Dr Vasudevan Ramesh.

School of Chemistry
Tel.: 0161 306 4539
Email: v.ramesh@manchester.ac.uk
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Background:

Appointed to UMIST with special interests in NMR methodology[1,2,3].

Research:

My group specialises in the study of the 3D structure and the interactions of proteins, nucleic acids and their complexes, based on high-resolution 2D and 3D NMR studies of fluorine-containing 'probe' compounds.

Recently, a conceptually new class of NMR methods has been developed to determine long-range constraints from internuclear dipolar coupling by dissolving the solute molecule in dilute liquid crystalline solvent and induce the former to acquire a very small degree of alignment with external magnetic field. We are developing the methodology for measuring 19F-1H dipolar coupling in dilute crystalline solvents which will enable the structures of both small organic compounds and large bio-molecules (ca. 10 kDa) to be determined.

In another project we have designed and synthesised a single-stranded 35mer RNAs (11 kDa), corresponding to the highly conserved secondary structural RNA motifs of Hh, E.coli and eukaryotic 23S rRNA, based on published sequence and biochemical data. The preliminary NMR data demonstrate that the designed, synthetic 35mer RNAs are endowed with the requisite stability and uniformly well folded A-RNA type tertiary conformation for amicetin antibiotic binding studies. Two salient features of the RNA sequence are :-

  • the highly conserved, two small, asymmetrical and unpaired nucleotide ‘bulges’ in the middle of the motif which have been implicated in binding to amicetin,
  • the occurrence of a spontaneous resistance mutant with a single nucleotide change, U2457-> C.


We propose to introduce 19F labels (e.g. 5-fluorouracil and 5-fluorocytosine) into the bulged bases constituting the RNA motifs (wild type and mutant) and carry out 19 F-NMR experiments in dilute liquid crystalline solvent to determine the conformation of amicetin binding site and elucidate the specificity of interaction.

References:

1. V. Ramesh, T. Brown, J Biochem., 1996, 315, 895.
2. V. Ramesh, S.E.H. Syed, R. Frederick, M.J. Sutcliff, M. Barnes, G.C.K. Roberts, Eur. J. Biochem., 1996, 235, 804.
3. Y-Z Xu, V. Ramesh, P.F. Swann, Biorg. Med. Chem. Lett., 1996, 6, 1179.

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