Daniel Summerer

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KEYWORDS: , ,'DNA damage • DNA polymerases • DNA replication • thymidine dimers • UV light Ultraviolet (UV) light causes a variety of damage in DNA. The most abundant lesions are pyrimidine dimers such as the pyrimidine (6-4) pyrimidone photo-product (6-4PP) and the eis,syn cyclo-butane-pyrimidine dimer ((PD)11J (Scheme 1). These lesions are often repaired(More)
We report a flexible method for selective capture of sequence fragments from complex, eukaryotic genome libraries for next-generation sequencing based on hybridization to DNA microarrays. Using microfluidic array architecture and integrated hardware, the process is amenable to complete automation and does not introduce amplification steps into the standard(More)
The fidelity of DNA polymerase activity is of central importance for numerous biotechnological applications.r1.2 1 The imperfect fidelity of DNA polymerases under the unnatural conditions of several techniques such as those of the polymerase chain reaction (PCR) either restricts the application of these enzymes or demands their tedious optimization. Thus, a(More)
We genetically encoded the photocaged amino acid 4,5-dimethoxy-2-nitrobenzylserine (DMNB-Ser) in Saccharomyces cerevisiae in response to the amber nonsense codon TAG. This amino acid was converted to serine in living cells by irradiation with relatively low-energy blue light and was used to noninvasively photoactivate phosphorylation of the transcription(More)
The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step(More)
Here, we report a generally applicable PEGylation methodology based on the site-specific incorporation of para-azidophenylalanine into proteins in yeast. The azido group was used in a mild [3+2] cycloaddition reaction with an alkyne derivatized PEG reagent to afford selectively PEGylated protein. This strategy should be useful for the generation of(More)
Sequence capture methods for targeted next generation sequencing promise to massively reduce cost of genomics projects compared to untargeted sequencing. However, evaluated capture methods specifically dedicated to biologically relevant genomic regions are rare. Whole exome capture has been shown to be a powerful tool to discover the genetic origin of(More)
Faithful transfer of genetic information from one generation to its offspring is crucial for the survival of any living species, Genomic integrity relies greatly upon the ability of DNA polymerases to efficiently catalyze selective DNA synthesis in a template-directed manner,11J Despite enormous efforts in structural and functional studies, the complex(More)
DNA polymerases are the key enzymes for DNA synthesis involved in DNA replication, recombination, and repair. These enzymes undergo manifold contacts with the primer-template-substrates reaching up to several nucleotide pairs beyond the catalytic centre. To evaluate these enzyme contacts with the DNA substrates we applied novel synthetic steric probes in(More)
The unnatural amino acid p-nitrophenylalanine (pNO2-Phe) was genetically introduced into proteins in Escherichia coli in response to the amber nonsense codon with high fidelity and efficiency by means of an evolved tRNA/aminoacyl-tRNA synthetase pair from Methanocuccus jannaschii. It was shown that pNO2-Phe efficiently quenches the intrinsic fluorescence of(More)