A chief focus of research in our laboratory is on design, synthesis, and study of molecules that mimic DNA and its functions in biological systems. The research can lead to basic understanding of biological mechanisms such as DNA replication and DNA repair, and to the development of molecules for detecting and treating disease.
One long-term goal of the group is to develop RNA-templated chemistries that can be used to diagnose human cancers and infections highly specifically and very early. Toward this goal, we have been pursuing the discovery of new chemical reactions that generate a fluorescence signal; we then modify DNAs to perform these reactions in a cell upon finding a specific RNA. Such molecules can detect a single base alteration in a DNA or RNA target; such mutations are causative in many diseases. We are developing these probe chemistries for use in identifying pathogenic bacteria and cancer-related sequences in human cells.
A second project involves the development of new fluorescent molecular assemblies built on a DNA scaffold. We synthesize new fluorescent nucleosides that can be strung together with a DNA synthesizer. These are assembled into DNA-like libraries and are being evaluated for unusual fluorescence and sensing properties. The resulting molecules are under development as new tools for biological reporting in cells. Using this approach, we have successfully developed intracellular sensors of esterases, proteases, and DNA repair enzymes.
A third research goal involves the design of new bases for DNA and RNA. Our group was the first to show that DNA base pairs could be replicated very efficiently by polymerase enzymes even when they lack Watson-Crick hydrogen bonds. As a result, we are now developing new DNA bases with varied structures, sizes, and shapes. New bases and base pairs could be used to expand nature's genetic system, or to develop entirely new genetic systems. Such molecules are also used as mechanistic tools in the study of biomolecular recognition.
1) "A Four-base Paired Genetic Helix with Expanded Size," H. Liu, J. Gao, S. Lynch, L. Maynard, D. Saito, and E.T. Kool, Science, 302, 868-871 (2003).
2) "Quenched Autoligating DNAs: Multicolor Identification of Nucleic Acids at Single Nucleotide Resolution," S. Sando, H. Abe, and E.T. Kool, J. Am. Chem. Soc., 126, 1081-1087 (2004).
3) "Assembly of the Complete Eight-Base Artifical Genetic Helix, xDNA, and Its Interaction With the Natural Genetic System," J. Gao, H. Liu, and E.T. Kool, Angew. Chem Int. Ed., 44, 3118-3122 (2005).
4) "Probing the Active Site Tightness of DNA Polymerase in Sub-Angstrom Increments," T.W. Kim, J.C. Delaney, J.M. Essigmann, and E.T. Kool,Proc. Natl. Acad. Sci. USA, 102, 15803-15808 (2005).
5) "The Roles of Hydrogen bonding and Sterics in RNA Interference", A. Somoza and E.T. Kool, Angew. Chem. Int. Ed., 45, 4994-4997 (2006).
6) "Polyfluorophores on a DNA Backbone: A Multicolor Set of Dyes Excited at a Single Wavelength," J.N. Wilson, Y.N. Teo, and E.T. Kool, J. Am. Chem. Soc., 131, 3923-3933 (2009).
7) "Efficient Nucleic Acid Detection by Templated Reductive Quencher Release," R.M. Franzini and E.T. Kool, J. Am. Chem. Soc, 131, 16021–16023 (2009).