Arash Ahmadi

• Ahmadi, Arash; Till, Katharina; Backe, Paul Hoff; Blicher, Pernille; Diekmann, Robin & Sch¨¹ttpelz, Mark [Vis alle 11 forfattere av denne artikkelen] (2021). Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Communications Biology. 4. doi: 10.1038/s42003-021-02400-x. Fulltekst i vitenarkiv Vis sammendrag

  Abstract The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged ¦Â-hairpin able to protrude into the major groove of DNA.

• Ahmadi, Arash; Till, Katharina; Hafting, Yngve; Schuttpelz, Mark; Bj?r?s, Magnar & Glette, Kyrre [Vis alle 9 forfattere av denne artikkelen] (2019). Additive manufacturing of laminar flow cells for single-molecule experiments. Scientific Reports. 9(1). doi: 10.1038/s41598-019-53151-z. Fulltekst i vitenarkiv Vis sammendrag

  A microfluidic laminar flow cell (LFC) forms an indispensable component in single-molecule experiments, enabling different substances to be delivered directly to the point under observation and thereby tightly controlling the biochemical environment immediately surrounding single molecules. Despite substantial progress in the production of such components, the process remains relatively inefficient, inaccurate and time-consuming. Here we address challenges and limitations in the routines, materials and the designs that have been commonly employed in the field, and introduce a new generation of LFCs designed for single-molecule experiments and assembled using additive manufacturing. We present single- and multi-channel, as well as reservoir-based LFCs produced by 3D printing to perform single-molecule experiments. Using these flow cells along with optical tweezers, we show compatibility with single-molecule experiments including the isolation and manipulation of single DNA molecules either attached to the surface of a coverslip or as freely movable DNA dumbbells, as well as direct observation of protein-DNA interactions. Using additive manufacturing to produce LFCs with versatility of design and ease of production allow experimentalists to optimize the flow cells to their biological experiments and provide considerable potential for performing multi-component single-molecule experiments.

• Ahmadi, Arash; Rosnes, Ida; Blicher, Pernille; Diekmann, Robin; Sch¨¹ttpelz, Mark & Glette, Kyrre [Vis alle 10 forfattere av denne artikkelen] (2018). Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V. Nature Communications. 9(1). doi: 10.1038/s41467-018-07797-4. Fulltekst i vitenarkiv
• Ahmadi, Arash & Reihani, S. Nader S. (2013). Axial potential mapping of optical tweezers for biopolymer stretching: the bead size matters. Optics Letters. ISSN 0146-9592. 38(5), s. 685¨C687. doi: 10.1364/OL.38.000685. Fulltekst i vitenarkiv

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• Ahmadi, Arash; Rosnes, Ida; Blicher, Pernille; Diekmann, Robin; Schuttpelz, Mark & Glette, Kyrre [Vis alle 10 forfattere av denne artikkelen] (2019). Publisher Correction: Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V (Nature Communications, (2018), 9, 1, (5381), 10.1038/s41467-018-07797-4). Nature Communications. 10(1). doi: 10.1038/s41467-019-10070-x. Fulltekst i vitenarkiv

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