The project proposed has two main goals. One of them is to study the conformational changes on nucleic acids that occur upon partial intercalation and bis-partial intercalation of aromatic amino acid residues using NMR, fluorescence and Raman spectroscopy. The second one is to synthesize a series of symmetrical bis-partial intercalating tetracationic peptide analogs containing the Tyr or Trp, which are expected to establish stacking interactions of equal strength with nucleic acids. Stacking interactions of aromatic amino acids upon complex formation with nucleic acids have been observed for both single stranded DNA binding proteins as well as for model oligopeptide systems. The stacking of aromatic amino acid residues produces partial intercalation of the ring in between DNA base pairs presumably as a result of stearic constraints posed by the peptide backbone. Stacking interactions may play an important role in protein-nucleic acid binding, recognition and conformation. Lys-Trp-Lys is even capable of promoting stand cleavage of apurinic DNA and has been used as a simple model for DNA damage recognition enzymes. Studies with a series of diastereometric tetrapeptides containing two aromatic residues with DNA, as well as with polynucleotides by 1H NMR, have shown that stacking interactions are enhanced when more than one aromatic residue is present with both rings engaging in stacking. Stacking interactions are found to be greater with alternating A-T polynucleotides. However, the stacking of one ring is stronger than the other due to its proximity to an N-terminal lysine, 1H and 31P NMR studies, in progress, with the hexanucleotide d(ATGCAT)2 have provided evidence of conformational changes that occur to the double stranded hexanucleotide in the presence of peptides containing aromatic residues. The detection of the conformational changes that occur to DNA as a consequence of partial interaction remains elusive. Viscometric results have led to the proposal of a bending of the DNA helix at the point of insertion of the aromatic amino acid, but this has not been confirmed by other methods. It is of interest to study these conformational changes by Raman spectroscopy. Raman studies on partial intercalator-nucleic acid complexes will complement the NMR studies.
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