Hongbin (Tony) Yan

Professor, Chemistry

Tony Yan

Office: Cairns 415
Lab: Cairns 542
Office Phone: 905 688 5550 x3545
Lab Phone: 905 688 5550 x3411

  • Natural and modified nucleic acids (DNA handedness, light-responsive nucleic acids, glycosylated nucleic acids, fluorine-containing nucleic acids)
  • Modulation of the STING (Stimulator of Interferon Genes) proteins (nucleic acid-based mucosal vaccine adjuvants, STING inhibitors)
  • Interaction of microwave with biomolecules and biological systems
  • Bacterial biofilm formation and autoinducers
  • Toxicological chemistry/biochemistry (DNA damage by reactive metabolic intermediates)

Undergraduate students interested in completing their CHEM/BTEC/BCHM/BMED

4F90/4F91 research projects in my lab are welcome to contact me.

Undergraduate students interested in an NSERC USRA summer research award are also welcome to contact me.

Research in this lab is focused on the chemistry and applications of biologically important molecules, such as nucleic acids and carbohydrates. Some directions of research are summarized below.


Chemical modification of nucleotides

Work is underway to introduce various modifications, such as fluorophores and photosensitive moieties to nucleosides, and to explore their biochemical applications. One such modification involves the incorporation of moieties that undergo conformational/configurational changes upon exposure to light of selected wavelength. As a consequence of these changes, hybridization/binding properties are altered. We are also working towards labelling nucleic acids using inverse electron demand Diels-Alder reaction. This approach will allow for nucleic acid labelling at rates that are relevant to cellular concentrations of nucleic acids.


Cyclic oligonucleotides and analogues as potential mucosal vaccine adjuvants

There is a largely unmet requirement for safe and effective mucosal vaccine adjuvants to combat the ever-increasing mucosal infectious and inflammatory diseases. In collaboration with immunologists, we are working on cyclic olignucleotides to screen their immunostimulatory activities and potentials to enhance the efficacy of vaccines against a number of bacterial infections. We are particularly interested in identifying cyclic oligonucleotides as suitable nasal and oral vaccine adjuvants.


Bacterial biofilm formation and quorum sensing

Bacteria undergo phenotypic transitions between planktonic and biofilm forms in response to changes in environmental conditions. The biofilm phenotype has attracted significant attention in healthcare and industry due to their unique traits, such as antibiotic resistance. We are interested in identifying compounds that interfere with the transition to the biofilm phenotype. We are also interested in the bacterial quorum sensing signalling cascade that allow bacteria to adapt as a result of cell density. In particular, work in is progress to identify autoinducers in particular bacterial species, and to establish links between the signalling pathways enabled by bacterial second messengers and autoinducers.


Interaction of microwave with biomolecules

We are interested in understanding the interactions of electromagnetic wave, particularly microwave, with molecules such as proteins and nucleic acids. Towards this end, work in is progress to determine the impact of microwave exposure on the enzyme activity and behaviours of nucleic acids.

Publications (*corresponding author)

Independent publications

  1. Encapsulation of dyes and DNA by silica nanoparticles, manuscript under preparation.
  2. Synchrotron radiation circular dichroism spectroscopy of DNA at millimolar concentrations, 2023, manuscript under preparation.
  3. DAPTEV: Deep Aptamer Evolutionary Modelling for COVID-19 Drug Design, 2023, manuscript submitted for publication.
  4. Joshi, D. K.; Betancourt, F.; Pilkington, M.; Yan, H.* Neutral BODIPY photosensitizers, 2023, revision under review.
  5. Bennett, H-A; Li, Y;* Yan, H.* Thermal treatment affects aptamers’ structural profiles. Med. Chem. Lett. 2023, in press
  6. Joshi, D. K.; Betancourt, F.; McAdorey, A.; Yalagala, R. S.; Poupon, A.; Yan, H.* BODIPY quaternary ammonium salt as photosensitizers, Photochem. Photobiol. A: Chem. 2023, 434, 114213.
  7. Wang, G.; Xu, J.; Traynor, S. M.; Wu, X.; Chen, H.; Eljabu, F.; Yan, H.; Li, F.* Weighing the thermodynamics and kinetics of chemically modified DNA using a rationally designed DNA balance, Am. Chem. Soc. 2021, 143, 13655.
  8. Yan, H.;* Chen, W.* The promise and challenges of cyclic dinucleotides as

