Determination of Allosteric Effects and Interstrand Bidentate Interactions in DNA‐Peptide Molecular Recognition

Abstract

To study DNA allostery, quantitative DNase I footprinting studies were carried out on a newly designed peptide His-Hyp-Lys-Lys-(Py) 4 -Lys-Lys-NH 2 (HypKK-10) containing the XHypKK (Hyp = hydroxyproline) and polyamide motifs. The interconnection of DNA footprints of peptides HypKK-10 and the parent peptide PyPro-12 supports the proposal that interaction network cooperativity is preferred in DNA-peptide interactions between multiple recognition sites. A simple method of determining interstrand bidentate interactions between the peptide moieties and DNA bases is introduced. It is envisaged that interstrand bidentate interactions also participate in the relay of conformational changes to recognition sites on the complementary strands. Circular dichroism studies of the titration of peptide HypKK-10 with an oligonucleotide duplex indicate that this peptide binds in a dimeric fashion to DNA in the minor groove. This work may prompt the design of new DNA binding ligands for the study of DNA-peptide allosteric interactions and DNA interaction network.

Thermochemical Study of the Interaction of Cytosine and Uracil with Peptides in a Buffered Saline: Complex Formation with beta-Endorphin 30-31 (Human), L-Glutathion (Reduced) and α-L-Alanyl-L-Tyrosine

“…Unsurprisingly, a lot of biochemical and physicochemical research is aimed at a comprehensive study of these interactions. Recently, the complexation between proteins and DNA, which underlie the effect of viruses on a living organism, has attracted the attention of researchers [1][2][3][4][5][6][7]. Due to the compact structure of the viral particle, proteins and nucleic bases are spatially close, due to which a large number of bonds and interactions arise (hydrophobic, hydrogen bonding, salt bridges, etc.).…”