• Article
    | Open Access

    Translesion Synthesis is a process that enables cells to overcome the deleterious effects of replication stalling caused by DNA lesions. Here the authors present a Cryo-EM structure of human Y-family DNA polymerase k (Pol k) bound to PCNA, P/T DNA and an incoming nucleotide; and propose a model for polymerase switching in which “carrier state” Pol k is recruited to PCNA.

    • Claudia Lancey
    • , Muhammad Tehseen
    •  & Alfredo De Biasio
  • Article
    | Open Access

    The versatility of DNA has inspired many single-molecule investigations utilizing nanotechnology. Harashima et al. have a somewhat different take on the subject and study a zipper configuration bridging electrodes that resembles an active electro-mechanical component instead.

    • Takanori Harashima
    • , Shintaro Fujii
    •  & Tomoaki Nishino
  • Article
    | Open Access

    DNA supercoiling can result in underwinding with negative supercoiling or overwinding with positive supercoiling of the DNA double helix. Here the authors reveal insights into the dynamic relationship between DNA supercoiling-induced sequence-dependent disruptions to base pairing, DNA looping, and the shape of the DNA molecule.

    • Jonathan M. Fogg
    • , Allison K. Judge
    •  & Lynn Zechiedrich
  • Article
    | Open Access

    How cells coordinate chromatin dynamics with the cell cycle machinery to promote genome duplication during S phase is still a matter of study. Here the authors reveal by in vitro reconstitution assays that the AAA + -ATPase containing Yta7 protein in S. cerevisiae promotes chromatin.

    • Erika Chacin
    • , Priyanka Bansal
    •  & Christoph F. Kurat
  • Article
    | Open Access

    Integration and communication of distinct chemical reaction networks is a biological strategy for controlling dynamics of hierarchical structures. Here, the authors report ATP-fuelled autonomous DNA nanotube assembly regulated by DNA strand displacement reactions, which are induced and controlled by an upstream enzyme reaction network of concurrent ATP-mediated ligation and restriction of DNA components.

    • Jie Deng
    •  & Andreas Walther
  • Article
    | Open Access

    DNA is becoming increasingly used as a medium to store non-genetic information. Here the authors present a dynamic stack data structure implemented as a DNA polymer chemistry able to record and retrieve signals in a last-in first-out order.

    • Annunziata Lopiccolo
    • , Ben Shirt-Ediss
    •  & Natalio Krasnogor
  • Article
    | Open Access

    DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-human sequencing panels.

    • Jinny X. Zhang
    • , Boyan Yordanov
    •  & David Yu Zhang
  • Article
    | Open Access

    Charting the landscape of 5hmC in human tissues is fundamental to understanding its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues and found 5hmC shows tissue-specific patterns.

    • Bo He
    • , Chao Zhang
    •  & Chengqi Yi
  • Article
    | Open Access

    Eukaryotic DNA replication is mediated by many proteins which are tightly regulated for an efficient firing of replication at each cell cycle. Here the authors report a cryo-EM structure of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA revealing additional insights into how Cdc6 contributes to origin DNA recognition.

    • Xiang Feng
    • , Yasunori Noguchi
    •  & Huilin Li
  • Article
    | Open Access

    CAPPs are putative Primase-Polymerases associated with CRISPR-Cas operons. Here, the authors show CAPPs genetic and physical association with Cas1 and Cas2, their capacity to function as DNA-dependent DNA primases and DNA polymerases, and that Cas1-Cas2 complex adjacent to CAPP has bona fide spacer integration activity.

    • Katerina Zabrady
    • , Matej Zabrady
    •  & Aidan J. Doherty
  • Article
    | Open Access

    Although chromatin remodelers have been shown to align nucleosome arrays to barriers and to generate spacing regularity among nucleosomes within arrays, it has remained unclear how the distance to barrier and the spacing length are determined in absolute terms. Here, the authors reveal that remodelers contain a ‘ruler’ element that sets remodeler-specific alignment and spacing distances when generating nucleosome arrays.

    • Elisa Oberbeckmann
    • , Vanessa Niebauer
    •  & Philipp Korber
  • Article
    | Open Access

    The poor bench stability of phosphoramidites is a drawback for fast automised chemical oligonucleotide synthesis. Here, the authors report a method for on-demand flow synthesis of phosphoramidites within short reaction times, in near-quantitative yields and sufficient purity for integration with DNA synthesizers.

    • Alexander F. Sandahl
    • , Thuy J. D. Nguyen
    •  & Kurt V. Gothelf
  • Article
    | Open Access

    It is challenging to develop DNA probes that allow staining of both organelle and nuclear DNA, are compatible with super resolution imaging and avoid UV-light photo-excitation. The authors overcome these issues with N-aryl pyrido cyanine derivatives showing high DNA specificity and membrane permeability.

