@article{KagelFrohmeGloekler2018, author = {Kagel, Heike and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Photoacids in biochemical applications}, series = {Journal of Cellular Biotechnology}, volume = {4}, journal = {Journal of Cellular Biotechnology}, number = {1-2}, publisher = {IOS Press}, issn = {2352-3697}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16123}, pages = {23 -- 30}, year = {2018}, abstract = {BACKGROUND: After excitation with light photoacids can change the pH in a solution by release of a proton. They have been used mostly for excited state proton transfer studies. In this review the general functionality and mechanisms and the subdivision of photoacids is explained. STATE OF THE ART: Different uses of photoacids are described, covering a wide range of various biochemical topics, focusing on biochemical applications. Examples for the introduced subdivisions are covered. CONCLUSIONS AND OUTLOOK: The areas in which photoacids can be employed are diverse. Photoacids have a promising future in biotechnology and biochemistry and should be considered for upcoming applications, especially in non-invasive control of biochemical reactions.}, language = {en} } @misc{SeifertPospisil2014, author = {Seifert, Felix and Pospisil, Heike}, title = {Reannotation des Maize oligonucleotide arrays}, series = {Wissenschaftliche Beitr{\"a}ge 2014}, volume = {18}, journal = {Wissenschaftliche Beitr{\"a}ge 2014}, issn = {0949-8214}, doi = {10.15771/0949-8214_2014_1_4}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-3315}, pages = {33 -- 35}, year = {2014}, abstract = {Die Microarray-Technologie hat sich zu einem etablierten Ansatz der Hochdurchsatz-Genexpressionsanalyse entwickelt. Das „maize oligonucleotide array" (maizearray) ist eine der wenigen Microarray-Plattformen, welche f{\"u}r die genomweite Genexpressionsanalyse von Mais (Zea mays L.) erzeugt wurden. Die Sonden wurden basierend auf ESTs (expressed sequence tags) generiert. Mittlerweile ist die Genomsequenz von Mais verf{\"u}gbar und erm{\"o}glicht eine genauere Annotation dieser Sonden. In dieser Arbeit wurden die Genompositionen aller Sonden und basierend darauf die zugrunde liegenden Gene sowie deren funktionelle Annotation bestimmt. Durch die Analyse konnten Redundanzen und nicht eindeutig bindende Sonden aufgedeckt und gleichzeitig die Zahl der Gene mit funktioneller Annotation verdoppelt werden. Unsere Reannotation wird funktionelle Analysen bereits existierender und zuk{\"u}nftiger Datens{\"a}tze stark verbessern.}, language = {de} } @article{MorlockSubramanianZounietal.2022, author = {Morlock, Sascha and Subramanian, Senthil Kumar and Zouni, Athina and Lisdat, Fred}, title = {Bio-inorganic hybrid structures for direct electron transfer to photosystem I in photobioelectrodes}, series = {Biosensors and Bioelectronics}, volume = {204}, journal = {Biosensors and Bioelectronics}, publisher = {Elsevier}, issn = {1873-4235}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16770}, year = {2022}, abstract = {Synthetic materials can be combined with biological components in many ways. One example that provides scientists with multiple challenges is a photobioelectrode that converts sunlight into electrons in a biohybrid approach. In the present study several key parameters are evaluated concerning their influence on the direct electron transfer from a 3D indium tin oxide (ITO) electrode material to photosystem I (PSI) as a light-harvesting biomolecule. In contrast to previous investigations, no mediating molecule is added to shuttle the electrons to the luminal side of PSI. Thus, this setup is less complex than foregoing ones. The solution composition drastically influences the interaction of PSI with the ITO surface. Here, the application of higher buffer concentrations and the addition of salts are advantageous, whereas the nature of the buffer ions plays a minor role. The artificial electrode material's thickness is adjustable since a spin-coating procedure is used for preparation. With a 30 μm thick structure