The “rigid” nucleotide concept in perspective

Abstract

The principles embodied in the “rigid” nucleotide concept contend that the highly correlated preferred conformations of 5′-nucleotides lead to helical conformations as the most predominant secondary structure, while their distortions induce the loops, bends, and kinks of the tertiary structure of nucleic acids. These principles have been amply corroborated by the crystal structure of tRNAphe and throughout the studies of nucleic acid conformations by numerous other techniques, although the choice of the term “rigid” was at times misunderstood or considered confusing. The “rigid” nucleotide concept helps understand the polymorphism of polynucleotides, the folding of DNA in chromatin, and the interactions between metals or drugs with nucleic acids. It provides also a rationale for the dynamics and flexibility (unwinding, unfolding, unpairing, etc.) of nucleic acids during replication, transcription, and translation as well as related processes like denaturation, thermal-or pH-induced melting.