Yingfu Li 

Assistant Professor
Department of Biochemistry 
& Department of Chemistr
Canada Research Council Chair Tier II

Ph.D. (Simon Fraser Uinversity)
Postdoctoral Fellowship (Yale University, U.S.A)
Location:    Health Sciences Centre (HSC), Room 4H28
Phone: (905) 525-9140, ext. 22462 FAX:   (905) 522-9033
E-mail:  liying@mcmaster.ca
Molecular Evolution and Biomedical Application of DNA and RNA Enzymes, DNA and RNA Aptamers
     My laboratory primarily focuses on the creation and in-depth 
study of DNA and RNA molecules that have interesting
properties, such as the ability to function as enzymes (i.e., enzymes
that are made of DNA and RNA) or bind other molecules (DNA 
and RNA aptamers). These special nucleic acid molecules may 
hold great promise for a variety of applications, including, new 
therapeutic agents to cure and control specific diseases.

     Instead of relying on Mother Nature to supply us with DNA
or RNA molecules for our study, we create them in our own 
hands using an evolution technology known as "In Vitro 
Selection". It is a combinatorial approach that mimics Darwinian 
evolution in a test tube. Typical experiments involve the following 
major procedures:

   (A) Construction of a random-sequence DNA pool.   A 
population containing up to 10E16 (10,000,000,000,000,000) 
different single-stranded DNA or RNA molecules is generated
by automated DNA synthesis as well as enzymatic manipulations.
This extraordinarily diverse DNA or RNA pool (or library)
unquestionably contains molecules with special functions to 
catalyze chemical reactions or to bind other molecules such as 

   (B) In vitro selection (see illustration).   The above DNA 
library is challenged to perform a specific task (such as catalysis 
for a biological reaction) in carefully designed in vitro evolution 
experiments. Strategies are implemented to allow the isolation 
of capable molecules from incapable ones; the selected molecules 
are amplified by PCR into a new generation for a new cycle of 
selection-amplification. The cycle is repeated for a number of 
times until the terminal population displays the desired properties.

   (C) Forced evolution (see illustration).   Usually, the above 
selection experiments lead to the isolation of many different 
molecules for any given task. Mutations are then introduced, 
and the mutagenized molecules are forced to compete with each 
other for the survival of the fittest under very demanding 
conditions. The winning molecules will again be selected and 
amplified, with more mutations being introduced. The process 
will be repeated until the surviving population is very proficient 
at completing the desired task. 

   (D) DNA cloning and sequencing.   The identity of the 
winning molecules in the terminal population will be revealed by 
DNA cloning and sequencing techniques. Sequence comparison 
studies will permit the identification of different classes of 
the fittest functional DNA and RNA molecules for further studies.

   (E) Biochemical analysis.   A variety of chemical, biochemical,
and physical methods will be used to probe the structure and 
function of the isolated molecules in order to understand the 
molecular mechanisms for catalysis or binding (see an example). 

   (F) Biomedical and other applications.   Thus created 
special DNA or RNA molecules will then be fully assessed for 
applications in biology, medicine and biotechnology. The potential 
end uses of these functional nucleic acid sequences include 
controlling the selective cellular functions, deactivating virus or 
disease-prone genes, establishing novel drug-screening 

Selected Publications

Capping DNA with DNA. Li, Y., Liu, Y. & Breaker, R. R. 
(2000). Biochemistry 39, 3106-3114. PubMed

Deoxyribozymes: New players in the ancient games of 
biocatalysis. Li, Y. & Breaker, R. R. (1999). Curr.Opin. 
Struct. Biol. 9, 315-323.PubMed 

Phosphorylating DNA with DNA. Li, Y. & Breaker, R. R. 
(1999).  Proc. Natl. Acad. Sci. U. S. A. 96, 2746-2751.
Kinetics of RNA degradation by specific base catalysis 
of transesterification involving the 2'-hydroxyl group. 
Li, Y. & Breaker, R. R. (1999). J. Am. Chem. Soc.121, 
DNA-enhanced peroxidase activity of DNA aptamer-
hemin complex. Travascio, P., Li, Y. & Sen, D. (1998).  
Chem. Biol. 5, 505-517.PubMed
The modus operandi of a DNA enzyme: Enhancement 
of substrate basicity. Li, Y. & Sen, D. (1998). Chem. 
Biol. 5, 1-12. PubMed
Towards an efficient DNAzyme. Li, Y. & Sen, D. (1997). 
Biochemistry 36, 5589-5599. PubMed

A catalytic DNA for porphyrin metallation.  Li, Y. & Sen, 
D. (1996). Nature Structural Biology 3, 743-747. 
Recognition of anionic porphyrins by DNA aptamers. 
Li, Y., Geyer, C. R. & Sen, D. (1996). Biochemistry 35, 
6911-6922. PubMed

Current Research 

Research Funding 


Research Training

Positions Available