and immobilized PSI cathodic photocurrents up to 10.1 μA cm-2 are obtained at 100 mW cm-2 illumination intensity and an applied potential of -0.1V vs. Ag/AgCl. Over a period of three days the photobioelectrodes are illuminated for a total of 90 min and stored between the measurements at ambient temperature. The stability of the setup is noteworthy as still about 90\% of the photocurrent is retained. The photocathode described here offers many positive features, including a high onset potential for the photocurrent starting sligthly above the redox potentail of P700, and applicability in a wide pH range from pH 5 to 8.}, language = {en} } @article{GloeklerLimIdaetal.2021, author = {Gl{\"o}kler, J{\"o}rn and Lim, Theam Soon and Ida, Jeunice and Frohme, Marcus}, title = {Isothermal amplifications - a comprehensive review on current methods}, series = {Critical Reviews in Biochemistry and Molecular Biology}, journal = {Critical Reviews in Biochemistry and Molecular Biology}, publisher = {Taylor \& Francis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15154}, pages = {1 -- 44}, year = {2021}, abstract = {AbstractThe introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.}, language = {en} } @article{MorlockSubramanianZounietal.2023, author = {Morlock, Sascha and Subramanian, Senthil Kumar and Zouni, Athina and Lisdat, Fred}, title = {Closing the green gap of photosystem I with synthetic fluorophores for enhanced photocurrent generation in photobiocathodes}, series = {Chemical Science}, volume = {14}, journal = {Chemical Science}, publisher = {Royal Society of Chemistry (RSC)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-17022}, pages = {1696 -- 1708}, year = {2023}, abstract = {One restriction for biohybrid photovoltaics is the limited conversion of green light by most natural photoactive components. The present study aims to fill the green gap of photosystem I (PSI) with covalently linked fluorophores, ATTO 590 and ATTO 532. Photobiocathodes are prepared by combining a 20 μm thick 3D indium tin oxide (ITO) structure with these constructs to enhance the photocurrent density compared to setups based on native PSI. To this end, two electron transfer mechanisms, with and without a mediator, are studied to evaluate differences in the behavior of the constructs. Wavelength-dependent measurements confirm the influence of the additional fluorophores on the photocurrent. The performance is significantly increased for all modifications compared to native PSI when cytochrome c is present as a redox-mediator. The photocurrent almost doubles from -32.5 to up to -60.9 μA cm-2. For mediator-less photobiocathodes, interestingly, drastic differences appear between the constructs made with various dyes. While the turnover frequency (TOF) is doubled to 10 e-/PSI/s for PSI-ATTO590 on the 3D ITO compared to the reference specimen, the photocurrents are slightly smaller since the PSI-ATTO590 coverage is low. In contrast, the PSI-ATTO532 construct performs exceptionally well. The TOF increases to 31 e-/PSI/s, and a photocurrent of -47.0 μA cm-2 is obtained. This current is a factor of 6 better than the reference made with native PSI in direct electron transfer mode and sets a new record for mediator-free photobioelectrodes combining 3D electrode structures and light-converting biocomponents.}, language = {en} } @article{MorlockSubramanianZounietal.2021, author = {Morlock, Sascha and Subramanian, Senthil Kumar and Zouni, Athina and Lisdat, Fred}, title = {Scalable Three-Dimensional Photobioelectrodes Made of Reduced Graphene Oxide Combined with Photosystem I}, series = {ACS Applied Materials \& Interfaces}, volume = {13}, journal = {ACS Applied Materials \& Interfaces}, number = {9}, publisher = {American Chemical Society (ACS)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-16760}, pages = {11237 -- 11246}, year = {2021}, abstract = {Photobioelectrodes represent one of the examples where artificial materials are combined with biological entities to undertake semi-artificial photosynthesis. Here, an