The School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign

Our laboratory studies the nucleic acids, DNA and RNA. In these efforts, we use concepts and techniques from biochemistry, chemical biology, and organic chemistry. The primary focus of our laboratory is the identification and application of DNA as a catalyst (deoxyribozyme) for various chemical reactions. In other efforts, we apply double-stranded DNA as a macromolecular structural constraint, and we pursue DNA as an integral component of sensors for compounds such as toxins and pollutants.

DNA enzymes as catalysts. Catalytic RNA plays an important role in fundamental biochemistry. Although catalytic DNA is not known in nature, in vitro selection is a powerful approach to identify artificial DNA enzymes (deoxyribozymes), which are specific DNA sequences with catalytic activity. We study deoxyribozymes both as a means to explore the catalytic power of nucleic acids and as an experimental approach to catalyze desirable chemical reactions, many of which may have practical applications. Our early efforts focused on deoxyribozymes that ligate RNA, which we used to synthesize large RNA molecules that have site-specific modifications or interesting and biochemically relevant topologies (e.g., branched and lariat RNA). Our current efforts pursue deoxyribozymes for reactions other than RNA ligation. For example, we seek DNA enzymes that can join nucleic acids to proteins, forming oligonucleotide-peptide conjugates that may have utility for drug delivery or encoding. Similarly, we seek DNA enzymes that can join sugars to proteins. The resulting glycopeptides are very difficult to synthesize by other means, and they are integral to many normal and pathological biochemical processes. More generally, we seek deoxyribozymes that can site-specifically modify proteins in any desired fashion; e.g., specific phosphorylation of a tyrosine residue or acetylation of a lysine residue. In other experiments, we have recently identified deoxyribozymes that sequence-specifically cleave DNA. With continued development, these DNA catalysts may be alternatives to conventional restriction enzymes, while avoiding the challenges of absent or undesired recognition sites. For all of our new deoxyribozymes, we are interested in studying their structures and catalytic mechanisms.

Other novel applications of DNA. (1) Double-stranded DNA has many favorable properties that make it an excellent candidate for a structural constraint upon other macromolecules. We use double-stranded DNA to constrain and control RNA folding. The basic concept is that covalent attachment of two complementary DNA strands onto RNA (one strand at each of two different positions) imposes a geometrical constraint upon the RNA. This DNA constraint may either stabilize or destabilize the natively folded RNA structure, thereby allowing control of the RNA folding landscape. (2) We also investigate the use of DNA as a sensor component. A DNA aptamer is a particular sequence of DNA that can bind a specific molecular target, ranging from metal ions and small organic compounds to proteins, which may even be present on the surface of a living cell. We seek to combine molecular recognition by DNA aptamers with practical signal generation approaches. For example, in collaboration with colleagues in Civil & Environmental Engineering, we are developing microfluidic-based devices that integrate DNA binding of water pollutants such as steroid hormones with colorimetric or fluorescent signal generation. These devices will enable real-time on-site detection of such compounds.