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GRK 2039 Blog

With our new GRK 2039 blog we want to invite you, no matter you are a student, a young researcher, a cooperation partner or an interested guest, to follow our latest GRK activities. Our members frequently share here their scientific progresses, new  GRK events and updates but also their personal ideas and thoughts. With this we hope to give you detailed insights into our research training group and keep you up to date. Have fun to read!

* Frontiers in Delivery of Therapeutics

written by Tim Schober 2018/10/15
Tartu (Estonia), 21.-24.08.2018
This proceeding conference series is organized by Prof. Ülo Langel, who is the world key opinion leader in the field of cell-penetrating peptides for many years now. In this year edition, for the first time, the “peptides for intracellular delivery” topic has been expanded to all kinds of carriers, including liposomes, nanoparticles, exosomes, viral particles. The talks and posters presented current pharmacologically relevant examples of delivering medically relevant proteins, small molecules, SSO, siRMAs and plasmids. Combining the expertise from other-than peptides-only fields and strong focus on therapeuticall cargoes leads to a better understanding of fundamental delivery mechanisms and enables generation of new practically useful ideas.
Our member Tim Schober gave an oral presentation about his results on developing photocontrollable cell-penetrating peptides.
Towards photocontrol of the cell entry of cell-penetrating peptides
Tim Schober, Oleg Babii, Sergii Afonin, Igor V. Komarov and Anne S. Ulrich
Photoswitchable drugs can be delivered to their in vivo targets via illumination with non-invasive red light with unprecedented spatiotemporal resolution. Herein we expand this delivery concept to in-cell transport, by enabling photocontrol of peptide cell-penetrating ability. We designed several oligo-arginine-based cyclic cell-penetrating peptides, each of having a diarylethene-based photoswitch (DAE) in the backbone. For some amphipathic 10-mer peptides, we observed well-pronounced differences in uptake between the two photoforms. We explain the differences by the changes in rigidity/flexibility and in backbone exposure upon photoswitching, which differentially affect both, the entry-enabling preorganized charge display and peptide CPP-activity deteriorating intramolecular aggregation.

* Impressions about the microfluidics conference in Heidelberg

written by Sahana Sheshachala 2018/09/04

I recently participated in a three-day microfluidics conference at Heidelberg, Germany. The conference titled “Microfluidics 2018: New Technologies and Applications in Biology, Biochemistry and Single-Cell Analysis” is one of the biggest conferences in Europe organized by EMBL (European Molecular Biology Laboratory) focusing on current state-of-the art in the field of microfluidics and its applications in Molecular Biology. This was my first conference as a PhD student and I could not have asked for more. It was a great opportunity for an early researcher like me to get insights into the current trends and directions in the field of microfluidics, given that my doctoral studies involves microfluidic applications in the field of chemical biology.

Prior to the conference, I kept myself informed with the general information on the relevant lectures and keynote speakers. I was very impressed with the structuring and contents of the topics covered in the conference. The gathering was an amalgamation of some of the pioneer research groups in the field of microfluidics.

The conference hall at the EMBL center Heidelberg, the ARC Auditorium was fascinating in terms of its construction, perfectly designed for the scientific conferences. Particularly astonishing was the architecture of the hall way inspired by DNA double helix, through which the posters were aligned. The educational and product based stalls present there were from various companies, institutions and start up’s. The conference was attended by close to 200 people and one could say the gathering was quite international. The topics covered during conference were categorized into several segments covering sub topics. The poster sessions were distributed between two days and the large student gathering created a very vibrant atmosphere. The first lecture was delivered by Prof. Stephen Quake from Stanford, who provided a solid start to the conference through his engaging presentation about single cell genomics. The lectures throughout the day were very informative and inspiring at the same time, although I struggled a bit to process all the information that was coming through the fast moving slides. The next segment had some flash talk sessions from a set of students and I felt the flash talks were a great way to attract the audience to one’s poster. Imagining myself delivering one of these flash talks in the next conference, I eagerly waited for the poster sessions and took a note of the posters that were interesting to me.

