Selection of peptides with affinity for single stranded DNA using a phage display library

Area of Science:

• Molecular Biology
• Biochemistry
• Peptide Chemistry

Background:

• Oligonucleotides are crucial in biological processes and therapeutics.
• Phage display is a powerful technique for identifying peptide-nucleic acid interactions.
• Developing specific peptide binders for nucleic acids is of significant interest.

Purpose of the Study:

• To identify and characterize hexapeptides that specifically bind to single-stranded cytosine oligonucleotides (oligo-C).
• To compare the efficacy of selection in different buffer systems.
• To evaluate the binding affinity and specificity of selected peptide clones.

Main Methods:

• Affinity selection using a hexapeptide phage library against oligo-C.
• Phage selection performed in two buffer systems: 50 mM 2[N-Morpholino]ethanesulphonic acid (MES)-buffer (pH 5.5) and 50 mM Tris(hydroxymethyl)-aminomethane, 150 mM NaCl (pH 7.5).
• Characterization of selected clones through binding assays against oligo-C and other oligonucleotides (-G, -A, -T).

Main Results:

• Selection was more successful in MES-buffer (pH 5.5) compared to Tris-buffer (pH 7.5).
• Three distinct hexapeptide clones (Pro-Pro-Pro-Leu-Tyr-Phe, Arg-Phe-Cys-Asp-Thr-Ser, Arg-Ser-Arg-Leu-Ile-Trp) exhibited enhanced affinity for oligo-C.
• Selected peptides demonstrated differential binding specificity towards oligo-C over other oligonucleotide sequences.

Conclusions:

• MES-buffer at pH 5.5 is optimal for selecting peptides binding to oligo-C using this phage display system.
• Identified hexapeptides represent promising candidates for targeting cytosine-rich nucleic acid structures.
• The study highlights the potential of phage display for discovering specific peptide-oligonucleotide interactions.