approach is described that uses reduced graphene oxide (rGO) as an electrode material. This classical 2D material is used to construct a three-dimensional structure by a template-based approach combined with a simple spin-coating process during preparation. Inspired by this novel material and photosystem I (PSI), a biophotovoltaic electrode is being designed and investigated. Both direct electron transfer to PSI and mediated electron transfer via cytochrome c from horse heart as redox protein can be confirmed. Electrode preparation and protein immobilization have been optimized. The performance can be upscaled by adjusting the thickness of the 3D electrode using different numbers of spin-coating steps during preparation. Thus, photocurrents up to ∼14 μA/cm2 are measured for 12 spin-coated layers of rGO corresponding to a turnover frequency of 30 e- PSI-1 s-1 and external quantum efficiency (EQE) of 0.07\% at a thickness of about 15 μm. Operational stability has been analyzed for several days. Particularly, the performance at low illumination intensities is very promising (1.39 μA/cm2 at 0.1 mW/cm2 and -0.15 V vs Ag/AgCl; EQE 6.8\%).}, language = {en} } @article{IdaChanGloekleretal.2019, author = {Ida, Jeunice and Chan, Soo Khim and Gl{\"o}kler, J{\"o}rn and Lim, Yee Ying and Choong, Yee Siew and Lim, Theam Soon}, title = {G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing}, series = {Molecules}, volume = {24}, journal = {Molecules}, number = {6}, issn = {1420-3049}, doi = {10.3390/molecules24061079}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-11438}, year = {2019}, abstract = {G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.}, language = {en} } @article{KoelschHejaziStiegeretal.2018, author = {K{\"o}lsch, Adrian and Hejazi, Mahdi and Stieger, Kai Ralf and Feifel, Sven Christian and Kern, Jan F. and M{\"u}h, Frank and Lisdat, Fred and Lokstein, Heiko and Zouni, Athina}, title = {Insights into the binding behavior of native and non-native cytochromes to photosystem I from Thermosynechococcus elongatus}, series = {Journal of Biological Chemistry}, volume = {293}, journal = {Journal of Biological Chemistry}, number = {23}, issn = {1083-351X}, doi = {10.1074/jbc.RA117.000953}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-12780}, pages = {9090 -- 9100}, year = {2018}, abstract = {The binding of photosystem I (PS I) from Thermosynechococcus elongatus to the native cytochrome (cyt) c6 and cyt c from horse heart (cyt cHH) was analyzed by oxygen consumption measurements, isothermal titration calorimetry (ITC), and rigid body docking combined with electrostatic computations of binding energies. Although PS I has a higher affinity for cyt cHH than for cyt c6, the influence of ionic strength and pH on binding is different in the two cases. ITC and theoretical computations revealed the existence of unspecific binding sites for cyt cHH besides one specific binding site close to P700. Binding to PS I was found to be the same for reduced and oxidized cyt cHH. Based on this information, suitable conditions for cocrystallization of cyt cHH with PS I were found, resulting in crystals with a PS I:cyt cHH ratio of 1:1. A crystal structure at 3.4-{\AA} resolution was obtained, but cyt cHH cannot be identified in the electron density map because of unspecific binding sites and/or high flexibility at the specific binding site. Modeling the binding of cyt c6 to PS I revealed a specific binding site where the distance and orientation of cyt c6 relative to P700 are comparable with cyt c2 from purple bacteria relative to P870. This work provides new insights into the binding modes of different cytochromes to PS I, thus facilitating steps toward solving the PS I-cyt c costructure and a more detailed understanding of natural electron transport processes.