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- ItemDNAzymes as Catalysts for l-Tyrosine and Amyloid β Oxidation(Washington, DC : ACS Publications, 2020) Köhler, Tony; Patsis, Panagiotis A.; Hahn, Dominik; Ruland, André; Naas, Carolin; Müller, Martin; Thiele, JulianSingle-stranded deoxyribonucleic acids have an enormous potential for catalysis by applying tailored sequences of nucleotides for individual reaction conditions and substrates. If such a sequence is guanine-rich, it may arrange into a three-dimensional structure called G-quadruplex and give rise to a catalytically active DNA molecule, a DNAzyme, upon addition of hemin. Here, we present a DNAzyme-mediated reaction, which is the oxidation of l-tyrosine toward dityrosine by hydrogen peroxide. With an optimal stoichiometry between DNA and hemin of 1:10, we report an activity of 101.2 ± 3.5 μUnits (μU) of the artificial DNAzyme Dz-00 compared to 33.0 ± 1.8 μU of free hemin. Exemplarily, DNAzymes may take part in neurodegeneration caused by amyloid beta (Aβ) aggregation due to l-tyrosine oxidation. We show that the natural, human genome-derived DNAzyme In1-sp is able to oxidize Aβ peptides with a 4.6% higher yield and a 33.3% higher velocity of the reaction compared to free hemin. As the artificial DNAzyme Dz-00 is even able to catalyze Aβ peptide oxidation with a 64.2% higher yield and 337.1% higher velocity, an in-depth screening of human genome-derived DNAzymes may identify further candidates with similarly high catalytic activity in Aβ peptide oxidation.
- ItemPhotoswitching of DNA Hybridization Using a Molecular Motor(Washington, DC : ACS Publications, 2018) Lubbe, Anouk S.; Liu, Qing; Smith, Sanne J.; de Vries, Jan Willem; Kistemaker, Jos C. M.; de Vries, Alex H.; Faustino, Ignacio; Meng, Zhuojun; Szymanski, Wiktor; Herrmann, Andreas; Feringa, Ben L.Reversible control over the functionality of biological systems via external triggers may be used in future medicine to reduce the need for invasive procedures. Additionally, externally regulated biomacromolecules are now considered as particularly attractive tools in nanoscience and the design of smart materials, due to their highly programmable nature and complex functionality. Incorporation of photoswitches into biomolecules, such as peptides, antibiotics, and nucleic acids, has generated exciting results in the past few years. Molecular motors offer the potential for new and more precise methods of photoregulation, due to their multistate switching cycle, unidirectionality of rotation, and helicity inversion during the rotational steps. Aided by computational studies, we designed and synthesized a photoswitchable DNA hairpin, in which a molecular motor serves as the bridgehead unit. After it was determined that motor function was not affected by the rigid arms of the linker, solid-phase synthesis was employed to incorporate the motor into an 8-base-pair self-complementary DNA strand. With the photoswitchable bridgehead in place, hairpin formation was unimpaired, while the motor part of this advanced biohybrid system retains excellent photochemical properties. Rotation of the motor generates large changes in structure, and as a consequence the duplex stability of the oligonucleotide could be regulated by UV light irradiation. Additionally, Molecular Dynamics computations were employed to rationalize the observed behavior of the motor–DNA hybrid. The results presented herein establish molecular motors as powerful multistate switches for application in biological environments.
- ItemThe genomic data deficit : On the need to inform research subjects of the informational content of their genomic sequence data in consent for genomic research(Amsterdam [u.a.] : Elsevier Science, 2020) Hallinan, DaraResearch subject consent plays a significant role in the legitimation of genomic research in Europe – both ethically and legally. One key criterion for any consent to be legitimate is that the research subject is ‘informed’. This criterion implies that the research subject is given all relevant information to allow them to decide whether engaging with a genomic research infrastructure or project would be normatively desirable and whether they wish to accept the risks associated with engagement. This article makes the normative argument that, in order to be truly ‘informed’, the research subject should be provided with information on the informational content of their genomic sequence data. Information should be provided, in the first instance, prior to the initial consent transaction, and should include: information on the fact that genomic sequence data will be collected and processed, information on the types of information which can currently be extracted from sequence data and information on the uncertainties surrounding the types of information which may eventually be extractable from sequence data. Information should also be provided, on an ongoing basis, as relevant and necessary, throughout the research process, and should include: information on novel information which can be extracted from sequence data and information on the novel uses and utility of sequence data. The article argues that current elaborations of ‘informed’ consent fail to adequately address the requirements set out in the normative argument and that this inadequacy constitutes an issue in need of a solution. The article finishes with a set of observations as to the fora best suited to deliver a solution and as to the substantive content of a solution. © 2020 The Authors