Objective
Apical loops of at least six nucleotide residues are often distinguished by a cross-loop base pair leaving three nucleotides at the cap of the loop forming a well conserved motif called T-loop or lonepair triloop. Our previous studies have indicated the occurrence of such a loop pattern in the HIV-1 TAR RNA. The present project concerns molecular structure and dynamics of sequence-dependent modes of large loop stabilisation. We will focus on apical loop of the dimer initiation site (DIS) of the leader sequence of HIV-2 RNA, composed of 11-nucleotide residues and including a palindromic sequence. We suppose that prior to its involvement into loop-loop interaction via kissing hairpin mode, the HIV-2 DIS RNA hairpin undergoes intra-loop stabilisation.
Advanced molecular dynamics simulation techniques will be used in order to get an insight into the structure and dynamics of this model. In addition, possible contribution of magnesium cations to the loop stabilisation will be investigated by combined Brownian Dynamics/MD methods. The Molecular Dynamics Thermocycler protocol, recently proposed by us, will be simultaneously developed and applied for the project. At the level of conformational analysis, novel methods for description of the conformational space of the loops will be proposed, based on the cluster analysis approach. In order to confront our simulations results with physical data, the RNA models will also be chemically synthesised and their melting thermodynamics will be studied based on magnesium dependence. The picture of RNA/magnesium binding sites emerging from simulations will be confronted with results of Mg2+ ion-promoted RNA cleavages studied by electrophoresis.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences chemical sciences inorganic chemistry alkaline earth metals
- natural sciences physical sciences thermodynamics
- natural sciences biological sciences genetics nucleotides
- natural sciences biological sciences genetics RNA
- natural sciences chemical sciences electrochemistry electrophoresis
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP6-2002-MOBILITY-11
See other projects for this call
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Coordinator
POZNAN
Poland
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.