DNA articles within Nature Communications

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  • Article
    | Open Access

    During transcription, RNA polymerases may encounter protein roadblocks along template DNA. Here, Qian et al. use magnetic tweezers to show that RNA polymerases can backtrack and ram into longer lived roadblocks to transit through them.

    • Jin Qian
    • , Allison Cartee
    •  & Laura Finzi

  • Article
    | Open Access

    Physical unclonable functions provide algorithm-independent cryptography based on non-distributable unique tokens. Here, the authors introduce unclonable functions based on random DNA pools, enabling secure decentralized authentication.

    • Anne M. Luescher
    • , Andreas L. Gimpel
    •  & Robert N. Grass

  • Article
    | Open Access

    It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA.

    • Jack W. Shepherd
    • , Sebastien Guilbaud
    •  & Mark C. Leake

  • Article
    | Open Access

    The authors find that small circular DNA nanostructures which partially match gRNA sequences only minimally activate Cas12a. They report AutoCAR (Autocatalytic Cas12a Circular DNA Amplification Reaction) which allows a single nucleic acid target to activate multiple ribonucleoproteins, and increases reporter cleavage rates.

    • Fei Deng
    • , Yi Li
    •  & Ewa M. Goldys

  • Article
    | Open Access

    I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single stranded, cytosine-rich genomic region, but the specific contributions of several factors involved in their formation are unknown. Using in-cell NMR, the authors examined DNA i-motif formation in human cells at body temperature, suggesting i-M occur in a small portion (<1%) of genomic sites predisposed to its formation.

    • Pavlína Víšková
    • , Eva Ištvánková
    •  & Lukáš Trantírek

  • Article
    | Open Access

    Conventional CRISPR-based approaches to monitor genomic loci can be hampered by high background and nonspecific nucleolar signal. Here, the authors propose a fluorogenic CRISPR (fCRISPR) tool that allows for high-contrast and sensitive imaging of genomic DNA.

    • Zhongxuan Zhang
    • , Xiaoxiao Rong
    •  & Xing Li

  • Article
    | Open Access

    The PARylation activity of PARP recruits DNA repair proteins to damaged DNA, most likely via non-covalent protein-PAR interactions. Here, the authors show that PARP1 covalently PARylates base excision repair proteins to modulate their DNA transactions and thus promote active BER DNA demethylation.

    • Simon D. Schwarz
    • , Jianming Xu
    •  & Roland Steinacher

  • Article
    | Open Access

    Here, the authors use cryo-EM to capture nine intermediates along the DNA proofreading pathway using human mitochondrial DNA Polymerase Gamma. The results provide a step-by-step view of the DNA proofreading at single-nucleotide resolution.

    • Gina Buchel
    • , Ashok R. Nayak
    •  & Dmitry Temiakov

  • Article
    | Open Access

    Here, the authors show that a DnaA:origin complex promotes specific nucleobase capture from a single DNA strand. It is proposed that this mechanism may play a key role stimulating opening of bacterial chromosome origins.

    • Simone Pelliciari
    • , Salomé Bodet-Lefèvre
    •  & Heath Murray

  • Article
    | Open Access

    A common genetic cause of Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here the authors reveal that the RNA (GGGGCC)n expansion repeat associated with ALS/FTD can generate condensates in the absence of proteins, highlighting the potential relevance of targeting RNA-structures to treat neurodegenerative diseases.

    • Federica Raguseo
    • , Yiran Wang
    •  & Marco Di Antonio

  • Article
    | Open Access

    Inactivation of DNPH1 leads to hmdU incorporation into DNA, sensitising BRCA-deficient cells to PARP inhibitors. Crystal structures of DNPH1 bound to hmdU monophosphate reveal a two-step mechanism for hydrolysis via a glycosyl-enzyme intermediate.

    • Neil J. Rzechorzek
    • , Simone Kunzelmann
    •  & Stephen C. West

  • Article
    | Open Access

    Unnatural base pairing xenonucleic acids (XNAs) can be used to expand life’s alphabet beyond ATGC. Here, authors show strategies for enzymatic synthesis and next-generation nanopore sequencing of XNA base pairs for reading and writing 12-letter DNA (ATGCBSPZXKJV).

