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1. Tuning Chemical DNA Ligation within DNA Crystals and Protein–DNA Cocrystals

   https://doi.org/10.1021/acsnanoscienceau.4c00013  

   Orun, Abigail R; Slaughter, Caroline K; Shields, Ethan T; Vajapayajula, Ananya; Jones, Sara; Shrestha, Rojina; Snow, Christopher D (June 2024, ACS Nanoscience Au)

   Biomolecular crystals can serve as materials for a plethora of applications including precise guest entrapment. However, as grown, biomolecular crystals are fragile in solutions other than their growth conditions. For crystals to achieve their full potential as hosts for other molecules, crystals can be made stronger with bioconjugation. Building on our previous work using carbodiimide 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) for chemical ligation, here, we investigate DNA junction architecture through sticky base overhang lengths and the role of scaffold proteins in cross-linking within two classes of biomolecular crystals: cocrystals of DNA-binding proteins and pure DNA crystals. Both crystal classes contain DNA junctions where DNA strands stack up end-to-end. Ligation yields were studied as a function of sticky base overhang length and terminal phosphorylation status. The best ligation performance for both crystal classes was achieved with longer sticky overhangs and terminal 3′phosphates. Notably, EDC chemical ligation was achieved in crystals with pore sizes too small for intracrystal transport of ligase enzyme. Post assembly cross-linking produced dramatic stability improvements for both DNA crystals and cocrystals in water and blood serum. The results presented may help crystals containing DNA achieve broader application utility, including as structural biology scaffolds. 

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2. 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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3. 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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4. 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)
5. 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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