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.