Interaction energy studies for the specificity of transcription

Electrostatic interaction energy has been studied for the DNA base pair–RNA base complexes inside the deep groove of the DNA. The allowed region has been continuously scanned in order to find out a minimum energy configuration for each complex. A comparative study of the interactiion energy values and the site of association has been carried out. It has been found that the Watson–Crick GC base pair shows a definite specificity similar to the model proposed by Zubay or Riley, while for the AT pair, no specificity can be assigned on the basis of the interaction energy studies alone. Instead, an assumption for a hypothetical backbone directed by the GC pair specificity, has been adopted to assign a specificity to the AT pair. As a consequence of these studies, a model for transcription without unwinding of the DNA double helix has been developed.