Interactions of diastereomeric tripeptides of lysyl-5-fluorotryptophyllysine with DNA. 2. Optical, fluorine-19 NMR and strand cleavage studies of apurinic DNA complexes

Abstract

The interactions of the diastereomers lysyl-5-fluoro-L-tryptophyllysine and lysyl-5-fluoro-D-tryptophyllysine with apurinic DNA have been examined as a model for the action of DNA repair enzymes. The binding characteristics of the tripeptide diastereomers to DNA, modified to contain approximately 5% apurinic sites, were studied by measuring 19F NMR parameters, fluorescence quenching, and activity in promoting single-strand cleavage of plasmid DNA. The affinities of each of the peptides to apurinic DNA are similar to those for native DNA. However, the 19F NMR chemical shift and relaxation behavior indicates that both diastereomers form complexes with apurinic DNA that are distinct from those formed with native DNA. In addition, the 19F NMR measurements differ for the L-Trp and D-Trp complexes with apurinic DNA. In spite of these differences, when either of the tripeptide diastereomers is incubated with plasmid DNA containing apurinic sites, no difference in the rate of single-strand cleavage of the DNA is detectable.

Phosphorescence and Optically Detected Magnetic Resonance of Polynucleotide Complexes of Tryptophan- and 5-Methyltryptophan-Containing Peptide Stereoisomers

“…It is of interest to compare our results with previous studies of peptide binding to nucleic acids. From their NMR measurements of the complexes of the dipeptide diastereomers KF and KF* with duplex salmon sperm DNA, Gabbay et al 33 concluded that the phenylalanine was partially inserted between stacked bases in KF, but that it extended into the solvent in KF* Similarly, binding of K(5FW)K and K(5FW*)K to duplex DNA reveals 5FW-base interactions only with the l -isomer. , To explain their results on dipeptides and longer oligomers, Gabbay et al proposed 33,60 a binding model in which the N-terminal lysine, utilizing its α and ε NH 3 + groups binds in a stereospecific manner to the DNA backbone, directing the aromatic ring of lysylphenylalanine with the l−l designation toward the DNA helix while that of the l−d designation points outward. This binding model has been utilized to explain the results of more recent work 31,32 on binding of the peptides KWK, KGWK(O- tert- Bu), and KGWGK to DNA oligonucleotide hairpins and duplexes.…”

“…The binding of KF (F is phenylalanine) and KF* to salmon sperm DNA has been compared 33 with the result that aromatic stacking of KF exceeds that of KF*. Similar studies of the binding of K(5FW)K and K(5FW*)K (5FW is 5-fluorotryptophan) to duplex DNA 34 and DNA containing apurinic lesions 35 shows that fluorine is partially inserted into the base stack in the K(5FW)K complex, while there is no interaction of fluorine with bases in the K(5FW*)K complex. In this communication, we will use phosphorescence and ODMR spectroscopy to compare complexes formed between three polynucleotides [poly dT, poly(uridylic) acid (poly U), and poly(inosinic) acid (poly I)] and resolved peptide diastereomers that contain a single aromatic amino acid, W or 5-methyltryptophan (MeW).…”