Project description
A fast spectroscopy method for mutation detection
DNA sequencing and PCR comprise the gold standard methods for the identification of genetic mutations. However, there is a constant search for fast, inexpensive and accurate techniques to detect mutations at the molecular level. The EU-funded 2D-MES project proposes to detect base mutations in DNA or RNA using graphene-based biosensors. The molecules under test are attached to a graphene nanoribbon (GNR) in an aqueous environment, and their transport characteristics are recorded. The obtained transport molecular fingerprints of the mutated DNA/RNA on the GNR will lay the groundwork for the development of an innovative tool with high spatial resolution.
Objective
In this project, Dr. Reza Rezapour will address, by a combination of quantum mechanical and classical simulations combined with electronic transport techniques, the sensing capabilities of graphene-based biosensors to identify DNA and RNA mutations in PNA-functionalized graphene nanoribbons.
In the search for fast, inexpensive and accurate tools for DNA sequencing and mutation recognition, computational techniques are being fruitfully used to address detection at the molecular level. We will extended the 2D-MES method previously developed by Dr. Rezapour to the identification, not only of single normal and mutated nucleobases on graphene, but of base mutations in DNA or RNA fragments attached to a graphene nanoribbon (GNR) in an aqueous environment. To this aim, after the quantum mechanical (QM) calculation of the transport characteristics of a nucleobases-GNR system in vacuum, we will study: (1) large DNA/RNA fragments in a solvent by molecular mechanics (MM) classical methods (to study mutation stability in a given sequence) and (2) the most stable mutations on a GNR by novel hybrid QM/MM simulations combining the accuracy of QM with the speed of MM.
Besides providing new insight on fundamental aspects of physical processes at the interface between solids, liquids and biomolecules, the project will train Dr. Rezapour in advanced new techniques, complementary to his current expertise; and it will provide the community with a new and efficient QM/MM-electronic transport tool by the implementation of transport routines into the existent QM/MM package. The obtained QM/MM transport molecular fingerprints of the mutated DNA/RNA on the GNR will serve as a proof-of-concept for the design of a graphene-based bionsensor fast, inexpensive, and with high spatial resolution.
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Programme(s)
Funding Scheme
MSCA-IF - Marie Skłodowska-Curie Individual Fellowships (IF)Coordinator
18071 Granada
Spain