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Tue, 14 Nov 2017
Molecular interactions in gene-regulating RNAs and DNAs

Time: 11.00 AM - 12.00 PM

Venue: Cysteine, Level 7 (30 Biopolis Street, Matrix)

Speaker: Prof. Alessandra Villa, Associate Professor, Department of Biosciences and Nutrition, Karolinska Institute, Sweden


Ribonucleic acid (RNA) molecules can regulate gene expression. In bacteria, natural riboswitches, occurring within the untranslated region of messenger RNA, regulate gene expression after binding with a metabolite. In eukaryotic, one mechanism for gene regulation is the formation of triple helices between long non-coding RNA and double helical DNA. Synthetic oligonucleotides are also a promising strategy to modulate in vivo gene expression, for example by targeting specific genomic DNA molecules by triplex forming oligonucleotide (TFO). All those processes are regulated by interactions between RNA and/or DNA bases. Understanding the role of the molecular interactions, will help to define criteria for the design of new tools for biomedical and biotechnological applications.

In this lecture, I will discuss the role of base-base interactions on the stability and dynamics of the RNA and DNA molecules, with a particular attention to the environment (such as sequence, pH, and metabolites). Using atomistic simulations, we have identified the pivotal role of some RNA residues in the metabolite binding to the aptamer domain of purine riboswitches and made an hypothesis for the binding mechanism. We have also shown how consensus mutations affect the structure of RNA stem-loop hairpin of HBV virus and how DNA breathing is influenced by sequence. Recently we have investigated how DNA binding is affect by sugar and base mutations, and/or by base tautomerism and protonation. The findings will contribute the design of better anti-gene oligonucleotides.

About The Speaker
Current position: Associate Professor at Department of Biosciences and Nutrition, Karolinska Institute, Sweden.
1995 Degree in Chemistry, University of Milano, Italy.
2000 Ph.D. in Physical-Chemistry, University of Milano, Italy.
2000-2001 Marie Curie Fellowship, University of Groningen, The Netherlands.
2002-2004 Postdocs with Prof. Alan E. Mark, University of of Groningen, The Netherlands.
2004-2007 Postdocs with Prof. Gerhard Stock, Goethe University, Germany.
2007-2009 Postdocs in the polymer theory group, MPI for Polymer Research, Mainz, Germany.
2009- Senior researcher at the Department of Biosciences and Nutrition, Karolinska Institutet, Sweden.
2015 Associate Professor in Biochemistry

Dr. Hao Fan, Principal Investigator

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