    • Kakishi Uno
    • , Nagisa Sugimoto
    •  & Yoshikatsu Sato
  • Article
    | Open Access

    Current aptamer discovery approaches are unable to probe the complete space of possible sequences. Here, the authors use machine learning to facilitate the development of DNA aptamers with improved binding affinities, and truncate them without significantly compromising binding affinity.

    • Ali Bashir
    • , Qin Yang
    •  & B. Scott Ferguson
  • Article
    | Open Access

    The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.

    • Christopher R. Horne
    • , Hariprasad Venugopal
    •  & Renwick C. J. Dobson
  • Article
    | Open Access

    7,8-dihydro-8-oxoguanine and 7,8-dihydro-8-oxoadenine (oxoA) are generated upon oxidative damage to DNA, but the biological effects of oxoA are not well known. Here, the authors report that only oxoA forms DNA interstrand crosslinks (ICLs) upon secondary oxidation and that these ICLs can be induced by reactive halogen species, one-electron oxidants and the myeloperoxidase/H2O2/Cl- system.

    • Aaron L. Rozelle
    • , Young Cheun
    •  & Seongmin Lee
  • Article
    | Open Access

    The methods for investigation of DNA-binding proteins require site-selective chemical modifications to be introduced into oligonucleotides. Here, the authors report a chemo- and regioselective method for the modification of unpaired guanosines in single- and double-stranded oligonucleotides, based on Rh(I)-carbene catalysis.

    • Yang-Ha Lee
    • , Eunsoo Yu
    •  & Cheol-Min Park
  • Article
    | Open Access

    The APOBEC mutation signature contributes to a significant percentage of human cancers. Here the authors via biochemical and computational analyses shed light on how DNA primary sequence and secondary structure jointly influence A3A substrate optimality.

    • Adam Langenbucher
    • , Danae Bowen
    •  & Michael S. Lawrence
  • Article
    | Open Access

    A world preceding the prebiotic RNA-world may have been based on xeno nucleic acids (XNAs), but their replication likely did not require enzymes. Here, the authors demonstrate template-directed non-enzymatic synthesis of an XNA, acyclic l-threoninol nucleic acid, via chemical ligation mediated by N-cyanoimidazole, and achieve a pseudo-primer extension of this XNA with all four nucleobases.

    • Keiji Murayama
    • , Hikari Okita
    •  & Hiroyuki Asanuma
  • Article
    | Open Access

    C5-glyceryl-methylcytosine is a DNA modification that plays a role in the regulation of green alga photosynthesis and is catalysed by CMD1, using vitamin C (VC) as a co-substrate. Here, the authors provide insights into the catalytic mechanism of CMD1 by determining the crystal structures of apo CMD1 and CMD1 bound to either VC or DNA, as well as the ternary CMD1/VC/DNA complex structure.

    • Wenjing Li
    • , Tianlong Zhang
    •  & Jianping Ding
  • Article
    | Open Access

    Histone acetylation is a ubiquitous hallmark of transcription. Here the authors provide evidence that the majority of histone acetylation is dependent on transcription, specifically due to the requirement of RNAPII for the recruitment and activity of histone acetyltransferases.

    • Benjamin J. E. Martin
    • , Julie Brind’Amour
    •  & LeAnn J. Howe
  • Article
    | Open Access

    DNA three-way junctions are branched structures formed during replication, repair, and recombination, and are involved in models of repeat expansion. Here the authors use single-molecule Förster resonance energy transfer to reveal the dynamics of DNA three-way junctions containing slip-outs composed of CAG or CTG repeats.

    • Tianyu Hu
    • , Michael J. Morten
    •  & Steven W. Magennis
  • Article
    | Open Access

    Acidothermus cellulolyticus CRISPR-Cas9 (AceCas9) is a Type II-C enzyme that cleaves DNA in a Protospacer Adjacent Motif (PAM) methylation sensitive fashion. Biochemical analysis and crystal structures of AceCas9 in complex with sgRNA and DNA bearing the correct and incorrect PAM offer insight into the structural basis for the recognition of PAM and its methylation.

    • Anuska Das
    • , Travis H. Hand
    •  & Hong Li
  • Article
    | Open Access

    In type I-D CRISPR–Cas systems, the nuclease and helicase activities are carried out by separate subunits. The crystal structure of Sulfolobus islandicus type I-D large subunit Cas10d, containing a nuclease domain, reveals unusual architecture. The structure of Cas10d in complex with anti-CRISPR protein AcrID1 suggests that the latter sequesters Cas10d in a nonfunctional state.

