Protein-nucleic acid interactions: investigations on the peptide backbone interaction with polynucleotides

Abstract

Model building, difference spectroscopy, and 1H and 13C NMR experiments have been carried out to study the binding of poly(L-Ser) with the polyribonucleotides poly(A) and poly(U) at pH 7.1. Studies have also been carried out with base paired duplexes poly(A)m.poly(U). Peak doubling of Cα and carbonyl resonances in the 13C NMR spectrum of poly(L-Ser) in presence of polyribonucleotides is observed. From the chemical shifts and the linewidth, it is concluded that the interaction occurs through hydrogen bonding between the nucleic acid bases and the peptide backbone. In case of poly(A) and poly(U) the hydrogen bonding scheme with peptide backbone is different from that in the base paired poly(A)m.poly(U). The possible binding schemes of double stranded DNA and peptide backbone have been investigated using model building and potential energy calculations. The hydrogen bonding schemes discriminate between various base pairs and their sequence. It is concluded that protein backbone can play an important role in protein-nucleic acid recognition schemes