseph Bondy-Denomy

  • Article |

    A programmable transposase integrates donor DNA at user-defined genomic target sites with high fidelity, revealing a new approach for genetic engineering that obviates the need for DNA double-strand breaks and homologous recombination. 

    • Sanne E. Klompe
    • , Phuc L. H. Vo
    •  & Samuel H. Sternberg

  • Article |

    The cryo-electron microscopy structure of a paused transcription elongation complex of RNA polymerase II bound to DRB sensitivity-inducing factor and negative elongation factor is reported at 3.2 Å resolution.

    • Seychelle M. Vos
    • , Lucas Farnung
    •  & Patrick Cramer

  • Article |

    The cryo-electron microscopy structure of an activated transcription elongation complex of RNA polymerase II bound to DRB sensitivity-inducing factor and the elongation factors PAF1 complex and SPT6 is reported at 3.1 Å resolution.

    • Seychelle M. Vos
    • , Lucas Farnung
    •  & Patrick Cramer

  • Letter |

    In vitro experiments, using purified proteins and an assay that detects DNA unwinding, reveal the mechanism of activation of eukaryotic DNA replication.

    • Max E. Douglas
    • , Ferdos Abid Ali
    •  & John F. X. Diffley

  • Article |

    Detailed structures of yeast RNA polymerase III and its initiation complex shed light on how the transcription of essential non-coding RNAs begins and allow comparisons with other RNA polymerases.

    • Guillermo Abascal-Palacios
    • , Ewan Phillip Ramsay
    •  & Alessandro Vannini

  • Letter |

    All necessary strands for DNA origami can be created in a single scalable process by using bacteriophages to generate single-stranded precursor DNA containing the target sequences interleaved with self-excising DNA enzymes.

    • Florian Praetorius
    • , Benjamin Kick
    •  & Hendrik Dietz

  • Article |

    In Escherichia coli, the control of RNA polymerase backtracking by transcription elongation factors impairs DNA break repair by affecting RecBCD resection and consequently RecA loading at sites far removed from the original DNA break.

    • Priya Sivaramakrishnan
    • , Leonardo A. Sepúlveda
    •  & Christophe Herman

  • Article |

    The tumour suppressor complex BRCA1–BARD1, which facilitates the generation of a single-stranded DNA template during homologous recombination, also binds to the recombinase RAD51 and enhances its function.

    • Weixing Zhao
    • , Justin B. Steinfeld
    •  & Patrick Sung

  • Letter |

    The structure of E. coli Cascade bound to foreign target DNA is presented, revealing the basis of the relaxed Cascade PAM recognition specificity, which results from its interaction with the minor groove, and demonstrating how a wedge in Cascade forces the directional pairing of the target strand with CRISPR RNA while stabilizing the non-target displaced strand.

    • Robert P. Hayes
    • , Yibei Xiao
    •  & Ailong Ke

  • Letter |

    A high-throughput analysis of DNA binding in over 9,000 interacting transcription factor pairs reveals that the interactions are often actively mediated by the DNA itself and the composite DNA sites recognized are different from the individual motifs of each transcription factor.

    • Arttu Jolma
    • , Yimeng Yin
    •  & Jussi Taipale

  • Letter |

    Crystal structures of the DNA glycosylase AlkD with DNA containing various modified bases show that neither substrate recognition nor catalysis use a base-flipping mechanism; instead, AlkD scans the phosphodeoxyribose backbone for increased cationic charge imparted by the alkylated base, and then uses the positive charge to facilitate cleavage of the glycosidic bond, thus explaining the specificity of AlkD for cationic lesions.

    • Elwood A. Mullins
    • , Rongxin Shi
    •  & Brandt F. Eichman

  • Article |

    This study describes a new model of eukaryotic replication termination in which converging leading strands pass each other unhindered and the replicative DNA helicase is unloaded late, after all strands have been ligated.

    • James M. Dewar
    • , Magda Budzowska
    •  & Johannes C. Walter

  • Letter |

    Enzymes of the nucleotide salvage pathway are shown to have substrate selectivity that protects newly synthesized DNA from random incorporation of epigenetically modified forms of cytosine; a subset of cancer cell lines that overexpress cytidine deaminase (CDA) are sensitive to treatment with 5hmdC or 5fdC (oxidized forms of 5-methyl-cytosine), which leads to DNA damage and cell death, indicating the chemotherapeutic potential of these nucleoside variants for CDA-overexpressing cancers.

    • Melania Zauri
    • , Georgina Berridge
    •  & Skirmantas Kriaucionis

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