    • M. Cemre Manav
    • , Lan B. Van
    •  & Ditlev E. Brodersen
  • Article
    | Open Access

    The DNA helicase ASCC3 is the largest subunit of the activating signal co-integrator complex (ASCC), and its DNA unwinding activity is required for the AlkBH3/ASCC-dependent DNA de-alkylation repair pathway. Here, the authors identify a minimal stable complex of the two ASCC subunits ASCC2 and ASCC3, determine the complex crystal structure and further show that cancer-related mutations at the interface between both proteins reduce ASCC2–ASCC3 affinity.

    • Junqiao Jia
    • , Eva Absmeier
    •  & Markus C. Wahl
  • Article
    | Open Access

    Polymerase μ (Polμ) participates in the repair of DNA double-strand breaks (DSBs) via the nonhomologous end-joining (NHEJ) pathway. Here, the authors determine the crystal structure of a pre-catalytic ternary complex of human Polμ with a bound DSB substrate and they obtain further mechanistic insights by allowing the insertion reaction to proceed in crystallo, which enabled them to determine a Polμ structure with incomplete incorporation and the structure of the post-catalytic nicked state.

    • Andrea M. Kaminski
    • , John M. Pryor
    •  & Katarzyna Bebenek
  • Article
    | Open Access

    Single molecule force measurements have shed light on dynamic biological events, but rare events escape notice owing to low throughput of the methods. Here, the authors combine an array of magnetic tweezers with lateral flow to increase throughput 100-fold, and detect rare DNA breaks induced by gyrase.

    • Rohit Agarwal
    •  & Karl E. Duderstadt
  • Article
    | Open Access

    The origin recognition complex (ORC) is essential for loading the Mcm2–7 replicative helicase onto DNA during DNA replication initiation. Here, the authors describe several cryo-electron microscopy structures of Drosophila ORC bound to DNA and its cofactor Cdc6 and also report an in vitro reconstitution system for Drosophila Mcm2–7 loading, revealing unexpected features of ORC’s DNA binding and remodeling mechanism during Mcm2–7 loading.

    • Jan Marten Schmidt
    •  & Franziska Bleichert
  • Article
    | Open Access

    Cas12a-linked base editors can broaden the targeting scope of programmable cytidine deaminases. Here the authors assess their target specificity in an in vitro genome-wide assay.

    • Daesik Kim
    • , Kayeong Lim
    •  & Jin-Soo Kim
  • Article
    | Open Access

    G4 structure-interacting proteins have been linked to DNA repair processes. Here the authors reveal that in yeast, Zuo1 associates with G4 structures and plays a role in repair pathway choice by promoting nucleotide excision repair and ultimately contributing to maintenance of genome stability.

    • Alessio De Magis
    • , Silvia Götz
    •  & Katrin Paeschke
  • Article
    | Open Access

    During eukaryotic chromosome replication cells utilize ring-shaped CMG helicase that separates the two strands of the DNA double helix. Here the authors reveal that CMG helicase activity is inhibited by duplex DNA engagement at the fork, which is relieved by binding of RPA to the lagging-strand template.

    • Hazal B. Kose
    • , Sherry Xie
    •  & Hasan Yardimci
  • Article
    | Open Access

    Nucleic acid-based materials are usually only compatible with aqueous solutions. Here, the authors show a structural nucleic acid nanotechnology using gamma-modified peptide nucleic acids that enables formation of solvent-compatible, self-assembling nanostructures defined by Watson-Crick base pairing.

    • Sriram Kumar
    • , Alexander Pearse
    •  & Rebecca E. Taylor
  • Article
    | Open Access

    Some transcription factors have been proposed to functionally interact with RNA to facilitate proper regulation of gene expression. Here the authors demonstrate that human Sox2 interact directly and with high affinity to RNAs through its HMG DNA-binding domain.

    • Zachariah E. Holmes
    • , Desmond J. Hamilton
    •  & Robert T. Batey
  • Article
    | Open Access

    Pol δ bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand in eukaryotes and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. Here, the authors present a Cryo-EM structure of the human 4-subunit Pol δ bound to DNA and PCNA in a replicating state with an incoming nucleotide in the active site.

    • Claudia Lancey
    • , Muhammad Tehseen
    •  & Alfredo De Biasio
  • Article
    | Open Access

    The DNA duplex is known to be split apart in a steric exclusion manner during replication, but the specific mechanism has remained unclear. Here the authors present a cryo-EM structure of a eukaryotic replicative CMG helicase on forked DNA, revealing the mechanism of DNA unwinding.

    • Zuanning Yuan
    • , Roxana Georgescu
    •  & Michael E. O’Donnell
  • Article
    | Open Access

    To carry out their function, transcription factors must efficiently recognize specific DNA sequence targets, a complex problem in the context of eukaryotic chromatin. Here the authors use single-molecule biophysical experiments, statistical mechanical theory and bioinformatics analyses to conclude that interactions with non-target sequences near promoters serve to increase overall affinity and targeting efficiency.

    • Milagros Castellanos
    • , Nivin Mothi
    •  & Victor Muñoz