MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

Synthetic Biology and Biosensing


Sensor Technologies


prof. dr. Tamara Lah Turnšek
prof. dr. Henning Ulrich


• Comprehension of RNA and DNA biology and state-of-the art techniques for biosensors.
• Ability to design and evaluate approaches for biosensor development.
• How artificial circuits (synthetic biology) can be used for biosensor approaches.
• Understanding of the importance of interdisciplinary approaches.

• Independent use of tolls to develop the interdisciplinary approach in preparation of nuclear acids base biosensors.


• Introduction: Concept of biosensors: Biological mechanisms, detection and translation systems (more authors).
• Synthetic biology: Introducing the concept and construction of novel artificial biological pathways, organisms, or the redesign of existing natural biological systems for purposes of biotechnology, diagnostics and therapy.
• Application of DNA and RNA engineering principles to design the fundamental biological components.
• Engineering of biological substances, based on RNA regulatory loops.
• RNA molecules for programming gene expression in response to small molecules. Applications for biosensorics.
• RNA and DNA aptamers for biosensorics: Principles and applications vs. classical (antibody-based) assays.
• New approaches for sensing metabolites and proteins in live cells using RNA aptamers.
• Aptamers for detection of stem, cancer cells and pathogenic organisms.
• On-chip protein microarray for multiplexed SPRI biosensing measurements in research and clinical application.
• Allosteric ribozymes and deoxy-ribozymes as biosensors.
• RNA- and DNA-derived biosensors in environmental protection and food safety.
• Biosensors in cancer research: Biomarkers technologies.

Course literature:

• Arugula MA, Zhang Y, Simonian A. Biosensors as 21st Century technology for detecting Genetically Modified Organisms in food and feed. Anal Chem. 2013 Oct 2. [Epub ahead of print
• Bacchus W, Aubel D, Fussenegger M. Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol. 2013 Sep 24;9:691.
• Bacchus W, Fussenegger M. Engineering of synthetic intercellular communication systems. Metab Eng. 2013 Mar;16:33-41. doi: 10.1016/j.ymben.2012.12.001.
• Benenson Y. Synthetic biology with RNA: progress report. Curr Opin Chem Biol. 2012 Aug;16(3-4):278-84.
• Breaker RR. Engineered allosteric ribozymes as biosensor components. Curr Opin Biotechnol. 2002 Feb;13(1):31-9. Review.
• Chen Y, Nakamoto K, Niwa O, Corn RM. On-chip synthesis of RNA aptamer microarrays for multiplexed protein biosensing with SPR imaging measurements. Langmuir. 2012 Jun 5;28(22):8281-5.
• Liu J, Cao Z, Lu Y. Functional nucleic acid sensors. Chem Rev. 2009 May;109(5):1948-98.
• McKeague M, Giamberardino A, DeRosa MC. Advances in Aptamer-Based Biosensors for Food Safety. In: " Environmental Biosensors" , book edited by Vernon Somerset, ISBN 978-953-307-486-3, InTech, 2011
• Paige JS, Nguyen-Duc T, Song W, Jaffrey SR. Fluorescence imaging of cellular metabolites with RNA. Science. 2012 Mar 9;335(6073):1194.
• Robert S. Marks, Christopher R. Lowe, David C. Cullen, Howard H. Weetall, Isao Karube. Handbook of Biosensors and Biochips. Wiley 2007, ISBN: 978-0-470-01905-4.
• Šmuc T, Ahn IY, Ulrich H. Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics. J Pharm Biomed Anal. 2013 Jul-Aug;81-82:210-7
• Strehlitz B, Reinemann C, Linkorn S, Stoltenburg R. Aptamers for pharmaceuticals and their application in environmental analytics. Bioanal Rev. 2012 Mar;4(1):1-30.
• Ulrich H, Wrenger C. Disease-specific biomarker discovery by aptamers. Cytometry A. 2009 Sep;75(9):727-33
• Win MN, Liang JC, Smolke CD. Frameworks for programming biological function through RNA parts and devices. Chem Biol. 2009 Mar 27;16(3):298-310.
• Zimbres FM, Tαrnok A, Ulrich H, Wrenger C. Aptamers: Novel Molecules as Diagnostic Markers in Bacterial and Viral Infections? Biomed Res Int. 2013;2013:731516.

Significant publications and references:

• TORSVIK, Anja, PRIMON, Monika, LAH TURNŠEK, Tamara, MOTALN, Helena. Spontaneous malignant transformation of human mesenchymal stem cells reflects cross-contamination: putting the research field on track - letter. Cancer res. (Baltimore), 2010, 70, 15, 6393-6396.
• MOTALN, Helena, SCHICHOR, Christian, LAH TURNŠEK, Tamara. Human mesenchymal stem cells and their use in cell-based therapies. Cancer (Print), 2010, vol. 116, no. 11,. 2519-2530.
• SCHICHOR Christian , ALBRECHT Valerie , KORTE , Benjamin, BUCHNER, Alexander , BUCHNER Rainer, MYSLIWIETZ Josef, PARON Igor, MOTALN, Helena, LAH TURNŠEK, Tamara, JάRCHOTT Kathrin , SELBIG Joachim, TONN Joerg-Christian. Mesenchymal stem cells and glioma cells form a structural as well as a functional syncytium in vitro. Exp. neurol., 2012, vol. 234, issue 1,. 208-219.
• MOTALN, Helena, GRUDEN, Kristina, HREN, Matjaž, SCHICHOR, Christian, PRIMON, Monika, ROTTER, Ana, LAH TURNŠEK, Tamara. Human mesenchymal stem cells exploit the immune response mediating chemokines to impact the phenotype of glioblastoma. Cell transplant. 2012, vol. 21, no. 7, str. 1529-1545.
• TORKAR, Ana, BREGANT, S., DEVEL, Laurent, NOVINEC, Marko, LENARČIČ, Brigita, LAH TURNŠEK, Tamara, DIVE, Vincent. A novel photoaffinity-based probe for selective detection of cathepsin L active form. ChemBioChem. 2012, vol. 13, issue 17, 2616-2621.


Oral examination (50%)
Seminar (50%)
Project for biosensor-development.
Defense of seminar and projects.

Students obligations:

Oral examination.
Project for biosensor-development.
Defense of seminar and projects.