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Research Spanning Peptides and Oligonucleotide Chemistries
Our principle research activities involve the application of organic synthesis in the field of bio-organic chemistry. We specialize in oligonucleotide analogs and our work is focused on peptide nucleic acid (PNA) and nucleobase-modified DNA and RNA with particular interest in fluorescent analogs.
PNA and DNA/RNA Research Areas The term Peptide Nucleic Acid (PNA) now refers to a large number of nucleic acid mimics based on a synthetic amino acid monomer unit. The original design, as shown below in comparison to DNA, was disclosed by Peter Nielsen and coworkers in the early 1990's. Since that time a great deal of work has been done in the chemistry and biochemical/biological properties and applications of PNA. Our research program has mostly focused on the chemistry and effects of various nucleobase modifications on the properties of PNAs. As well, we are interested in similar modifications to DNA and RNA.
Nucleobase Modifications and Luminescent Nucleobases. The pyrimidine nucleobases uracil and cytosine are particularly attractive candidates for modification in PNA because of the wealth of established chemistry for them. For some time, we have pursued is via the cross-coupling between terminal alkynes and a halogenated nucleobase, either uracil or cytosine.
These studies lead us to the investigation of 5-alkynylpyrimidines and their cyclization to form fluorescent bicyclic nucleobases. We have found that the luminescent properties of these compounds varies with the nature of the substituent on the 5-membered ring ("R") and are currently investigating their use as DNA probes.
In DNA oligomers, 6-phenylpyrrolocytidine can selectively yield fluorometric detection of guanosine-containing sequences in complementary DNA. It is a very robust system, as the fluorescence is selectively quenched by guanosine but not mismatched bases.
Oligodeoxynucleotides incorporating structurally simple 5-alkynyl-2 -deoxyuridines fluorometrically respond to hybridization. The principle of selective recognition of adenosine by 5-alkynyluridines versus the known fluorescent, bicyclic derivative furanouracil is shown. Cyclization is not required for fluorescence given the proper choice of R', such as phenyl. Substitution on the phenyl ring leads to pyrrolocytosines that interact more strongly with guanosine through a tether designed to form a 4th Hydrogen bond, when incorporated into PNA oligomers. These modified pCs also fluorometrically respond to hybridization.
F. Wojciechowski and R.H.E. Hudson† "Fluorescence and Hybridization Properties of Peptide Nucleic Acid Containing a Substituted Phenylpyrrolocytosine Designed to Engage Guanine with an Additional H-Bond” Journal of the American Chemical Society, 2008, 130(38), 12574-12575." R.H.E. Hudson† and A. Ghorbani Choghamarani “Oligonucleotides Incorporating Structurally Simple 5-Alkynyl-2’-Deoxyuridines Fluorometrically Respond to Hybridization” Organic and Biomolecular Chemistry, 2007, 5(12), 1845-1848. R.H.E. Hudson† and A. Ghorbani-Choghamarani “Selective Fluorometric Detection of Guanosine-Containing Sequences by 6-Phenylpyrrolocytidine in DNA” Synlett, 2007, 6, 870-873. R.H.E. Hudson† and A.K. Dambenieks “Synthesis of N1-unsubstituted 5-alkynylcytosine and derivatives thereof” Heterocycles, 2006, 68(7), 1325 - 1328. R.H.E Hudson† and J.M. Moszynski “A facile synthesis of fluorophores based on 5-phenylethynyluracils” Synlett, 2006, 18, 2997-3000. R.H.E. Hudson†, A.K. Dambenieks, R.D. Viirre “Fluorescent 7-deazapurine derivatives from 5-iodocytosine via a tandem cross-coupling/annulation reaction” Synlett 2004, 13, 2400-2402. R.H.E. Hudson†, R.D. Viirre, Y.H. Liu, F. Wojciechowski, A.K. Dambenieks Pure & Applied Chemistry 2004, 76 (7-8), 1591-1598. R.H.E. Hudson†, G. Li and J. Tse Tetrahedron Letters 2002, 43 (8), 1381-1386.
