@article{DunceMilburnGurusaranetal.2018,
  author    = {Dunce, James M. and Milburn, Amy E. and Gurusaran, Manickam and da Cruz, Irene and Sen, Lee T. and Benavente, Ricardo and Davies, Owen R.},
  title     = {Structural basis of meiotic telomere attachment to the nuclear envelope by MAJIN-TERB2-TERB1},
  series = {Nature Communications},
  volume    = {9},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-018-07794-7},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-226416},
  year      = {2018},
  abstract  = {Meiotic chromosomes undergo rapid prophase movements, which are thought to facilitate the formation of inter-homologue recombination intermediates that underlie synapsis, crossing over and segregation. The meiotic telomere complex (MAJIN, TERB1, TERB2) tethers telomere ends to the nuclear envelope and transmits cytoskeletal forces via the LINC complex to drive these rapid movements. Here, we report the molecular architecture of the meiotic telomere complex through the crystal structure of MAJIN-TERB2, together with light and X-ray scattering studies of wider complexes. The MAJIN-TERB2 2:2 hetero-tetramer binds strongly to DNA and is tethered through long flexible linkers to the inner nuclear membrane and two TRF1-binding 1:1 TERB2-TERB1 complexes. Our complementary structured illumination microscopy studies and biochemical findings reveal a telomere attachment mechanism in which MAJIN-TERB2-TERB1 recruits telomere-bound TRF1, which is then displaced during pachytene, allowing MAJIN-TERB2-TERB1 to bind telomeric DNA and form a mature attachment plate.},
  language  = {en}
}
@article{BencurovaAkashDobsonetal.2023,
  author    = {Bencurova, Elena and Akash, Aman and Dobson, Renwick C.J. and Dandekar, Thomas},
  title     = {DNA storage-from natural biology to synthetic biology},
  series = {Computational and Structural Biotechnology Journal},
  volume    = {21},
  journal   = {Computational and Structural Biotechnology Journal},
  issn      = {2001-0370},
  doi       = {10.1016/j.csbj.2023.01.045},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-349971},
  pages     = {1227-1235},
  year      = {2023},
  abstract  = {Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macram{\´e} , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).},
  language  = {en}
}
@phdthesis{Neitz2024,
  author    = {Neitz, Hermann},
  title     = {Hydrophobic recognition motifs in functionalized DNA},
  doi       = {10.25972/OPUS-34838},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348382},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {In w{\"a}ssriger Umgebung spielen hydrophobe Wechselwirkungen eine wichtige Rolle f{\"u}r die DNA. Die Einf{\"u}hrung von Modifikationen, die auf hydrophoben aromatischen Einheiten basieren, kann die Erkennung und Reaktivit{\"a}t von funktionellen Gruppen in der DNA steuern. Modifikationen k{\"o}nnen durch ein k{\"u}nstliches R{\"u}ckgrat oder in Form einer Erweiterung der Nukleobasen eingebracht werden und so zu zus{\"a}tzlichen Eigenschaften der DNA f{\"u}hren. Diese Dissertation befasst sich mit der Verwendung von hydrophoben Einheiten zur Funktionalisierung von DNA. Im ersten Teil der Arbeit wurde das Tolanmotiv (Diphenylacetylen) in Kombination mit dem acyclischen R{\"u}ckgrat von GNA und BuNA verwendet, um Erkennungseinheiten im DNA-Kontext zu erzeugen. Die gezielte Fluorierung der aromatischen Ringe des Tolan-Bausteins bildete die Grundlage f{\"u}r eine supramolekulare Sprache, die auf Aren-Fluoroaren-Wechselwirkungen basiert. Die spezifische Erkennung wurde mittels thermodynamischer, kinetischer und NMR-spektroskopischer Methoden untersucht. Im zweiten Teil der Arbeit wurden Desoxyuridin-Derivate mit einer hydrophoben aromatischen Modifikation hergestellt und in die DNA-Doppelhelix eingebaut. Die Bestrahlung mit UV-Licht f{\"u}hrte zu einer [2+2]-Cycloaddition zwischen zwei modifizierten Nukleosiden in der DNA. Das Reaktionsprodukt wurde strukturell charakterisiert und die Reaktion in verschiedenen biochemischen und nanotechnologischen DNA-Anwendungen eingesetzt.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}
@article{NeitzBessiKachleretal.2022,
  author    = {Neitz, Hermann and Bessi, Irene and Kachler, Valentin and Michel, Manuela and H{\"o}bartner, Claudia},
  title     = {Tailored tolane-perfluorotolane assembly as supramolecular base pair replacement in DNA},
  series = {Angewandte Chemie International Edition},
  volume    = {62},
  journal   = {Angewandte Chemie International Edition},
  number    = {1},
  doi       = {10.1002/anie.202214456},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-312575},
