An affinity scale for the interaction of amino acid residues with nucleic acids

✍ Scribed by Dietmar Porschke; Jorg Ronnenberg

• Publisher: Wiley (John Wiley & Sons)
• Year: 1983
• Tongue: English
• Weight: 751 KB
• Volume: 22
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360221209

✦ Synopsis

Republic of Germany

Synopsis

The affinity of amino acid residues to nucleic acids is probed by measurements of melting temperatures t , for the helix-coil transition a t various concentrations of amino acid amides.

The increase oft, on addition of ligand is described by the equation t , = t k + CY log(1 + &A), where t ; is the melting temperature in the absence of ligand, C A the ligand concentration, and Kt the "t,-onset"constant, which is analogous to an equilibrium constant. It is shown that K t is closely related to the affinity of the ligands to the double helix, whereas the slope CY mainly reflects the preference of the ligand binding to the helix versus the coil form. In the case of the amino acid amides, CY is found to be virtually independent of the nature of the side chain with few exceptions, e.g., aromatic amides. The t , -onset constant, however, strongly depends on the nature of the amino acid side chain. For simple aliphatic amino acids, the relative free energy of binding decreases with increasing hydrophobic free energy, e.g., a high affinity is found for Gly-amide and a low affinity for Leu-amide. This relation is modified by functional groups like OH in Ser-amide. The helices poly[d(A-T)], poly[d(I-C)], and poly[d(A-C)]-poly[d(G-T)] exhibit similar affinity scales with relatively small variations. Our results demonstrate that the hydrophilic character of double helices a t their surface disfavors binding of hydrophobic ligands unless special contacts can be formed. From our results we establish an affinity scale for the binding of amino acids to double helices.