Nucleic Acid Aggregation Research Articles

Nucleic acid aggregation geometry and the possible evolutionary origin of ribosomes and the genetic code

It is proposed that the primitive translational complex responsible for the evolutionary origin of the genetic code was an ordered RNA aggregate, stabilized not only by base-pairing, but also by the multivalent ionic interactions known to be responsible for bundle aggregation and condensation of DNA. A triplet code is the logical consequence of the structural symmetry and information coding capacity and efficiency of the proposed class of aggregates. The model requires rod-like adaptor, or primitive transfer RNA, molecules, and predicts that they were about 42 nucleotides in length. There are plausible reasons for preferring 5′ → 3′ reading of the message, and for favoring a primitive GNC code. It is further proposed that the primitive coding aggregate was the starting point for the evolution of ribosomes, and that the vestigial skeleton of the early translational complex may be discernible in present ribosomes. Amino acid specificity in coding interactions could have been generated spontaneously in a “bootstrap” process, given formation of an RNA aggregate in which RNA adaptors act as catalytic cofactors in the synthesis of peptides having appreciable catalytic activity for RNA synthesis and amino acid activation.

Interpretation of the kinetics of helix formation

This chapter focuses on recent biochemical and biophysical studies that examine the nucleic acid chaperone function of HIV‐1 nucleocapsid protein (NC) and its critical role in facilitating specific and efficient reverse transcription. This chapter also describes the effect of NC on individual steps in viral DNA synthesis. This chapter also summarizes what is known about NC structure, NC nucleic acid binding properties, and the contribution of the zinc fingers to chaperone activity. In addition, this chapter also discusses new evidence that provides a model to explain the mechanism of NC's nucleic acid chaperone activity at the molecular level. Characterization of the mechanism of NC's chaperone activity in molecular terms has been invaluable for understanding NC's effect on specific steps in reverse transcription. NC binds nucleic acids noncooperatively and does not rely on protein– protein interactions to drive aggregation and annealing. Instead, NC‐induced nucleic acid aggregation appears to be facilitated by simple polyelectrolyte attraction, similar to that observed for many multivalent cations.