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Joanne Macdonald

Joanne Macdonald

Assistant Professor in Clinical Medical Sciences (in Medicine)
Division of Experimental Therapeutics, Department of Medicine, Columbia University

Molecular Engineering

Molecular engineering involves the construction of new molecules and molecular networks that would otherwise not exist in nature. Often this process begins from a known molecule, and can include the enhancement of known characteristics, adaptation to new environments, the conjunction of known molecular motifs, or the evolution of entirely new functions.

My research is focused on the application of molecular engineering as a tool to solve mathematical and biological problems. My current research projects toward this aim are a natural extension of my background in molecular computation, enzymology, virology, and molecular biology.

Molecular Engineering Research Projects

  • Molecular Computation:
    • Logic gate circuits and game-playing automata.
    • Visual interfaces for molecular computation
    • Smart Diagnostic devices:
      • Rapid computational arrays for multiplex SNP detection (including A-i mutations),
      • Viral lineage attribution (including West Nile virus, Ebola, Rabies)
      • Small molecule discrimination (including Vasopressin).

  • Enzymology:
    • Artificial enzymes for substance abuse (including Cocaine & Nerve agents)
    • High throughput screening for small molecule effectors
      • Reactivation of Cholinesterases inhibited by nerve agents
      • Inhibitors of Glutaminase for schizophrenia treatment

  • Molecular biology:
    • Vasopressin partial agonists to treat vasodilatory shock.



  • I host an National Science Foundation (NSF) funded student internship program, which runs during the summer, after school, and on weekends to provide state-of-the-art science education to interested students. More information can be obtained here
  • Five students are currently participating
  • Past participants of our program have greatly contributed to our laboratory’s success; several students’ contributions were outstanding, and were acknowledged in the form of authorship in top-tier scientific publications (underlined):
    • Macdonald J., Li Y., Sutovic M., Lederman H., Pendri K., Lu W., Andrews B.L., Stefanovic D., and Stojanovic M.N. (2006) Medium Scale Integration of Molecular Logic Gates in an Automaton. Nano Letters, 6 (11), 2598 -2603
    • Lederman H., Macdonald J., Stefanovic D., Stojanovic M.N. (2006) Deoxyribozyme-Based Three-Input Logic Gates and Construction of a Molecular Full Adder. Biochemistry, 45(4):1194-9.
  • Congralations to Pavithra Vijayakumar, semifinalist in the 2011 Intel Science Talent search (January 2011) and the 2010 Siemans Competition in Math, Science and Technology (October 2011).
  • Congratulations to Julia Poje, finalist at the Intel Science and Engineering Fair (May 2010, San Jose, CA). Julia won two awards, Engineering: Materials and Bioengineering "Second Award" ($1500), and Patent and Trademark Society "Second Award" ($150), for her project entitled "A Molecular Automaton with Built-in Visual Display for Filovirus Identification."

Grants and Contracts

  • 2011 Allosteric effectors of cholinesterase as pre-treatments for nerve agent exposure (Grant) 4/1/11-3/30/14, $1,098,296 USD. Department of Defense/Defense Threat Reduction Agency
  • 2010 Biological stability of CocE, 8/1/09 - 6/30/11, $113,050 USD. Reckitt Benckiser Pharmaceuticals Inc
  • 2010 Research Experiences for High School Students, $16,000 USD. NSF supplement CCF-0829793 Amendment #002
  • 2010 Research Experiences for Undergraduates, $16,000 USD. NSF supplement CCF-0829793 Amendment #001
  • 2008 Collaborative Research: EMT/MISC: Making Molecular Computation Practical for Biodetection Applications (Grant). 9/1/08 – 8/31/11, $548,000 USD. NSF award CCF-0829793: Emerging Models & Technologies


  • 2009: Thermostabilization of proteins, Pub. No.: WO/2009/009669, International Application No.: PCT/US2008/069659; Publication Date: .01.2009; International Filing Date: 10.07.2008; IPC: A61K 38/46 (2006.01)
  • 2009: Medium Scale integration of Molecular Logic gates in an automaton, Provisional application for Patent; Docket number 0575/76943-PRO/JPW/AJM/JCS; App# 20090275027
  • 2008: System and method for displaying output of a computation performed by DNA logic, Pub. No.: WO/2008/141279; International Application No.: PCT/US2008/063414; Publication Date: 20.11.2008; International Filing Date: 12.05.2008; IPC: H03K 19/00 (2006.01)
  • 2008: Anti-Cocaine Compositions and Treatment, Pub. No.: WO/2008/008358; International Application No.: PCT/US2007/015762 ; Publication Date: 17.01.2008; International Filing Date: 10.07.2007; IPC: A61K 38/46 (2006.01)



