Research & Publications
Nucleic acids carry out numerous tasks in organisms that range from the
long-term storage and transfer of genetic information to molecular recognition
and biological catalysis. It is now apparent that both RNA and DNA have a
tremendous untapped potential for biochemical function that can be accessed
using molecular engineering strategies. Existing ribozymes can be altered
by using test tube evolution, and entirely new enzymes made of RNA or DNA
can be isolated from pools of trillions of sequence variants. In addition,
we are finding that some types of functional RNAs though to be extinct are
present in modern cells where they perform fundamental biochemical tasks.
For example, we are discovering new examples of “riboswitches” that
sense metabolites and control gene expression. We will continue to explore
the functional potential of RNAs and DNAs that have been isolated from natural
sources and that have been created outside the confines of cells.
Extensive Research Description
The Breaker laboratory uses a variety of approaches to explore the
fundamental properties of nucleic acids. For example, the laboratory
develops new techniques for in vitro selection to create new functional
RNAs and DNAs. In vitro selection is patterned after natural Darwinian
evolution, but where "survival-of-the-fittest" is played out at the
molecular level in the absence of living cells. Up to 100 trillion
different molecules can be subjected to this test-tube evolution
process to isolate or engineer molecules that perform tasks such as
catalysis and molecular sensing.
Previous molecular engineering projects have provided evidence that both RNA and DNA have substantial untapped potential for sophisticated biochemical function. For example, we have produced a variety of new DNA enzymes, some that operate under cell-like conditions and perform reactions that mimic important biochemical transformations. In addition, we have generated dozens of examples of RNAs that function as designer molecular switches that respond to specific small molecules. These findings demonstrate that the primary roles of RNA and DNA in nature might be greater than currently appreciated, and suggests that the function of nucleic acids could be expanded via molecular engineering.
Inspired by these molecular engineering demonstrations, we have more
recently begun to search for novel types of non-coding RNAs that
perform undiscovered catalytic or molecular sensing tasks in cells. We
have identified numerous classes of "riboswitches", which are
metabolite-binding mRNA domains that control genes responsible for
biosynthesis of essential compounds. Among the first dozen riboswitches
classes identified are representatives that sense coenzymes,
nucleobases, amino acids or sugars. Some riboswitch classes exhibit
complex biochemical behaviors including ribozyme activity, cooperative
ligand binding, and logic gate function. In addition, we have
identified other non-coding RNAs that are not riboswitches, but whose
biological functions remain to be established. We will continue to use
bioinformatics, genetics, and biochemistry techniques to discover new
types of non-coding RNAs and to establish the functions of these
complex-folded nucleic acids.The Breaker laboratory is working to discover novel non-coding RNAs in all three domains of life. Bioinformatics systems are used to identify candidate structured RNAs, and the functions of these new-found RNAs are validated using genetic and biochemical techniques.
In addition, the Breaker laboratory is exploring the functional capability and utility of nucleic acids when engineered outside the confines of cells.
Bacteria; Biochemistry; Biology; Biotechnology; Fungi; Genetics, Microbial; Microbiology; Molecular Biology; Computational Biology; Genomics; Metabolomics