molecular adjuvants for vaccine development, Vaccines 2021, 9, 917. (invited review)

  1. McAdorey, A.; Bennett, H.; Vanloon, J.; Yan, H.* Use of anion-exchange (AEX) HPLC to study nucleic acid polymorphism, Chromatogr. B 2021, 1180, 122890.
  2. Betancourt, F.; Valente, A.; Yan, H.* 1,8-Naphthalimide derivatives as probes for protein surface hydrophobicity. Photochem. Photobiol. A: Chem. 2021, 418, 113386.
  3. Vanloon, J.; Harroun, T.;* Yan, H.* Circular dichroism spectroscopy of DNA duplexes at near-biological concentrations. Med. Chem. Lett. 2021, 43, 128053.
  4. Betancourt, F.; Helmkay, J.; Yan, H.* Microwave-assisted synthesis and fluorescent properties of 4-phenyl-1,8-naphthalimide. Molbank 2020, M1127.
  5. Solodinin, A.; Ollivier, S.; Helmkay, J.; Yan, H.* N-2-Isobutyryl-8-fluoro-2’-deoxyguanosine: synthesis and reactivity. Molbank 2020,
  6. Sun, J.; Joshi, D.; Betancourt, F.; Solodinin, A.; Woodland, B.; Yan, H* Anion exchange chromatography of oligonucleotides under denaturing conditions. Nucleosides, Nucleotides and Nucleic acids. 2020, 1-11.
  7. Huang, C. Y.; Yan, H.; Chiou, Y.-R.; Wan, C.-F.; Wu, A.-T.* A Schiff-based fluorescence sensor for the detection of Cu2+ and its application in living cells. Photochem. Photobiol. A: Chem. 2020, 390, 112326.
  8. Li, J.; Kuo Lee, R.; Chen, W.; Yan, H.* 2’-Fluoro-c-di-GMP as an oral vaccine adjuvant.RSC Advances 2019, 9,
  9. Solodinin, A.; Gautrais, A.; Yan, H.* Incorporation of 5-fluoro-2’-deoxycytidine into oligonucleotides for the study of DNA structures by 19F NMR spectroscopy. ACS Omega 2019, 4, 19716 (invited).
  10. Sun, J.; Vanloon, J.; Yan, H.* Influence of low-power microwave irradiation on DNA hybridization and polymerase reactions. Tetrahedron Lett. 2019, 60, 151060.
  11. Mazinani, S. M.; Noaman, N.; Pergande, M. R.; Cologna, S. M.; Coorssen, J.;* Yan, H.* Exposure to microwave irradiation at constant culture temperature slows the growth of Escherichia coli DE3 cells, leading to modified metabolic profiles. RSC Advances 2019, 9, 11810.
  12. Bordeleau, E.; Mazinani, S. A.; Nguyen, D.; Betancourt, F.; Yan, H.* Abrasive treatment of microtiter plates improves the reproducibility of bacterial biofilm assays – preliminary study of the roles of flavonoids in biofilm formation in subtilis. RSC Advances 2018, 8, 32434.
  13. Mazinani, S. A.; Stuart, J. A.; Yan, H.* Microwave-assisted delivery of an anticancer drug to cancer cells. RSC Advances 2018, 8, 31465.
  14. Jun, M.; Joshi, D. J.; Yalagala, R.; Valoon, J.; Lough, A. J.; Gordon, H. L.; Yan H.* Spectroscopic characterization of cyclic azobenzene analogues and confirmation of the structure of trans-cyclic azobenzene by X-ray crystallography, ChemistrySelect 2018, 3, 2697.
  15. Joshi, D. J.; Jun, M.; Yang, L.; Lough, A. J.;* Yan H.* Further investigation on the nitration of BODIPY with cupric nitrate, Acta Crystallogr. E. 2018, E74, 103.
  16. Sie, Y.-W.; Li, C.-L.; Wan, C.-F.; Yan, H.; Wu, A.-T.* A novel colorimetric probe for dual sensing of Hg2+ and Cu2+ ions in water. Photochem. Photobiol. A: Chem. 2018, 353, 19.