Collaborations
Medical Imaging.
We are involved in a multi-partner collaboration with coworkers in both the London Health Sciences and the Robarts Research Institute (in conjunction with Prof. H. Azab, Suez Canal University, Egypt). These works span the synthesis of materials for radioisotopic, optical and magentic resonance imaging for potential clinical applications.
We have recently developed peptide-decorated lanthanide metal chelators as MRI contrast agents that operate on the basis of paramagnetic chemical exchange saturation transfer (PARACEST). These ligands are similar to the well-known DOTA and DOTAM ligands.
A PARACEST spectrum, w denotes the bound water signal, separated from the bulk water signal. The intensity, approx. 45% at physiologic pH and temperature is the most intense yet developed. This signal is used to generate contrast in PARACEST-based MR imaging.
Mojmír Suchý,Alex X. Li, Robert Bartha and Robert H.E. Hudson† “Analogs of Eu3+ DOTAM-Gly-Phe-OH and Tm3+ DOTAM-Gly-Lys-OH: Synthesis and Magnetic Properties of Potential PARACEST MRI Contrast Agents” Bioorganic and Medicinal Chemistry, 2008, in press. Alex X. Li, Filip Wojciechowski, Mojmir Suchy, Robert H.E. Hudson, Ravi Menon and Robert Bartha† “A Sensitive PARACEST Contrast Agent for In-vivo Temperature MRI: Eu3+-DOTAM-Gly-Phe” Magnetic Resonance in Medicine, 2008, 59, 374-381. Filip Wojciechowski, Mojmir Suchy, Alex X. Li, Hassan Azab, Robert Bartha and Robert H.E. Hudson† “A Robust and Convergent Synthesis of Dipeptide-Cyclen Conjugates as Chelators for Lanthanide Ions: New Paracest MRI Agents” Bioconjugate Chemistry, 2007, 18, 1625-1636. Synthesis of Cystamine Modified Eu3+ DOTAM-Gly-Phe-OH: A Conjugation Ready Temperature Sensitive MRI Contrast Agent. Modification of the ligand yet retention of the most desirable PARACEST effects has been achieved. 
Applications of PNAs.
Using chimeric, modified DNA/RNA and PNA to examine the HIV RNAse H enzyme. Chemical structures used:
Inhibition of HIV Integrase: The ability of PNAs to prevent the integration of the viral genome into host DNA is being investigated with Dr. J.-F. Mouscadet, Ecole Normale Supérieure de Cachan, France.
Radiosensitized Damage to DNA: PNAs containing halogenated nucleobases are being investigated with Prof. Darel Hunting at the Université de Sherbrooke, Quebec.
Pt-based Anticancer Agents.
In collaboration with our Inorganic colleagues (Prof. Westcott, MTA and Prof. Jones, UWO), we have investigated the reactivity of novel cis-dichloroplatinum complexes with DNA. The archetypal compound, cisplatin (cis-diammineplatinum dichloride) is a very successful and widely used anticancer drug, but has significant side-effects and limitations - thus the search for new compounds with similar action.
L.G. Nikolcheva, C.M. Vogels, R.A. Stefan, H.A. Darwish, S.J. Duffy, R.J Ireland, A. Decken, R.H.E. Hudson†, S.A Westcott† Canadian Journal of Chemistry 2003, 81 (4), 269-274. A.S. King, L.G. Nikolcheva, C.R. Graves, A. Kaminski, C.M. Vogels, R.H.E. Hudson, R.J. Ireland, S.J. Duffy, S.A. Westcott† Canadian Journal of Chemistry 2002, 80, 1217-1222.
Find out more about our group,
facilities,
research and publications by following these links.
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Department of Chemistry Chemistry Building Laboratory 226 The University of Western Ontario
Tel: 519-661-2111x86349 Fax: 519-661-3022 Email: Robert.Hudson
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