The binding of the peptide Lys-Trp-Lys to various single-stranded copolymers of adenine and cytosine has been investigated using circular dichroism (CD) and fluorescence measurements. Two types of complexes are formed, both involving electrostatic interactions between lysyl residues and phosphate groups. The fluorescence quantum yield of the first complex is identical with that of the free peptide. The other complex involves a stacking of the polynucleotide bases with the tryptophan residue whose fluorescence is quenched. The binding of the peptide leads to a conformational change of the copolymers as shown by the CD variations. The fluorescence and CD data have been analyzed according to the model involving the two types of complexes. The values of the binding constants have been studied as a function of the cytosine content of the copolymers. Analysis of the stacking process in term of nearest neighbor frequency demonstrates that this binding is sequence dependent and is favored in AA sequence as compared with AC, CA, and CC sequence. Thus this simple tripeptide is able to distinguish between various base sequences in a single-stranded nucleic acid.

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