Synthesis and nucleic acid binding studies of novel pyrrolidinyl PNA carrying an N-amino-N-methylglycine spacer

Two novel pyrrolidinyl peptide nucleic acids comprising alternating sequences of thymine-modified d- or l-proline and an N-amino-N-methylglycine spacer were synthesized using solid-phase methodology. UV and CD titrations together with a gel-binding shift assay revealed that neither of the homothymine PNA decamers bind to their complementary DNA or RNA. This was considered to be due to an unfavorable secondary structure which could not be alleviated by the presence of the positively charged protonated amine in the PNA backbone.     

Tryptophan receptors containing acridine-based thiourea

Four derivatives of acridine and acridinium compounds (L1, L2, L1H and L2H) comprised thiourea-binding sites were synthesised. The binding abilities of receptors L1, L2, L1H and L2H towards amino acids (l-Trp, l-Phe, l-Leu, l-Ala and l-Gly) were studied by ¹H NMR spectroscopy, UV–vis and fluorescence spectrophotometry. Hydrogen bonding interactions between thiourea-binding site of the ligand and the carboxylate groups in zwitterionic amino acids were found to be the main interactions driving complexation to take place. The stoichiometry of 1:1 ligand to amino acid was observed in all cases. Neutral ligands L1 and L2 showed weak binding towards all studied amino acids. The cyclic ligand L1 showed better binding ability towards tryptophan (Trp) than the acyclic ligand L2 did (K for Trp is 307 and 266 M^? 1 for L1 and L2, respectively). Interestingly, binding abilities of the protonated ligands, L1H and L2H, towards studied amino acids, especially Trp (K for Trp is 3157 and 2873 M^? 1 for L1H and L2H, respectively), were increased due to R–COO^? …H…N⁺–acridinium interactions. Calculated structures of L1H·Trp and L2H·Trp showed that the polyglycol moiety in L1H provided a hydrophobic cavity for binding Trp resulting in a stronger binding affinity of L1H over L2H.