    • Hinako Kawabe
    • , Christopher A. Thomas
    •  & Jorge A. Marchand

  • Article
    | Open Access

    APOBEC3A mutates its host DNA in human cancers to evolve drug resistance. Modified-DNA inhibitors suppress this mutagenic activity in cells, suggesting use as conjuvants in anti-cancer therapies. Here the authors reveal structural insights into how these inhibitors bind APOBEC3A.

    • Stefan Harjes
    • , Harikrishnan M. Kurup
    •  & Geoffrey B. Jameson

  • Article
    | Open Access

    Mediator proteins such as BRCA2 and Rad52 direct formation of Rad51 filaments in Homologous Recombination. Here, the authors present cryoEM structures of Saccharomyces cerevisiae Rad52 revealing a homodecamer and Rad51 binding to two regions in Rad52.

    • Jaigeeth Deveryshetty
    • , Rahul Chadda
    •  & Edwin Antony

  • Article
    | Open Access

    Archiving data in synthetic DNA offers unprecedented storage density and longevity. To understand how experimental choices affect the integrity of digital data stored in DNA, the authors study the evolution of errors and bias and with a digital twin they supply tools for experimental planning and design of error-correcing codes.

    • Andreas L. Gimpel
    • , Wendelin J. Stark
    •  & Robert N. Grass

  • Article
    | Open Access

    Limited delivery of therapeutic cells to diseased tissue hampers the effective application of mesenchymal stromal cells (MSCs). Here, authors modify the cell surface with polyvalent antibodies using DNA-templated assembly, and show that polyvalent interactions can be used to improve the targeting efficiency of MSCs.

    • Tenghui Ye
    • , Xi Liu
    •  & Peng Shi

  • Article
    | Open Access

    The development of dynamic DNA nanodevices, whose configuration and function are regulated by specific chemical inputs, represents a rapidly growing area in molecular science. Herein, the authors report the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner.

    • Yusuke Takezawa
    • , Keita Mori
    •  & Mitsuhiko Shionoya

  • Article
    | Open Access

    The lack of a universal platform for PROTAC development remains a major bottleneck. Here, the authors report modular DNA framework-based PROTACs (DbTACs) that enable precise control of the linker length and selective degradation of diverse targets in different cellular compartments using various warheads.

    • Li Zhou
    • , Bin Yu
    •  & Yi Ma

  • Article
    | Open Access

    The binding of small molecules to the double stranded DNA may significantly alter its stability and functionality, which is the basis for many therapeutic and sensing applications. Here, the authors report that DNA binders can be used to program reaction pathways of a dynamic DNA reaction, where DNA strand displacement can be tuned quantitatively according to the affinity, charge, and concentrations of a given DNA binder.

    • Junpeng Xu
    • , Guan Alex Wang
    •  & Feng Li

  • Article
    | Open Access

    DNA data storage has gained recent interest due to the high information density of DNA. Here, the authors have developed a method to directly capture information in the form of light and encode it into DNA via bacteria, analogous to a digital camera.

    • Cheng Kai Lim
    • , Jing Wui Yeoh
    •  & Chueh Loo Poh

  • Article
    | Open Access

    Here the structure of transposase from Tn3 family is reported in apo form and bound to the transposon ends. The activation of the transposase induces metamorphic refolding of the catalytic domain suggesting the family-specific regulation mechanism.

    • Alexander V. Shkumatov
    • , Nicolas Aryanpour
    •  & Rouslan G. Efremov

  • Article
    | Open Access

    Poly-ADP-ribosylation (PARylation) is a well-known posttranslational modification of proteins. Here the authors show that beyond proteins also mammalian single-stranded DNA is PARylated in vitro and in vivo.

    • Michael U. Musheev
    • , Lars Schomacher
    •  & Christof Niehrs

  • Article
    | Open Access

    The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. Herein, the authors report the NMR solution structures of a bulge-containing KRAS-G4 that bound to two small molecules. The study provides molecular details of ligand interactions with KRAS-G4 and contributes insight into the design of specific KRAS-G4-interactive drugs.

