Current Research and Scholarly Interests
One major focus of our laboratory is the design, synthesis and study of unnatural DNA and RNA bases. These are used as tools for basic study of biochemical and biological mechanisms (see our work with "hydrophobic isosteres"), and as the basis for a new genetic system design (see "xDNA").
An area in which we make extensive use of designer DNA bases is in "DNA polyfluors", which are short segments of synthetic DNA in which the bases are replaced by fluorescent structures. These have been developed into a large palette of fluorescent labels for biology, offering benefits that current fluorescent labels do not have. They are also being built into sensors: short synthetically modified DNAs are being used to sense metal ions in water, and toxic gases in air. We are building arrays of fluorescent DNAs that can “smell” the metabolites that different bacteria emit, allowing us to distinguish disease-causing bacteria in a Petri dish. Our lab is also designing a broad array of multicolor sensors for different classes of enzymes, from esterases to proteases and DNA repair enzymes. These can function in living cells to report on biological activities there.
Our lab has been developing a new, functional genetic set that is orthogonal to the natural DNA system. Our design is based on expanded size (expanded DNA, or "xDNA"). We have shown that xDNA assembles into helices selectively, much like DNA, except that it is more stable and is also highly fluorescent. We have found polymerase enzymes that can copy bases of xDNA, and have shown that E. coli replication machinery can read the genetic information stored in xDNA. Very recently, we have begun to synthesize and study xRNA as well.
Our group also has an ongoing interest in finding simple and rapid ways to detect the cellular genetic mutations that cause cancer and drug resistance. Our approach is to use RNA-templated chemistry, in which chemically modified probes perform a fluorogenic reaction when they hybridize to their genetic target. Our laboratory was the first to use nucleic acid templated chemistry for detection of genetic sequences in solution, and the first to apply it in intact bacterial and human cells. New ways to improve this chemistry and monitor the output signal of these sensor molecules are under research. We are collaborating with clinical laboratories and physicians to test these molecules for applications in identifying pathogenic bacteria and in monitoring genetic changes in cells from patients with leukemias.
We have a general interest in the design of small-molecule probes and reagents that are useful in the study of cellular biomolecules. For example, we are developing cell-permeable reagents that can be used to map structure and contacts of RNAs in vivo. We are also developing tools for investigating RNA base modifications as well as DNA damage, and the enzymes that process these structural alterations. Finally, we are developing reagents for performing efficient and orthogonal bioconjugations in intact cells.