Review articles

  • Pei R., Macdonald J., and Stojanovic M.N.* (2011) Development of Trainable Deoxyribozyme-based Game Playing Automaton, in Methods in Molecular Biology: Ribozymes (Hartig,J., Ed.), in press.
  • Macdonald J.*, Stefanovic D., Stojanovic, M.N. (2009) Molecular Automata, in Encyclopedia of Complexity and Systems Science (Meyers R. Ed.), Springer, Entry 00126 337/337, Chapter 13 (M) p5631-5655
  • Macdonald J. and Stojanovic M.N.* (2009) Nucleic acids for computation, in Functional Nucleic Acids for Analytical Applications (Lu, Y. and Li, Y., Ed.) Chapter 14, p355-376, Springer-Verlag New York, LLC
  • Macdonald J., Stefanovic D., Stojanovic M.N. (2008) DNA computers for work and play. Scientific American November:84-91.
  • Macdonald J., Stefanovic D., and Stojanovic M.N. (2006) Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts, in Methods in Molecular Biology, vol 335: Fluorescent energy transfer nucleic acid probes: designs and protocols (Didenko, V.V., Ed.) Chapter 22, pp 343-363, Humana Press Inc., Totowa, NJ.

Posters & Presentations

  • Daffu G, Macdonald J, Lopez P, Katz F, Vinogradov M, Deng SX, Lenz D, Kasten S and Landry D* (2010) Site-specific PEGylation of bacterial phosphotriesterase - an approach to nerve agent detoxification. Chemical and biological defense science and technology conference, Orlando, Florida. Poster.
  • Daffu G, Macdonald J, Lopez P, Katz F, Vinogradov M, Deng SX, Lenz D, and Landry D.* (2010) Site-specific PEGylation of bacterial phosphotriesterase - an approach to nerve agent detoxification. 41st American Society for Neurochemistry meeting Santa Fe, New Mexico. Poster. PTW02-15
  • Macdonald J* (2009) Molecular Automata. VBC PhD Symposium 2009; Android and Eve: Bridging Biology, Medicine and Technology Vienna, Austria. Invited speaker - session #4: Biological microdevices.
  • Fanning ML, Macdonald J, Stefanovic D* (2009) Advancing the Deoxyribozyme-Based Logic Gate Design Process, in DNA 15, LNCS, 5877, pp. 45–54.
  • Zhu Z, Deng S-X, Macdonald J, Vinogradov M, and Landry DW,* Autophosphonylating peptides as the scavengers of nerve gas agents (2008) ACS 235th National Meeting New Orleans, Louisiana. Poster MEDI 280.
  • Macdonald J* (2007) DNA-based calculators with 7-segment displays. The 13th International Meeting on DNA Computing, Memphis, Tennessee, June 2007, Session E3
  • Yashin R, Macdonald J, Korkina O, Stojanovic MN, Rudchenko S* (May 2006) Flow Cytometry Analysis of Modular Aptameric Sensors Conjugated to Microspheres. ISAC XXIII International Congress, Québec, Canada. Poster P240.
  • Macdonald J, Li Y, Sutovic M, Stefanovic D, Stojanovic MN* (March 2006) Oligonucleotide-detecting automata for games and genome analysis. Genomes to Systems Conference, Manchester, U.K. Poster BN-2.
  • Macdonald J, Terry TD, Harris JM, Mackenzie JM, and Hall RA* (2001). Phage display and the study of flaviviral protein interactions. 6th International Symposium on Positive Strand RNA viruses, Paris, France. Poster P2-02.
  • Peake J, Hall RA, Mackenzie JS, Broom AK, Poidinger M* (1997) An investigation into the phylogeny of Edge Hill virus. Microbiology Australia 18(4):Oral presentation A79.


Contact Information

Dr. Joanne Macdonald
Assistant Professor in Clinical Medical Sciences
Division of Experimental Therapeutics
Department of Medicine, Columbia University
630 W 168th St, Rm P&S10-502/Box 84
New York, NY 10032 USA

Tel: 212-305-0351
Fax: 212-305-3475

Topic revision: r37 - 2011-03-09 - JoanneMacdonald
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