Interaction of oligopeptides containing aromatic amino acids with nucleic acids. Fluorescence and proton magnetic resonance studies

Abstract

1. introduction A study of interactions between amino acids and nucleic acid bases is required to explain the nature and specificity of recognition of nucleic acids by enzymes and proteins and to shed some light on the origin of the genetic code. We previously reported that aromatic amino acids could form complexes with nucleic acid bases either in frozen aqueous solutions [ 1,2] or in concentrated fluid solutions [3]. More recently, evi- dence has been provided for the interaction of nucleo- tides with immobilized amino acids [4]. A study of complex formation between tyramine [2] or trypt- amine [5] and nucleic acids in single-stranded or double-stranded conformations demonstrated a direct interaction of the phenol or indole rings with the purine and pyrimidine bases. Proton magnetic reso- nanee studies provided evidence for intercalation of the indole ring between thebases of single-stranded poly A [2, 5,6] and of double-stranded DNA [7]. This led us to propose that aromatic amino acids could be involved in the binding of enzymes or proteins to nucleic acids by direct interaction with the bases [8]. Such a proposal was also made in the case of trypt- ophan upon indirect evidence based upon changes in the denaturation temperature of DNA [9]. A study of the binding of oligopeptides containing aromatic amino acids to nucleic acids was undertaken to provide evi- dence for this direct interaction with the bases. In order to increase the affinity of the oligopeptides for nucleic acids, the aromatic amino acid was linked to lysine res- idues. The techniques of fluorescence and proton magne- tic resonance were used to investigate the binding process. 6 2. Experimental Most of the experimental conditions can be found in earlier publications [2,3,5]. The oligopeptides were purchased either from Schwarz-Mann (Lys Trp Lys, Trp Lys, Lys Tyr Lys) or from Cycle Chemical Corporation (Lys Tyramide, Lys Lys Lys). Calf thy- mus DNA samples used in the PMR experiments were sonicated until the sedimentation coefficient was de- creased to about 7. All measurements were carried out in a buffer containing 1 mM Na cacodylate and 1 mM NaCl at pH 7. The temperature was maintained at 20”. Tryptophan-containing peptides were excited at 295 nm and fluorescence intensity measured at 370 run. For tyrosine-containing peptides, the corres- ponding wavelengths were 275 and 3 10 nm. Proton magnetic resonance experiments were carried out in Dz 0 with a Briiker HFX 90 MHz spectrometer. Chem- ical shifts were measured with respect to an external reference (HMS). 3. Results 3.1.