  17. Sie, Y.-W.; Li, C.-L.; Wan, C.-F.; Chen, J.-H.; Hu, C.-H.; Yan, H.; Wu, A.-T.* A colorimetric probe for dual sensing of Hg2+ and Cu2+ ions in water, Chim. Acta 2017, 467, 325.
  18. Mazinani, S. A.; Moradi, F.; Stuart, J. A.; Yan, H.* Microwave Irradiation of PC3 Cells at Constant Culture Temperature Alters the Incorporation of BODIPY into Cells and the Reduction of MTT, ChemistrySelect, 2017, 2, 7983.
  19. Yang, L.; Drew, B.; Yalagala, R.; Chaviwala, R.; Simionescu, R.; Lough, A.;* Yan, H.* Solvent-dependent behaviours of 3-amino-1,6-diethyl-4,4-diphenyl-2,5,7-trimethyl-1,5,7,8-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene, Acta Crystallogr. E. 2017, E73, 378.
  20. Yan, H.;* Powers, R.; Gibbons, A.; Joshi, D. (2017) Z-DNA: Chemistry and Biological Relevance. In: Reedijk, J. (Ed.) Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. Waltham, MA: Elsevier. 20-Mar-17 doi: 10.1016/B978-0-12-409547-2.12656-3 (invited).
  21. Yang, L.; Liao, D.-J.; Wu, A.-W.;* Yan, H.* Synthesis and fluorescent properties of aza-crown ether tethered BODIPY fluorophores, Tetrahedron Lett. 2017, 58, 889.
  22. Qiu, H.; Li, Z.; KuoLee, R.; Harris, G.; Gao, X.; Yan, H.; Xu, H.; Chen, W.* Host resistance to intranasal Acinetobacter baumannii reinfection in mice, Dis. 2016, 74, pii: ftw048. doi: 10.1093/femspd/ftw048.
  23. Mazinani, S. A.; Yan, H.* Impact of microwave irradiation on enzymatic activity at constant bulk temperature is enzyme-dependent, Tetrahedron Lett. 2016, 57, 1589.
  24. Yalagala, R.; Mazinani, S. A.; Maddalena, L. A.; Stuart, J. A.; Yan, F.; Yan, H.* Microwave assisted synthesis of BODIPY-sugar conjugates through the Click chemistry and assembly of the conjugate into bilayers. Carbohydrate Res. 2016, 424, 15.
  25. Eljabu, F.; Dhruval, J.; Yan, H.* Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization. Med. Chem. Lett. 2015, 25, 5594.
  26. Mazinani, S. A.; DeLong B.; Yan, H.* Microwave radiation accelerates trypsin-catalyzed peptide hydrolysis. Tetrahedron Lett. 2015, 56, 5804.
  27. Yan, H.;* Yalagala, R.; Yan, F. Fluorescently labelled glycans and their applications, J. 2015, 32, 559.
  28. Kuolee, R.; Harris, G.; Yan, H.; Xu, H. H.; Conlan, W. J.; Patel, G. B.; Chen, W.* Intranasal immunization protects against Acinetobacter baumannii-associated pneumonia in mice, Vaccine 2015, 33, 260.
  29. Bordeleau, E.; Oberc, C.; Ameen, E.; Mendes da Silva, A.; Yan, H.* Identification of cytidine 2’,3’-cyclic monophosphate and uridine 2’,3’-cyclic monophosphate in Pseudomonas fluorescens pfo-1 culture. Med. Chem. Lett. 2014, 24, 4520.
  30. Yang, L.; Yalagala, R. S.; Hutton, S.; Lough, A. J.; Yan, H.* Reactions of BODIPY with nitrates, Synlett 2014, 25, 2661.
  31. Yalagala, R. S.; Yan, H.* Reactions of alkynes with trisubstituted (Z)-bromoalkenyl-pinacolboronates towards the synthesis of 1,2,4,6-tetrasubstituted benzenes. Tetrahedron Lett. 2014, 55, 4830.
  32. Yalagala, R. S.; Zhou, N.; Yan, H.* Palladium(II)–copper(I) mediated homotrimerization and homotetramerization of terminal alkynes, Tetrahedron Lett. 2014, 55, 1883.
  33. Yang, L.; Li, J.; Simionescu, R.; Yan, H*. Observation of two N2-isobutyrylguanine tautomers by NMR spectroscopy, Reson. Chem. 2013, 51, 60–64.