  year      = {2022},
  abstract  = {Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.},
  language  = {en}
}
@article{AydinliLiangDandekar2022,
  author    = {Aydinli, Muharrem and Liang, Chunguang and Dandekar, Thomas},
  title     = {Motif and conserved module analysis in DNA (promoters, enhancers) and RNA (lncRNA, mRNA) using AlModules},
  series = {Scientific Reports},
  volume    = {12},
  journal   = {Scientific Reports},
  number    = {1},
  doi       = {10.1038/s41598-022-21732-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301268},
  year      = {2022},
  abstract  = {Nucleic acid motifs consist of conserved and variable nucleotide regions. For functional action, several motifs are combined to modules. The tool AIModules allows identification of such motifs including combinations of them and conservation in several nucleic acid stretches. AIModules recognizes conserved motifs and combinations of motifs (modules) allowing a number of interesting biological applications such as analysis of promoter and transcription factor binding sites (TFBS), identification of conserved modules shared between several gene families, e.g. promoter regions, but also analysis of shared and conserved other DNA motifs such as enhancers and silencers, in mRNA (motifs or regulatory elements e.g. for polyadenylation) and lncRNAs. The tool AIModules presented here is an integrated solution for motif analysis, offered as a Web service as well as downloadable software. Several nucleotide sequences are queried for TFBSs using predefined matrices from the JASPAR DB or by using one's own matrices for diverse types of DNA or RNA motif discovery. Furthermore, AIModules can find TFBSs common to two or more sequences. Demanding high or low conservation, AIModules outperforms other solutions in speed and finds more modules (specific combinations of TFBS) than alternative available software. The application also searches RNA motifs such as polyadenylation site or RNA-protein binding motifs as well as DNA motifs such as enhancers as well as user-specified motif combinations (https://bioinfo-wuerz.de/aimodules/; alternative entry pages: https://aimodules.heinzelab.de or https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/aimodules). The application is free and open source whether used online, on-site, or locally.},
  language  = {en}
}
@article{SanyalWallaschekGlassetal.2018,
  author    = {Sanyal, Anirban and Wallaschek, Nina and Glass, Mandy and Flamand, Louis and Wight, Darren J. and Kaufer, Benedikt B.},
  title     = {The ND10 Complex Represses Lytic Human Herpesvirus 6A Replication and Promotes Silencing of the Viral Genome},
  series = {Viruses},
  volume    = {10},
  journal   = {Viruses},
  number    = {8},
  doi       = {10.3390/v10080401},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227337},
  pages     = {401, 1-11},
  year      = {2018},
  abstract  = {Human herpesvirus 6A (HHV-6A) replicates in peripheral blood mononuclear cells (PBMCs) and various T-cell lines in vitro. Intriguingly, the virus can also establish latency in these cells, but it remains unknown what influences the decision between lytic replication and the latency of the virus. Incoming virus genomes are confronted with the nuclear domain 10 (ND10) complex as part of an intrinsic antiviral response. Most herpesviruses can efficiently subvert ND10, but its role in HHV-6A infection remains poorly understood. In this study, we investigated if the ND10 complex affects HHV-6A replication and contributes to the silencing of the virus genome during latency. We could demonstrate that ND10 complex was not dissociated upon infection, while the number of ND10 bodies was reduced in lytically infected cells. Virus replication was significantly enhanced upon knock down of the ND10 complex using shRNAs against its major constituents promyelocytic leukemia protein (PML), hDaxx, and Sp100. In addition, we could demonstrate that viral genes are more efficiently silenced in the presence of a functional ND10 complex. Our data thereby provides the first evidence that the cellular ND10 complex plays an important role in suppressing HHV-6A lytic replication and the silencing of the virus genome in latently infected cells.},
  language  = {en}
}
@phdthesis{Hoeflein2023,
  author    = {H{\"o}flein, Felix},
  title     = {Kinetik der Schistosomen-spezifischen DNA nach Behandlung mit Praziquantel und Bestimmung der Schistosomiasis-Pr{\"a}valenz einer in einem Nicht-Endemiegebiet lebenden Risikopopulation sowie der Evaluation ausgew{\"a}hlter diagnostischer Verfahren},