}, language = {en} } @misc{KoberHanschkeMacholzetal.2018, author = {Kober, Liane and Hanschke, Christian and Macholz, Rainer and Frohme, Marcus}, title = {Die einfache Extraktion und Quantifizierung von sprengstofftypischen Verbindungen in Bodenproben {\"u}ber LC-MS/MS}, series = {Wissenschaftliche Beitr{\"a}ge 2018}, volume = {22}, journal = {Wissenschaftliche Beitr{\"a}ge 2018}, issn = {0949-8214}, doi = {10.15771/0949-8214_2018_1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-10219}, pages = {7 -- 16}, year = {2018}, abstract = {Die Kontamination von Fl{\"a}chen mit R{\"u}stungsaltlasten durch sprengstofftypische Verbindungen (STV) wie 2,4,6-Trinitrotoluol (TNT) ist nach wie vor ein großes Risiko f{\"u}r Gesundheit und Umwelt. Die Hochdruckfl{\"u}ssigchromatographie (HPLC) ist in Kombination mit der Tandem-Massenspektrometrie (MS/MS) ein besonders sensitives und exaktes Verfahren zur Konzentrationsbestimmung derartiger Umweltkontaminanten. Jedoch ben{\"o}tigen die derzeit eingesetzten Methoden zur Extraktion und Quantifizierung viel Zeit und Bodenmaterial. Wir haben daher eine 20-min{\"u}tige LC-MS/MS-Methode entwickelt, die in einer Probe simultan acht STV qualitativ und quantitativ nachweisen kann. Im Vergleich zur EPA-Referenzmethode konnte bei der Extraktion die eingesetzte Bodenmenge von 10 g auf 2 g reduziert und die Extraktionsdauer von 18 h auf 30 min verk{\"u}rzt werden. Die abschließende Validierung zeigte eine gute Reproduzierbarkeit und mit etablierten Protokollen vergleichbare Detektions- (LOD) und Quantifizierungslimits (LOQ), so dass die optimierten Methoden f{\"u}r eine schnelle und zuverl{\"a}ssige Analyse von Realproben eingesetzt werden konnten.}, language = {de} } @article{FischbachLohBieretal.2017, author = {Fischbach, Jens and Loh, Qiuting and Bier, Frank Fabian and Lim, Theam Soon and Frohme, Marcus and Gl{\"o}kler, J{\"o}rn}, title = {Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/srep45085}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-9248}, year = {2017}, abstract = {We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate.}, language = {en} } @inproceedings{RiedelGoebelParaketal.2014, author = {Riedel, Marc and G{\"o}bel, Gero and Parak, Wolfgang J. and Lisdat, Fred}, title = {Light-addressable amperometric electrodes for enzyme sensors based on direct quantum dot-electrode contacts}, publisher = {Society of Photo-Optical Instrumentation Engineers (SPIE)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:526-opus4-15266}, pages = {195 -- 200}, year = {2014}, abstract = {Quantum dots allow the generation of charge carriers upon illumination. When these particles are attached to an electrode a photocurrent can be generated. This allows their use as a light-switchable layer on the surface. The QDs can not only exchange electronics with the electrode, but can also interact with donor or acceptor compounds in solution providing access to the construction of signal chains starting from an analytic molecule. The magnitude and the direction of the photocurrent depend on several factors such as electrode polarization, solution pH and composition. These defined dependencies have been evaluated with respect to the combination of QD-electrodes with enzyme reactions for sensorial purpose. CdSe/ZnS-QD-modified electrodes can be used to follow enzymatic reactions in solution based on the oxygen sensitivity. In order to develop a photoelectrochemical biosensor, e.g. glucose oxidase is immobilized on the CdSe/ZnS-electrode. One immobilization strategy applies the layer-by-layer-technique of GOD and a polyelectrolyte. Photocurrent measurements of such a sensor show a clear concentration dependent behavior. The principle of combing QD oxidase. The sensitivity of quantum dot electrodes can be influenced by additional nanoparticles, but also by multiple layers of the QDs. In another direction of research it can be influenced by additional nanoparticles, but also by multiple layers of the QDs. In another direction of research it can be demonstrated that direct electron transfer from excited quantum dots can be achieved with the redox protein cytochrome c. This allows the detection of the protein, but also interaction partners such as a enzymes or superoxide.}, language = {en} }