Project summary DNA analogs that contain latently reactive electrophilic functionalities can selectively form covalent bonds with target biomolecules such as DNA, mRNA, and protein through affinity induced reactions. Therefore, they can be used as probes in research areas such as chemical biology, and have the potential to become a new class of therapeutic agents that have advantages over drugs based on small organic molecules, peptides and DNA analogs that lack such functionalities. In addition, DNA derivatives that contain base-labile and electrophilic groups have been found in cells. They are intermediates of important cellular processes and may play important cellular functions. To study these processes and functions, the availability of the derivatives can be crucial for success. Consequently, chemical synthesis of base-labile and electrophilic DNA analogs is important in health related research. Traditional DNA synthesis technologies use strongly basic and nucleophilic reagents, which are not compatible with base-labile and electrophilic groups, are not suitable for the purpose. A few reported methods intended to solve the problem have serious drawbacks including contamination of product by toxic transition metal, high cost of excessively used precious metal, damage of DNA by UV light, complicated post-DNA synthesis procedure, and narrow applications. The objective of this project is to develop a universally useful technology for the synthesis of DNA analogs that contain a wide range of base-labile and electrophilic functionalities. To achieve the objective, protecting groups and linkers based on the 1,3-dithian-2-yl-methoxy organic function will be employed during DNA synthesis. With these groups and linkers, the technology does not require using any strong base, nucleophile, transition metal, and UV light in the entire process. The technology does not need any tedious and complicated post-DNA synthesis manipulations either. As a result, it will be practically useful for the synthesis of DNA analogs containing base-labile and electrophilic groups. In the previous funding period, we have proven that the objective is achievable by synthesizing natural DNA under non-nucleophilic conditions. In the next funding period, our specific aims include evaluating the scope of the technology for the synthesis of DNA analogs that contain different electrophilic groups and further advancing the technology to a new level so that it is more convenient to use and potentially has broader substrate scope. We will also study the protecting groups invented in this project in the context of small molecule synthesis. Our long-term goal is to develop a new generation of antisense drugs based on latently reactive electrophilic DNA analogs. Successful completion of this project will build the foundation for us to achieve the goal. The PI believes that cultivating next generation biomedical researchers is equally important as meritorious research. This project will help the PI to train one postdoc, at least one PhD student and about seven undergraduate researchers in nucleic acid chemistry. They will learn techniques including organic synthesis, automated DNA synthesis, and more. With this project, undergraduate students majoring in our pharmaceutical chemistry, biochemistry & molecular biology, and other programs will have a chance to participate in NIH-supported research, which will enhance their interest and qualification in pursuing a career in biomedical field.

Project narrative DNA analogs that contain latent electrophilic groups can selectively form covalent bonds with protein, mRNA and DNA through affinity induced reactions. They can be used as probes in chemical biology, and have the potential to become a new class of therapeutic agents. This project will develop a universal and practically useful technology for their chemical synthesis.