Poster sessions turned out to be more enjoyable and resourceful than I imagined and I was able to have some very insightful interactions with many graduate students from various institutions around the globe. We did exchange a lot of information and discussed scientific problems concerning our research. Personally, for me, the interaction was very beneficial as I got answers and insights into new approaches for a few of the practical problems that I was facing in the lab. This to me was the best part of the conference as I found out how one approaches a particular scientific problem with a creative mind.

On the other hand, I was still trying to gather my courage to talk to the Professor I wanted to talk to, and saved it for the next day. Thanks to the organizers, in the evening everyone enjoyed the live telecast of the football world cup and then dispersed for the dinner.

The second and third day lectures were more relevant to my line of research about droplet-based microfluidics and its implications in the field of single cell analysis, antibody discovery and other related fields.I thoroughly enjoyed the talk by Prof. David A. Weitz from Harvard University on single cell analysis using droplet microfluidics and was fascinated to know how the microfluidic droplets can be manipulated for a particular application using simple chip designs. An interesting segment of the conference that intrigued me as a chemist was the topics on new microfluidic modules and designs which largely implied the exponential growth of new microfluidic modules and their ability to cross the scientific barrier in solving more complex phenomena in biomedical field. And I finally managed to have short interaction with one of the professors in the tea session and the interaction boosted my confidence for further networking and social interaction.

At the end, I would like to express my sincere gratitude to the GRK 2039 for providing funding for my very first conference and EMBL for structuring the conference so well.

* „Was genau passiert in Lebewesen und wie können wir es sichtbar machen?“

written by Larissa Doll and Samatha Wörner 2018/08/28

Am Girls´ Day 2018 hatte das „GRK 2039 - Molekulare Architekturen für die fluoreszente Bildgebung von Zellen“ die Chance, Schülerinnen einen Einblick in unser Forschungsprogramm zu ermöglichen. Um ihnen die Themengebiete Chemie, Biologie und Physik näher zu bringen, wurden verschiedene Stationen durchlaufen. Dabei konnten sie auch einen Einblick in die Quervernetzung dieser Themen und somit auch in das GRK 2039 bekommen und es wurde deutlich, wie wichtig das Zusammenarbeiten im Rahmen eines Graduiertenkollegs ist. An der ersten Station wurde den Schülerinnen die Eigenschaften von Photoschaltern durch Bestrahlung mit Licht bildlich vorgeführt. Auch die Theorie dahinter wurde mit Anwendungsbeispielen aus der Photopharmakologie erklärt. Um einen Einblick in den Laboralltag zu bekommen, konnten die Mädchen anschließend ausprobieren, wie beispielsweise das Arbeiten an einer Glove-Box oder HPLC funktioniert. Noch mehr praktische Erfahrung wurde an der dritten Station durch die Isolierung von DNA aus Zwiebeln gewonnen. Diese wurde durch Anfärben sichtbar gemacht. Zur weiteren Veranschaulichung für die zuvor erklärten und gezeigten Systeme von organischen und bioorganischen Molekülen, wurden abschließend angefärbte Zellen im Fluoreszenzmikroskop betrachtet. Dabei konnten die verschiedenen Zellorganellen farblich unterschieden werden. Final konnte sogar ein lebender Zebrafischembryo im Mikroskop untersucht werden.

Zusammenfassend war es eine gelungene Möglichkeit, schon jungen Menschen die Wichtigkeit des naturwissenschaftlichen Zusammenarbeitens zu vermitteln. Wir hatten viel Spaß dabei und freuen uns auf weiteres Interesse am GRK 2039.

* Welcome Julia Leier!

written by Julia Leier 2018/08/21

We also want to welcome Julia Leier!

She just started  her PhD in the group of PD Andreas Unterreiner:



I’m Julia, a new member of the GRK 2039.