    • Kai-Bo Wang
    • , Yushuang Liu
    •  & Ling-Yi Kong

  • Article
    | Open Access

    Locating a four-way junction in a high background of genomic DNA is likely to be the rate-limiting step of the resolution process. This study captures the entire reaction trajectory of a nuclease targeting and resolving a DNA junction at single-molecule level.

    • Artur P. Kaczmarczyk
    • , Anne-Cécile Déclais
    •  & David S. Rueda

  • Article
    | Open Access

    AP endonuclease 1 (APE1) processes genomic AP sites during base excision repair. Here, the authors determine the structural mechanism used by APE1 to process nucleosomal AP sites, providing new insight into DNA repair in chromatin.

    • Tyler M. Weaver
    • , Nicole M. Hoitsma
    •  & Bret D. Freudenthal

  • Article
    | Open Access

    The single stranded DNA binding protein RPA coordinates DNA metabolism using multiple protein and DNA interaction domains. Here, the authors show that the chaperone-like protein Rtt105 staples RPA domains to prevent untimely protein interactions.

    • Sahiti Kuppa
    • , Jaigeeth Deveryshetty
    •  & Edwin Antony

  • Article
    | Open Access

    The MuvB family of protein complexes regulate cell cycle-dependent transcription, and MuvB in complex with the transcription factors B-MYB and FOXM1 activate mitotic genes during G2. Here the authors present cryo-EM data of a MuvB:B-MYB (MMB) complex in the process of remodelling a nucleosome, and define its stoichiometry, assembly, and chromatin binding.

    • Marios G. Koliopoulos
    • , Reyhan Muhammad
    •  & Claudio Alfieri

  • Article
    | Open Access

    Methods for fluorescently labelling DNAs are expensive and labour-intensive. Here the authors report an in situ DNA labelling strategy for oligonucleotides as well as dsDNA that makes use of aldehyde-reactive rotor dyes to trap AP sites resulting from excision of deaminated DNA bases.

    • Yong Woong Jun
    • , Emily M. Harcourt
    •  & Eric T. Kool

  • Article
    | Open Access

    Next-generation lipid nanoparticles that target non-hepatocytes could be important clinical tools. Using in vivo DNA barcoding, the authors identify piperazine-containing lipids deliver mRNA to immune cells without targeting ligands.

    • Huanzhen Ni
    • , Marine Z. C. Hatit
    •  & James E. Dahlman

  • Article
    | Open Access

    CRISPR-Cas induced HDR methods tend to have a low efficiency. Here the authors report an HDR improvement strategy, Recursive Editing, that selectively retargets undesired indel outcomes to create additional opportunities for HDR; they introduce REtarget, a tool for Recursive Editing experimental design.

    • Lukas Möller
    • , Eric J. Aird
    •  & Jacob E. Corn

  • Article
    | Open Access

    It remains unclear how BRCA1-associated mutational sigantures are generated in cancer. Here, the authors develop nCas9-based approaches to uncover that aberrant repair of one-ended DSBs converted from DNA nicks by replication, not that of two-ended DSBs, induces such mutational signatures.

    • Yi-Li Feng
    • , Qian Liu
    •  & An-Yong Xie

  • Article
    | Open Access

    DNA replication of repetitive sequences was recreated in a test tube using purified components. DNA alone was sufficient to induce stalling. Both stalling and recovery were dictated by the capacity of DNA to fold into unusual secondary structures.

    • Corella S. Casas-Delucchi
    • , Manuel Daza-Martin
    •  & Gideon Coster

  • Article
    | Open Access

    Signal processing for downstream functional and morphological adaptations is crucial for understanding and re-enacting features of living systems. Here, the authors show DNAzyme-containing, metabolic protocells that induce prototissue formation via chemical messenger communication due to in situ cleavage of upstream DNA signals.

    • Avik Samanta
    • , Maximilian Hörner
    •  & Andreas Walther

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