  34. Dhruval, J.; Mitchell, M.; Bruce, D.; Lough, A.; Yan, H.* Synthesis of cyclic azobenzene analogues, Tetrahedron, 2012, 68, 8670.
  35. Zhou, N.; Wang, Q.; Lough, A.; Yan, H.* Preparation of (Z)-1,2-dichloroalkenes from terminal alkynes, J. Chem. 2012, 90, 625.
  36. Yang, L.; Yan, H.* A Mannich-type reaction at the meso-methyl position of the BODIPY fluorophore, Synlett.2012, 23, 1526.
  37. Cheng, H-J; Yan, H.; Sun, Y-L; Lu, C-Y; Huang, T-Y; Chen, S-J; Hu, C-H; Wu, Y-Y; Wu, A-T.* A simple and highly selective receptor for iodide in aqueous solution, Analyst 2012, 137, 571.
  38. Yang, L.; Simionescu, R.; Lough, A.; Yan, H.* Some observations relating to the stability of the BODIPY fluorophore under acidic and basic conditions, Dyes Pigments 2011, 91, 264.
  39. Zhao L, KuoLee R, Harris G, Tram K, Yan H, Chen W.* c-di-GMP protects against intranasal Acinetobacter baumannii infection in mice by chemokine induction and enhanced neutrophil recruitment, Immunopharmacol. 2011, 11, 1378.
  40. Tram, K.; Sangvi, Y.; Yan, H.* Further studies on the detritylation in solid phase oligodeoxyribonucleotide synthesis, Nucleoside, Nucleotides & Nucleic Acids. 2011, 30, 12.
  41. Tram, K.; Twohig, D.; Yan, H.* Oligonucleotide labeling using BODIPY phosphoramidite, Nucleoside, Nucleotides & Nucleic Acids. 2011, 30, 1.
  42. Chen, W.*; Patel, G.; Yan, H. Zhang, J. Recent advances in the development of novel mucosal adjuvants and antigen delivery systems, Human Vaccines, 2010, 6, 683.
  43. Yan, H.*; Chen, W. 3’,5’-Diguanylic acid-a small nucleotide that makes big impact, Soc. Rev. 2010, 39, 2914.
  44. KuoLee, R.; Yan, H.; Chen, W.* cdiGMP as a mucosal vaccines adjuvant. Vaccine, 2010, 28, 3080.
  45. Zhao, Y.; Tram, K.; Yan, H.* Synthesis and characterization of mannosylated oligoribonucleotides, Carbohydrate Res. 2009, 344, 2137.
  46. Yan, H.;* KuoLee, R.; Tram, K.; Qiu, H.; Zhang, J.; Patel, G.B.; Chen, W.* Intranasal immunization of mice with bacterial second messenger cdiGMP elicits protective immunity against nasopharyngeal carriage of Streptococcus pneumoniae, Biophys. Res. Commun. 2009, 387, 581.
  47. Tram, K.; Yan, H.;* Jenkins, H.; Vassiliev, S.; Bruce, D. The synthesis and crystal structure of unsubstituted 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY), Dyes Pigm. 2009, 82, 392.
  48. Tram, K.; McIntosh, W.; Yan, H*. Synthesis of glycosyl dipyrromethanes, Tetrahedron Lett. 2009, 50, 2278.
  49. Yan, H.;* Wang, X.; Kuolee, R.; Chen, W. Synthesis and immunostimulatory properties of the phosphorothioate analogues of cdiGMP, Med. Chem. Lett. 2008, 18, 5631.
  50. Tram, K.; Wang, X.; Yan, H.* Facile synthesis of oligonucleotide phosphoroselenoates, Lett. 2007, 9, 5103.
  51. Yan, H.;* Anguilar, A. L.; Zhao, Y. Preparation of carbohydrate–oligonucleotide conjugates using the squarate spacer, Med. Chem. Lett. 2007, 17, 6535.
  52. Yan, H.;* Anguilar, A. L. Synthesis of 3’,5’-cyclic diguanylic acid (cdiGMP), Nucleoside, Nucleotides & Nucleic Acids 2007, 26, 189.
  53. Yan, H.;* Tram, K. Glycotargeting to improve cellular delivery efficiency of nucleic acids, J. 2007, 24, 107.


