Synthetic and enzymatic preparation of chemically modified nucleic acids

All projects in DyNACo require synthetic oligonucleotides with chemical modifications for their experiments or for benchmarking new theory methods. Furthermore, some projects require the synthesis of long RNA oligonucleotides with reporter groups, which need advanced semi-synthetic strategies for their preparation.^P1-3,P6-10 Commercial vendors offer only limited selections of chemical modifications and cannot provide all required post-synthetic modifications or long oligonucleotides prepared by semi-synthetic approaches such as ligation. Service project Z2 will provide the CRC with nucleic acid constructs using solid-phase synthesis, in vitro transcription, and ligation of synthetic oligonucleotides according to published standard protocols.^P1,2,6-10 Commercially available building blocks such as phosphoramidites or nucleoside triphosphates bearing non-natural modifications will be introduced, allowing monitoring of structural dynamics in nucleic acid complexes. All project planning and synthesis of complex modified oligonucleotides will be performed in the Kath-Schorr group at the University of Cologne. Those oligonucleotides that contain 2’-methoxy or 2’-fluorine, will be synthesized at the NA synthesis lab at the University Hospital Bonn, led by Dr. Christine Wuebben.^P4-P6 Z2 will also in part provide large quantities of modified oligonucleotides for the CRC, which can in principle also be obtained from commercial suppliers. Establishing thereby an in-house service will reduce the costs for the large amounts of nucleic acids needed, reduce the delivery time, and provide the CRC with easy access to custom-made nucleic acids with specific modifications.