  doi       = {10.25972/OPUS-29790},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-297909},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In dieser Arbeit wurden Bewohner/-innen der W{\"u}rzburger Gemeinschaftsunterk{\"u}nfte f{\"u}r Gefl{\"u}chtete auf das Vorliegen einer Schistosomiasis gescreent. Lag eine behandlungsd{\"u}rftige Infektion vor, wurden die Teilnehmenden mit Praziquantel behandelt, um im nachfolgenden Verlauf freiwillig an der Erstellung einer Schistosomen-DNA-Kinetik mitzuwirken. Eine Besonderheit der Studie lag dabei in der fehlenden M{\"o}glichkeit einer Reinfektion, da sich die Betroffenen w{\"a}hrend des Follow-ups in einem Endemie-freien Gebiet aufhielten. F{\"u}r das Screening kamen ein CCA-Urin-Schnelltest sowie ein ICT zum Einsatz. Die Diagnosesicherung wurde durch die Mikroskopie oder die qPCR angestrebt. Es zeigte sich, dass die Kombination von CCA-Test und ICT einen positiven pr{\"a}diktiven Wert von 80 \% f{\"u}r das tats{\"a}chliche Vorliegen einer Schistosomen-Infektion liefert. Die Schistosomiasis-Pr{\"a}valenz der hier untersuchten, in einem Nicht-Endemiegebiet lebenden Risikopopulation, wurde auf 3,9 \% bestimmt und ist im Vergleich zu bisherigen Ver{\"o}ffentlichungen als niedrig anzusehen. Dabei ist zu beachten, dass die Pr{\"a}valenz zum Teil deutlich {\"u}bersch{\"a}tzt werden kann, sofern der CCA-Urin-Schnelltest als alleiniges Diagnosekriterium eingesetzt wird (Pr{\"a}valenzCCA = 27,6 \%). Die Erstellung der DNA-Kinetik mittels qPCR zeigte, dass die Behandlung mit Praziquantel einen nach 3 Tagen messbaren, signifikanten (p < 0,05) Anstieg der DNA-Konzentration im Serum zur Folge hatte, welcher im weiteren Verlauf kontinuierlich abfiel. Im Mittel wurde nach 48 Tagen der Schwellenwert der DNA-Konzentration unterschritten, der ohne vorausgegangene Behandlung als positiv und therapiebed{\"u}rftig gewertet worden w{\"a}re. Durch Inter- und Extrapolation der gewonnen Daten, konnte eine Funktion errechnet werden, die den zeitlichen Verlauf des Zerfalls der Schistosomen-DNA beschreibt und somit zur Ermittlung weiterer Therapie- und Kontrollm{\"o}glichkeit der Schistosomiasis beitragen kann.},
  subject      = {Schistosomiasis},
  language  = {de}
}
@phdthesis{Siewert2021,
  author    = {Siewert, Aaron},
  title     = {Nucleotide analogs as rigid spin labels for DNA and RNA},
  doi       = {10.25972/OPUS-24765},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247657},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Nucleic acids are one of the important classes of biomolecules together with carbohydrates, proteins and lipids. Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are most well known for their respective roles in the storage and expression of genetic information. Over the course of the last decades, nucleic acids with a variety of other functions have been discovered in biological organisms or created artificially. Examples of these functional nucleic acids are riboswitches, aptamers and ribozymes. In order to gain information regarding their function, several analytical methods can be used. Electron paramagnetic resonance (EPR) spectroscopy is one of several techniques which can be used to study nucleic acid structure and dynamics. However, EPR spectroscopy requires unpaired electrons and because nucleic acids themselves are not paramagnetic, the incorporation of spin labels which carry a radical is necessary. Here, three new spin labels for the analysis of nucleic acids by EPR spectroscopy are presented. All of them share two important design features. First, the paramagnetic center is located at a nitroxide, flanked by ethyl groups to prevent nitroxide degradation, for example during solid phase synthesis. Furthermore, they were designed with rigidity as an important quality, in order to be useful for applications like pulsed electron double resonance (PELDOR) spectroscopy, where independent motion of the spin labels relative to the macromolecule has a noticeable negative effect on the precision of the measurements. Benzi-spin is a spin label which differs from most previous examples of rigid spin labels in that rather than being based on a canonical nucleoside, with a specific base pairing partner, it is supposed to be a universal nucleoside which is sufficiently rigid for EPR measurements when placed opposite to a number of different nucleosides. Benzi-spin was successfully incorporated into a 20 nt oligonucleotide and its base pairing behavior with seven different nucleosides was examined by UV/VIS thermal denaturation and continuous wave (CW) EPR experiments. The results show