This is how I got here: After finishing school I moved to Gießen to study ecotrophology (nutritional science) at the Justus-Liebig-University with the focus on biochemistry. There I got very interested in chemistry, which initiated my decision to study chemistry and mathematics for a teaching profession at the Karlsruhe Institute of Technology after finishing my bachelor degree. Here I specialised in physical chemistry, where I wrote my scientific work in the research group of PD Dr. A.-N. Unterreiner.


For my PhD I joined this research group within the GRK in June 2018. My aim is to analyse the photophysical and -chemical properties of various molecules on an ultrashort time scale. Therefore I’m using a femtosecond broadband transient absorption spectrometer as well as steady-state methods like absorption spectroscopy in the UV and visible spectra region and fluorescence spectroscopy. After photo-excitation there is typically a manifold of possible relaxation pathways. Whereby the fluorescence and its competing pathways are of special interest. In order to additionally enable the investigation of fluorescence lifetimes of up to a few picoseconds, I’m building an experimental setup called fluorescence up-conversion.


Currently I collaborate with two GRK members to analyse the properties of flavine derivatives for electron transfer in the DNA and the environmental influence of photoswitchable peptides.

* Welcome Monja Kunkel!

written by Monja Kunkel 2018/07/19

We are happy to welcome Monja as a new member in our research training group!

I asked her to introduce herself so that we all know a little bit more about her background and her new doctoral project:


Hi all,

my name is Monja and I‘m from Lahr, a small town only about 100 km to the south of Karlsruhe. For my bachelor‘s degree in chemistry I went to the Albert-Ludwigs-Universität Freiburg. Afterwards, I decided to move to Karlsruhe because of the great offering of physical and theoretical chemistry lectures at the Karlsruhe Institute of Technology. During my Master‘s at the KIT I also learned much about chemical biology, which was very interesting to me.

In the group of Prof. M. Elstner, chemical and biological problems are studied at various levels of theory, which perfectly fits to my interests. Hence, I chose this group for writing my master thesis. Finally, in May I joined the group starting my PhD.

My new project in the GRK deals with the development of a blood glucose sensor working by means of fluorescence. The basic idea is to link a fluorescent dye molecule to a natural glucose binding system, in this case the glucose binding protein (GBP). The conformation of the protein changes by binding a glucose molecule, so that also the fluorescent dye is moved. Due to the various environment of the dye, its optical properties change, too.

My part in this collaborative project is to find a good position for the dye in the protein by means of molecular dynamics simulations and quantum chemical calculations of the fluorescence.

I‘m happy to be a member of the GRK due to the close collaboration between the research groups.

* Paper Update: Photoaktivierbare Nanopartikel lösen gezielt den programmierten Zelltod aus!

written by Anna Meschov 2018/07/04
In der vorliegenden Publikation handelt es sich um photoaktivierbare, anorganisch-organische Gd43+[AlPCS4]34− Hybridnanopartikel. Diese Nanopartikel sind ohne Lichteinwirkung nicht toxisch, lösen jedoch nach einer Behandlung mit nahinfrarotem Licht eine Bildung von reaktiven Sauerstoffspezies (ROS) in der Zelle aus, was zum programmierten Zelltod (Apoptose) führt. Solche Nanopartikel könnten unter anderem bei der Krebsbehandlung im Rahmen der photodynamischen Therapie Einsatz finden. In der Publikation sind die analytische Charakterisierung der Nanopartikel sowie in vitro und in vivo Experimente dargestellt, die deren Wirkung sowohl in den Zellen, als auch in einem lebenden Organismus (Zebrafisch) bestätigen.

Original Publikation: Gd43+[AlPCS4]34− Nanoagent Generating 1O2 for Photodynamic Therapy

Authoren: Marieke Poß, Eva Zittel, Carmen Seidl, Anna Meschkov, Leonel Muñoz, Ute Schepers and Claus Feldmann