Research

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Introduction

Our genetic system is constructed on the basis of the four nucleobases: adenine, cytosine, guanine and thymine. In RNA the base thymine is replaced by uracil. Although all cells in a human body contain the same DNA molecules with the same base sequence, we know that around 200 different cell types of the human body (among them neurons and fibroblasts) possess different functions and properties. It is consequently clear that we need another level of information alongside the sequence information in order to program the individual genomes. The control of genetic regulation at the DNA and RNA level is often achieved by modified DNA and RNA bases. In these compounds, the chemical structures of the canonical nucleobases are heavily altered. The presence of modified bases in either DNA or RNA represents a second layer of information in our genome that is so far not understood.

A) The Carell group uses modern synthetic organic chemistry to synthesize the naturally occurring modified nucleobases. We convert these structures into phophoramidite building blocks and subsequently utilize solid phase synthesis procedures in order to synthesize small DNA and RNA strands, which contain specific modifications at defined sites. These oligonucleotides are used for physical organic studies in order to elucidate how the modified bases change the structure and stability of DNA and RNA. In addition, we use the oligonucleotides for modern mass spectrometry based proteomics research in order to find the proteins which recognize the modified bases. By identifying the proteins which bind to the modified bases and read their information, we aim to elucidate their functional interplay.

B) In a second line of research we are synthesizing the modified DNA and RNA bases in an isotopically labelled form. By incorporating the stable isotopes 13C, D, 15N we are able to create isotopologues which are subsequently used in modern UHPLC mass spectrometry in order to quantify the levels of the modified bases in different tissues and for example differentiating stem cells. This approach allows us to follow dynamic changes of the modification content in genomes at various cellular states.

C) Modified DNA and RNA bases are not only biochemically generated in our cells in order to encode a second layer of information, but they are also created in the framework of DNA and RNA damage. Our genome is constantly threatened through the attack of for example reactive oxygen species, activated amino compounds or simply by UV-light. The generated DNA lesions are very often defined chemical products that harm the cellular integrity and are the reason for spontaneous mutations which finally may lead to cancer development. The Carell group is again using the tools of synthetic organic chemistry to synthesize the DNA lesions. We are using analytical chemistry to discover and incorporate new DNA lesions into oligonucleotides in order to study how they modify the structure and stability of the DNA duplex. In addition, we are using modern biotechnology in order to produce the proteins that are responsible for the repair of these DNA lesions in our genome. Using X-ray crystallography, we obtain detailed mechanistic insight into the mechanisms that allow cells to recognize and remove DNA lesions from the genome.

In summary: The Carell group uses modern synthetic organic chemistry to synthesize naturally occurring modified DNA and RNA bases. These may be bases that are generated as part of a genetic system beyond the DNA sequence code to program the activity of the genome in different cell types. These DNA bases are of fundamental importance for cellular differentiation and de-differentiation, which is the reason the Carell group operates a stem cell laboratory. We are synthesizing DNA lesions and study how these lesions lead to cellular degeneration and how cells are able to repair these DNA lesions. In our group, organic chemistry is linked to cell biology, biochemistry and molecular biology. Currently, 50% of the PhD students and postdocs are synthetic organic chemists interested in studying organic chemistry connected to biology. The other 50% are biologists, biochemists, biotechnologists and cell biologists, which are interested in studying how chemistry on DNA and RNA bases influence life. We are operating in small interdisciplinary subgroups where each subgroup focusses on a specific biological question. The chemists are providing the synthetic material, the molecular biologists the respective proteins and the mass spectrometrists collect data concerning the protein networks. Alongside our weekly group seminar we have bi-weekly subgroup meetings, where we discuss the research results and future directions of our projects. The highly interdisciplinary character of our research encourages the members of the Carell group to think beyond their own discipline and to adapt quickly to new technologies and scientific challenges.