Other independent publications

  1. Yan, H.; Chen, W.; KuoLee, R. United States Patent No. 10,092,644, October 9, 2018.
  2. Yan, H.; Chen, W.; KuoLee, R. WO Patent No. 2015/074145A1, May 28, 2015.
  3. Yan, H.; Tram, K. Compounds for fluorescent labelling. United States Patent No. 8,519,153. Issued on August 27,2013.
  4. Tram, K.; Jenkins, H. A.; Yan, H.* (2010) Private communication to the Cambridge Structural Database, deposition number CCDC 793318.
  5. Millar, S; Yan, H.; Sanghvi, Y. S.; Pon, R. Some observations on detritylation in solid-phase oligonucleotide synthesis. Nucleic Acids Symp. Ser. 2008, 52, 311.
  6. Zhao, Y.; Yan, H. Preparation of Mannosylated Oligoribonucleotides, Nucleic Acids Symp. Ser. 2008, 52, 89.
  7. Yan, H.; Humes, E. Convenient synthesis of 3’,5’-cyclic diguanylic acid (cdiGMP), Nucleic Acids Symp. Ser.2006, 50, 5.


Post-doctoral and graduate publications

  1. Yan, H.; Jennings, H. J. Synthesis of mono- and di-sialophospholipids via the H-phosphonate approach, J. Chem. 2006, 84, 540.
  2. Reese, C. B.; Yan, H. Alternatives to the 4,4′-dimethoxytrityl (DMTr) protecting group, Tetrahedron Lett. 2004,45, 2567–2570.
  3. Reese, C. B.; Yan, H. Further studies with adenosine 5′-dithiophosphoromorpholidate. A convenient preparation of nucleoside phosphorodithioates by a triester approach, Tetrahedron Lett. 2004, 45, 2653.
  4. Reese, C. B.; Yan, H. An approach to the desulfurization of oligonucleotide phosphorothioates, Tetrahedron Lett.2003, 44, 2501.
  5. Reese, C. B.; Yan, H. Solution phase synthesis of ISIS 2922 (Vitravene) by the modified H-phosphonate approach. Chem. Soc., Perkin. Trans. 1 2002, 23, 2619.
  6. Reese, C. B.; Yan, H. Xanthen-9-ylidene protecting groups in glycerol chemistry. Chem. Soc., Perkin Trans. 12001, 15, 1807.
  7. Reese, C. B.; Yan, H. Reaction between pyrrole and orthoesters: preparation of tri-(pyrrole-2-yl)alkanes. Tetrahedron Lett. 2001, 42, 5545.
  8. Reese, C. B.; Song, Q.; Yan, H. Xanthen-9-ylidene and 2,7-dimethylxanthen-9-ylidene protecting groups. Tetrahedron Lett. 2001, 42, 1789.

