Recognition schemes for protein-nucleic acid interactions.

The molecular forces involved in protein-nucleic acid interaction are electrostatic, stacking and hydrogen-bonding. These interactions have a certain amount of specificity due to the directional nature of such interactions and the spatial contributions of the steric effects of different substituent groups. Quantum chemical calculations on these interactions have been reported which clearly bring out such features. While the binding energies for electrostatic interactions are an order of magnitude higher, the differences in interaction energies for structures stabilised by hydrogen-bonding and stacking are relatively small. Thus, the molecular interactions alone cannot explain the highly specific nature of binding observed in certain segments of proteins and nucleic acids. It is therefore logical to assume that the sequence dependent three dimensional structures of these molecules help to place the functional groups in the correct geometry for a favourable interaction between the two molecules. We have carried out 2D-FT nuclear magnetic resonance studies on the oligonucleotide d- GGATCCGGATCC. This oligonucleotide sequence has two binding sites for the restriction enzyme Bam H1. Our studies indicate that the conformation of this DNA fragment is predominantly B-type except near the binding sites where the ribose ring prefers a 3E conformation. This interesting finding raises the general question about the presence of specificity in the inherent backbone structures of proteins and nucleic acids as opposed to specific intermolecular interactions which may induce conformational changes to facilitate such binding.

Interaction of two LAC repressor protein segments with polynucleotides.

The interaction of the oligopeptides Ala-Gln-GIn-Leu-Ala-Gly-OH and Gln-Leu- Ala-Gly-OMe corresponding, respectively, to the sequence 53–58 and 55–58 of lac repressor protein with four polynucleotides was studied. The two peptides did not interact with poly dA. poly dT, poly d(A-T).poly d(A-T) or poly d(A-G).poly d(C-T). But they interacted in a characteristic way with poly d(A-C). poly d (G-T), the sequences of which are in abundance in the lac operator region. Both the peptides stabilised the melting of poly d (A-C). poly d (G-T) at a peptide to nucleotide ratio (P/N) of 4; at lower ratios, they destabilised the DNA slightly. The circular dichroism of the alternating polynucleotide with CAC/GTG sequences was perturbed by both the oligopeptides. The hexapeptide at a P/N of 4 caused the transformation of the Bform circular dichroism spectrum to a new state, characterised by strong 220 and 240 nm bands, and a rather weak long wavelength spectrum.