DNA articles within Nature Communications

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  • Article
    | Open Access

    Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction.

    • Jeroen F. van Dyck
    • , Jonathan R. Burns
    •  & Frank Sobott

  • Article
    | Open Access

    DNA N6-adenine methylation (6 mA) plays a crucial role in epigenetic regulation in eukaryotes. Here, the authors determined nine crystal structures of the ciliates 6 mA methyltransferase complexes, providing the molecular basis for understanding the functions of 6 mA.

    • Jiyun Chen
    • , Rong Hu
    •  & Liang Liu

  • Article
    | Open Access

    Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.

    • Chad R. Simmons
    • , Tara MacCulloch
    •  & Hao Yan

  • Article
    | Open Access

    Artificial systems to control the transport of molecules across biomembranes can be useful for biosensing or drug delivery. Here, the authors assemble a DNA channel enabling the precisely timed, stimulus-controlled transport of functional proteins across bilayer membranes.

    • Swarup Dey
    • , Adam Dorey
    •  & Hao Yan

  • Article
    | Open Access

    Here the authors digested chromatin with DNA fragmentation factor (DFF) prior to chromatin immunoprecipitation (DFF-ChIP) to depict transcription complex interactions with neighboring nucleosomes in cells. Applying this method to human cytomegalovirus (HMCV)-infected cells, they find that the viral genome is underchromatinized, leading to fewer transcription complex interactions with nucleosomes.

    • Benjamin M. Spector
    • , Mrutyunjaya Parida
    •  & David H. Price

  • Article
    | Open Access

    HIV-1 integration sites are biased towards actively transcribed genes, likely mediated by binding of the viral integrase (IN) protein to host factors. Here, Winans et al. show that the K258R point mutation in IN eredirects viral DNA integration to the centromeres of host chromosomes, which may affect HIV latency.

    • Shelby Winans
    • , Hyun Jae Yu
    •  & Stephen P. Goff

  • Article
    | Open Access

    The actin-based molecular motors, myosins, have also been linked to transcription, but their precise role has remained elusive. Here the authors show RNA polymerase II (RNAPII) is lost from chromatin upon myosin perturbation and that myosin acts as a molecular anchor to maintain RNAPII spatial organisation.

    • Yukti Hari-Gupta
    • , Natalia Fili
    •  & Christopher P. Toseland

  • Article
    | Open Access

    While prime editing is a promising technique, some genomic sites remain difficult to edit. Here the authors present fluoPEER, fluorescent prime editing and enrichment reporter, to rank the efficiency of pegRNAs and prime editor variants.

    • I. F. Schene
    • , I. P. Joore
    •  & S. A. Fuchs

  • Review Article
    | Open Access

    Synthetic DNA is the basis for promising technologies in data storage, barcoding, computing 62 and sercurity. In this review, the authors provide an overview of the field and its future.

    • Linda C. Meiser
    • , Bichlien H. Nguyen
    •  & Robert N. Grass

  • Article
    | Open Access

    Chiral communication can propagate in secondary structures within the effective intermolecular force (IMF) range but it is not known whether long-range chiral communication exists between tertiary peptide structures. Here, the authors use single-molecule force spectroscopy to investigate chiral interaction between DNA duplexes/triplexes and peptide coiled-coils and demonstrate chiral communication beyond the IMF distance.

    • Shankar Pandey
    • , Shankar Mandal
    •  & Hanbin Mao

  • Article
    | Open Access

    Whether G-quadruplexes (G4s) regulate stem cell self-renewal and fate determination during embryonic development is not well understood. Here, the authors reveal that the embryonic stem cell state is defined by very high G4 abundance. G4s are progressively lost during differentiation as cells transit to lower lineage potential while artificial G4 stabilisation leads to delayed differentiation.

    • Katherine G. Zyner
    • , Angela Simeone
    •  & Shankar Balasubramanian

  • Article
    | Open Access

    Nucleosomes form arrays with even spacing between them in virtually all eukaryotes; however, their biogenesis is incompletely understood. Here the authors show that nucleosome density and DNA sequence along with the Ino80 chromatin remodeling complex play a role in nucleosome array formation in yeast and that the transcriptional machinery disrupts evenly-spaced nucleosomes.

    • Ashish Kumar Singh
    • , Tamás Schauer
    •  & Felix Mueller-Planitz

  • Article
    | Open Access

    Ty3 retrotransposon integrates with an exquisite specificity upstream of RNA Polymerase III-transcribed genes, such as transfer RNAs. Here the authors resolve a cryo-EM structure of an active Ty3 intasome in complex with a TFIIIB-bound tRNA promoter, shedding light into the molecular determinants of harmless retrotransposition.

    • Guillermo Abascal-Palacios
    • , Laura Jochem
    •  & Alessandro Vannini

  • Article
    | Open Access

    Bacteria-based therapy has shown promise for cancer treatment. To enhance tumor accumulation, here the authors describe the design of tumor specific aptamer-conjugated bacteria, to improve intratumor localization and enhance therapeutic efficacy.

    • Zhongmin Geng
    • , Zhenping Cao
    •  & Weihong Tan

  • Article
    | Open Access

    An enzymatic ensemble including Dna2 functions in DNA end resection; the function of the single-stranded DNA binding protein RPA in this complex has been underappreciated. Here the authors employ molecular modeling, biochemistry, and single molecule biophysics to reveal RPA directly promotes Dna2 recruitment, nuclease and helicase activities.

    • Ananya Acharya
    • , Kristina Kasaciunaite
    •  & Petr Cejka

  • 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

  • Comment
    | Open Access

    While genomic instability is a hallmark of cancer, its genetic vulnerabilities remain poorly understood. Identifying strategies that exploit genomic instability to selectively target cancer cells is a central challenge in cancer biology with major implications for anti-cancer drug development.

    • Craig M. Bielski
    •  & Barry S. Taylor

  • 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

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