only minor differences between the different nucleosides, thus confirming the ability of benzi-spin to act as a universally applicable spin label. Lumi-spin is derived from lumichrome. It features a rigid scaffold, as well as a free 2'-hydroxy group, which should make it well suited for PELDOR experiments once it is incorporated into RNA oligonucleotides. E{\c{C}}r is based on the {\c{C}} family of spin labels, which contains the most well known rigid spin labels for nucleic acids to this day. It is essentially a version of E{\c{C}}m with a free 2'-hydroxy group. It was converted to triphosphate E{\c{C}}rTP and used for primer extension experiments to test the viability of enzymatic incorporation of rigid spin labels into oligonucleotides as an alternative to solid-phase synthesis. Incorporation into DNA by Therminator III DNA polymerase in both single-nucleotide and full-length primer extensions was achieved. All three of these spin labels represent further additions to the expanding toolbox of EPR spectroscopy on nucleic acids and might prove valuable for future research.},
  subject      = {Nucleins{\"a}uren},
  language  = {en}
}
@unpublished{WohlgemuthMitric2020,
  author    = {Wohlgemuth, Matthias and Mitric, Roland},
  title     = {Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping},
  series = {Physical Chemistry Chemical Physics},
  journal   = {Physical Chemistry Chemical Physics},
  edition   = {submitted version},
  doi       = {10.1039/D0CP02255A},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-209467},
  year      = {2020},
  abstract  = {Absorption of ultraviolet light is known as a major source of carcinogenic mutations of DNA. The underlying processes of excitation energy dissipation are yet not fully understood. In this work we provide a new and generally applicable route for studying the excitation energy transport in multi-chromophoric complexes at an atomistic level. The surface-hopping approach in the frame of the extended Frenkel exciton model combined with QM/MM techniques allowed us to simulate the photodynamics of the alternating (dAdT)10 : (dAdT)10 double-stranded DNA. In accordance with recent experiments, we find that the excited state decay is multiexponential, involving a long and a short component which are due to two distinct mechanisms: formation of long-lived delocalized excitonic and charge transfer states vs. ultrafast decaying localized states resembling those of the bare nucleobases. Our simulations explain all stages of the ultrafast photodynamics including initial photoexcitation, dynamical evolution out of the Franck-Condon region, excimer formation and nonradiative relaxation to the ground state.},
  language  = {en}
}
@article{ReynoldsHofmeisterCliffeetal.2016,
  author    = {Reynolds, David L. and Hofmeister, Brigitte T. and Cliffe, Laura and Siegel, T. Nicolai and Andersson, Britta A. and Beverley, Stephen M. and Schmitz, Robert J. and Sabatini, Robert},
  title     = {Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination},
  series = {Molecular Microbiology},
  volume    = {101},
  journal   = {Molecular Microbiology},
  number    = {4},
  doi       = {10.1111/mmi.13408},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187727},
  pages     = {559-574},
  year      = {2016},
  abstract  = {The genomes of kinetoplastids are organized into polycistronic gene clusters that are flanked by the modified DNA base J. Previous work has established a role of base J in promoting RNA polymerase II termination in Leishmania spp. where the loss of J leads to termination defects and transcription into adjacent gene clusters. It remains unclear whether these termination defects affect gene expression and whether read through transcription is detrimental to cell growth, thus explaining the essential nature of J. We now demonstrate that reduction of base J at specific sites within polycistronic gene clusters in L. major leads to read through transcription and increased expression of downstream genes in the cluster. Interestingly, subsequent transcription into the opposing polycistronic gene cluster does not lead to downregulation of sense mRNAs. These findings indicate a conserved role for J regulating transcription termination and expression of genes within polycistronic gene clusters in trypanosomatids. In contrast to the expectations often attributed to opposing transcription, the essential nature of J in Leishmania spp. is related to its role in gene repression rather than preventing transcriptional interference resulting from read through and dual strand transcription.},
  language  = {en}
}