Research
Our research group is interested in the chemical synthesis, biochemical properties and molecular behaviour of nucleic acids and their analogues. We are particularly interested in developing new methods for the synthesis of nucleoside building blocks and RNA, including modified siRNA/miRNA, branched RNA and lariat RNA. We also devote an enormous effort to study nucleic acid structure.
More recently, our group reported the in situ synthesis of
RNA on microarrays for the study and discovery of protein-RNA
interactions that are relevant to important biological processes
(e.g., RNAi, transcription, etc).
Our research encompasses 4 main areas:
I. Chemical synthesis of nucleosides and oligonucleotides for drug development.
This work has involved biochemical studies with novel chemically modified nucleic acids. Aspects of these studies include modifications that either (i) augment nuclease stability; (ii) improve catalytic cleavage of mRNA by RNase H or within the RNA-Induced Silencing Complex (RISC); or (iii) increase target hybridization accessibility.
Recent examples synthesized in our group are arabinonucleic acids [see 2'-fluoro-ANA (FANA) and ANA above] and oligonucleotides with a 7-membered carbohydrate ring (oxepane nucleic acids, ONA; see Scheme below).
In
collaboration, we are presently examining these compounds as
antiviral agents and their ability of to kill primary human leukemia
cells in immune compromised mice using antisense and RNAi
approaches. We are also adopting the SELEX technique (Systematic
Evolution of Ligands by Exponential Enrichment) as a method for
generating chemically-modified aptamers with therapeutic utility.
II. Nucleic acid structure and function.
Current efforts are also focused on understanding the recognition of (a) branched RNA (bRNA) by the lariat debranching enzyme and spliceosomal factors, (b) siRNA duplexes by the RNA-induced silencing complex (RISC), and RNA hairpins by the HIV-1 Reverse Transciptase. This research goals include gaining a detailed understanding of inter- and intramolecular interactions between various nucleic acid components or between nucleic acids and proteins as these key biochemical processes occur. We approach all of these studies through the use of chemically-modified oligonucleotides.
III. New methods for the synthesis and fabrication of RNA and RNA microarrays.
Our work in this area is aimed at finding ribonucleoside synthons that potentially benefit three critical aspects of RNA manufacturing: yield, cost and “green” methods of synthesis. In collaboration with the Chan group (McGill), we have explored the conjugation of ionic tags to RNA that allows easy isolation of the product from a reaction mixture through simple precipitations or extractions. We have demonstrated that RNA oligomers may be grown (via Ogilvie's TBDMSi chemistry) on a dialkylimidazolide tag in high yields and purity, without the need for chromatography until the desired length polymer is obtained and deprotected. We believe that ionic tags will continue to be versatile and their applicability to biopolymer synthesis as soluble supports will continue to be a source of interest for some time to come.
More recently, in collaboration with researchers at the University of Wisconsin-Madison, we reported the first in situ synthesis of RNA on microarrays. These “RNA chips” will have immediate applications in the study (and discovery of) protein-RNA interactions that are relevant to important biological processes (e.g., RNAi, etc).
IV. Design and Synthesis of HIV-1 Reverse Transcriptase Inhibitors.
Our work in this area was first published in 2006
and was featured on the cover of
Nucleic Acids Research
(2006). We made the
exciting discovery that short hairpin RNAs interfere specifically
with the function of the RNase H domain of HIV-1 Reverse
Transcriptase (RT) at the low μM range, without affecting
E. coli or human RNase H. Remarkably,
the
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