CHEM 1P00: Introductory Chemistry

CHEM/BTEC 5P28/4P28: Bioorganic chemistry – carbohydrates and nucleic acids

CHEM/BTEC 3P93: Protein and nucleic acid chemistry

CHEM/BTEC 4P26: Toxicological chemistry and biochemistry

Current members:

Sina Mazinani (PhD student)

Joshi Dhruval (PhD student)

Frank Betancourt (MSc student)

Andrei Solodinin (MSc student)

Jesse Vanloon (MSc student)

Sunny Sun (Visiting scholar)

Jagandeep Saraya (Co-op)

Hind Kunna (Honours thesis)

Oyin Azeez (Honours thesis)

Breyer Woodland

Grant Trojner (Honours thesis)

Shirley Olumba (Honours thesis)


Past members:


Kha Tram (2016-2017)

Ningzhang Zhou (2011-2012)

Qiang Wang (2011)

Nasser Ali (2009)



Meesook Jun

Ravi Yalagala (2012-2016)



Khatma Milah (2016-2018)

Emily Bordeleau (2014-2017)

Christopher Oberc (2012-2015)

Fatma Eljabu (2013-2015)

Nazanin Heidari (2013-2015)

Dhruval Joshi (2011-2013)

Viola Yang (2010-2013)

Yuyan Zhao (2009-2011)

Kha Tram (2009-2011)

Jia Li (2009-2012)


BSc Honours

Mohamed Mahrouse (2018)

Kaitie Kean (2017-2018)

Courtney Farno (2017-2018)

Heather Hendrik (2017-2018)

Harris Sheihk (2017-2018)

Ashley Gibbons (2016-2017)

Eve Ameen (2016-2017)

Frank Betancourt (2016-2017)

Rhys Power (2016-2017)

David Nguyen (2015-2016)

Anastasia Burdilov (2015)

Matt Bell (2014-2015)

Ben DeLong (2013-2014)

Emily Bordeleau (2013-2014)

Scott Henderson (2013-2014)

Jassey Gosal (2013-2014)

Sukhmani Gill (2013-2014)

Brett Drew (2012-2013)

Rameez Chaviwala (2012-2013)

Matt Mitchell (2010-2011)

Ken Ellens (co-supervised)

Kha Tram (2008-2009)

Shannon Millar (2008-2009)

Aime Aguilar Lopez (2005-2007)



Michelle Giroux

Jagandeep Saraya


Summer and CHEM 2/3P98

Frank Lu (USRA summer student, 2011 and 2012)

Hany Ibrahim (CHEM 3P98)

Daniel Twohig (undergraduate research assistant, 2009)


High school mentorship

Stephanie Hutton (2013)

Westen McIntosh (2009)



Angeline Gautrais (Rennes, 2018)

Karoline Wantz (Rennes, 2018)

Milene Franzetti (Rennes, 2018)

Melissa Lallier (Rennes, 2018)

Alexandre Quelhas (Rennes, 2017)

Dylan Chapeau (Rennes, 2017)

Andy Poupon (Rennes, 2015)

Amanda Mendes Silvia (Canada-Brazil Ciência Sem Fronteiras (CsF) Scholarship Program, 2014)

Justine Vinet (Rennes, 2014)

Clair Languitin (Rennes, 2014)

Julient Vinet (Rennes, 2015)

Soufyan Jerhaoui (Rennes, 2013)