STRUCTURAL CHANGES AND (SUB)PICOSECOND DYNAMICS IN DNA MOLECULES PROBED WITH ULTRASENSITIVE RAMAN SPECTROSCOPIC TECHNIQUES

National Institute for Research and Development of Isotopic and Molecular Technologies Cluj-Napoca

 

Objectives / Expected results:

 

 

1. Structural characterization of a natural DNA recognition site molecular subgroups, at reduced and low pH values, in the absence of divalent metal cations: a spectroscopic and theoretical assessment.

 

A. On the basis of characteristic spectral markers we will comparatively analyse the structure of nucleosides and bases of a DNA oligomer, at reduced and low pH values, in the absence of divalent metal cations.

B. A detailed description of different spectral modifications, which can occur when correcting the theoretical vibrational spectra of GC base pairs, by including the anharmonic and solvent effects in the calculations will be given.

 

 

2. Study of experimental and theoretical vibrational properties of a natural DNA recognition site molecular subgroups, at reduced and low pH values, in the presence of divalent metal cations.

 

A. Based on the characteristic UV resonance Raman vibrations, the DNA oligomer nucleosides and bases structure will be comparatively analysed, at reduced and low pH values, in the presence of divalent metal cations.

B. Determine the vibrational frequencies of metal cations attached to the  DNA GC base pairs. Establishing the spectral shifts caused by metal ions upon characteristic marker modes of  GC base pairs.

 

 

3. Surface-enhanced Raman spectroscopy (SERS) structural characterization of genomic DNA molecules extracted from leaf tissues: nucleoside conformation, DNA backbone geometry and PO2- interaction.

 

A. Establishing the spectra-structure correlations in the vibrational (SERS) spectra of DNA molecules. Description of the wavenumber range corresponding to nucleoside conformation, DNA backbone geometry and PO2- interaction.

B. Based on the characteristic SERS spectra, we will analyse comparatively the nucleosidic residues and the conformational changes of the DNA backbone, in genomic DNA molecules from different leaf tissues.

 

 

4. Surface-enhanced Raman spectroscopy of genomic DNA extracted from leaf tissues: base electronic structures and base pairing.

 

A. Establishing the spectra-structure correlations in the SERS spectra of DNA molecules. Description of the wavenumber range corresponding to base electronic structures and base pairing.

B. Based on the SERS bands characteristic to adenine, guanine, cytosine and thymine, the structure of nucleic acids bases in genomic DNA from different leaf tissues will be comparatively analyzed.

 

 

5. (Sub)picosecond molecular relaxation processes in DNA-metal complexes, at different pH values.

 

A. Determine the FWHHs (full-widths at half height), characterizing the purinic, pyrimidinic nucleosides and the bases, respectively, in DNA-metal complexes, at different pH values.

B. Determine the molecular relaxation times of some DNA-metal structural  subgroups, at different pH values.

 

 

6. (Sub)picosecond surface dynamics in DNA molecules.

 

A. Determine the FWHHs (full-widths at half height) of the SERS bands, characterizing the purinic, pyrimidinic nucleosides and the bases, respectively, in different DNA molecules.

B. Determine the molecular relaxation times of some DNA structural subgroups near the surface of metallic nanoparticles.

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