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Alice Ghidini

  • PhD student
  • Group of Roger Strömberg
  • Department of Bioscience and Nutrition, Karolinska Institutet, Sweden
  • Contact email: alice.ghidini (please add @ki.se)

Background: I did my Bachelor and Master degrees in Chemistry at the Università degli Studi di Parma in Italy where I joined the group of Prof. Roberto Corradini and Prof. Angela Marchelli for my thesis about PNAs modifications as disease detection tools.

Training and Transferable Skills:
- Lab assistant for the Food Chemistry Course (1 week every year)

Research Projects: My main goal is to develop oligonucleotide based artificial nucleases (OBANs) to the state of becoming useful tools in molecular biology and biotechnology also in a cellular environment and to move closer to being able to use these artificial enzymes for disease therapy.
We have developed oligonucleotide based artificial nucleases (OBANs) with the aim to produce artificial enzymes that can cleave mRNA sequences arising from genetic or viral diseases. Through the developed Cu2+ based PNAzymes, we have obtained single site cleavage of the target RNA and rate is also bulge sequence dependent. These PNAzymes displays real catalytic behavior and turnover of RNA substrate even when used in 100 times excess of substrate vs enzyme. Moreover, single site cleavage and excellent mismatch rejection is achieved.
Most interesting for the further development is that metal ion catalyzed cleavage of phosphate diesters can be up to 1012 times faster in methanol than in aqueous solution. It is of course not feasible to have this environment in vivo but it may be possible to create a local solvent effect around the cleavage site. Our plans to achieve this local solvent effect, involve the conjugation of the PNA (and perhaps other oligonucleotide analogs) with polyethers and/or polyols to form a partial cage around the active site that would render the environment less aqueous.


alicediag02

The complex between PNAzyme and substrate RNA, as well as the IE-HPLC chromatogram displaying selective cleavage of the target RNA (3 h incubation time, 1:1 PNAzyme /RNA 4 µM of each, 10 µM Cu2+, pH 7.4, 37 °C). The cleavage site is indicated by the dashed line.


alicediag03

Possible structure of the active site created by local solvent effect.