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1. IMG-DNA: Approximate DNA Storage for Images

   Bingzhe Li, Li Ou (June 2021, International Systems and Storage Conference (SYSTOR’21))

   null (Ed.)

   Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are error-prone. Images widely used in social media have the properties of fault tolerance which are well fitted to the DNA storage. However, prior work simply investigated the feasibility of DNA storage storing different types of data and simply store images in DNA storage, which did not fully investigate the fault-tolerant potential of images in the DNA storage. In this paper, we proposed a new image-based DNA system called IMG-DNA, which can efficiently store images in DNA storage with improved DNA storage robustness. First, a new DNA architecture is proposed to fit JPEG-based images and improve the image’s robustness in DNA storage. Moreover, barriers inserted in DNA sequences efficiently prevent error propagation in images of DNA storage. The experimental results indicate that the proposed IMG-DNA achieves much higher fault-tolerant than prior work. 

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2. Localized DNA Hybridization Chain Reactions on DNA Origami

   https://doi.org/10.1021/acsnano.7b06699  

   Bui, Hieu; Shah, Shalin; Mokhtar, Reem; Song, Tianqi; Garg, Sudhanshu; Reif, John (January 2018, ACS Nano)
3. Plant DNA repair and Agrobacterium T-DNA integration.

   https://doi.org/doi.org/10.3390/ijms22168458  

   Gelvin, S.B. (July 2021, International journal of molecular sciences)

   Agrobacterium species transfer DNA (T-DNA) to plant cells where it may integrate into plant chromosomes. The process of integration is thought to involve invasion and ligation of T-DNA, or its copying, into nicks or breaks in the host genome. Integrated T-DNA often contains, at its junctions with plant DNA, deletions of T-DNA or plant DNA, filler DNA, and/or microhomology between T-DNA and plant DNA pre-integration sites. T-DNA integration is also often associated with major plant genome rearrangements, including inversions and translocations. These characteristics are similar to those often found after repair of DNA breaks, and thus DNA repair mechanisms have frequently been invoked to explain the mechanism of T-DNA integration. However, the involvement of specific plant DNA repair proteins and Agrobacterium proteins in integration remains controversial, with numerous contradictory results reported in the literature. In this review I discuss this literature and comment on many of these studies. I conclude that either multiple known DNA repair pathways can be used for integration, or that some yet unknown pathway must exist to facilitate T-DNA integration into the plant genome. 

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4. Structural predictions of protein–DNA binding: MELD-DNA

   https://doi.org/10.1093/nar/gkad013  

   Esmaeeli, Reza; Bauzá, Antonio; Perez, Alberto (February 2023, Nucleic Acids Research)

   Abstract Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein–DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein–DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein–DNA interactions). 

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5. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair

   https://doi.org/10.3390/biology10060530  

   Thompson, Marlo K.; Sobol, Robert W.; Prakash, Aishwarya (June 2021, Biology)

   The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples. 

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