Introduction

CARL C. CORRELL AND PHOEBE A. RICE

1.1 Overview

Nucleic acids are the information storehouse of life and in many cases serve as the regulators and construction workers as well. Indeed, self-replicating RNAs may have been the beginning of life itself, predating evolution of the first protein. Modern organisms, however, depend on a complex interplay between nucleic acids and proteins. This chapter reviews the basic features of the structures that nucleic acids can adopt and highlights the ways that nucleic acids and their cognate proteins interact with one another.

1.2 Fundamentals of DNA and RNA Structure

1.2.1 Stabilizing Forces

The fundamental forces that stabilize nucleic acid and protein structure are the same. The hydrophobic effect drives folding of these molecules as they attempt to simultaneously satisfy multiple goals: minimizing the exposure of hydrophobic surfaces to water, satisfying all the hydrogen bond donors and acceptors that become buried from solvent, maximizing van der Waals interactions, and ensuring that all charges are either solvated or neutralized with opposing charges. Nucleic acids differ from proteins in that the hydrogen bonds that are key to secondary structure formation are between the variable moieties (the bases) rather than the constant ones (the backbones). The backbone of nucleic acids is more flexible than that of proteins, with six variable torsion angles rather than two (Figure 1.1). Nucleic acid backbones also differ from proteins in that their backbones are uniformly negatively charged. To form large tertiary structures with buried backbones nucleic acids must rely on external sources of positive charge such as solvent cations or helper proteins. Relative to tertiary structure, secondary structure is more stable in nucleic acids than proteins. As a consequence, nucleic acid folding is generally less cooperative than protein folding, with the formation of tertiary structure following that of secondary structure.

1.2.2 Chemical Differences between DNA and RNA

The defining difference between RNA and DNA is the presence of the 2'-hydroxyl group on the pentose ring of RNA. This group is distinctive in two fundamental ways. First, it is an Achilles heel that renders the RNA chain more susceptible to cleavage than the DNA chain (Figure 1.2). Apparently, susceptibility to cleavage is the reason why the 2'-hydroxyl is removed, at considerable metabolic expense, to make a more stable molecule (DNA) for information storage. Second, the 20-hydroxyl is the glue permitting RNA to readily fold: it is the only group on the entire phosphodiester backbone that can donate as well as accept hydrogen bonds (Figure 1.1). This hydrogen-bonding capacity plays an important role in stabilizing the large variety of structures adopted by RNA molecules.

DNA also differs from RNA in that the pyrimidine base with two keto groups is thymine rather than uracil. Chemically, the difference is minor: thymine is merely 5-methyluracil, and the additional methyl group does not change the overall structure, but does provide a recognition opportunity. However, like the removal of the sugar ring's 2'-hydroxyl group, the addition of this methyl group requires considerable metabolic expense. Mother Nature's presumed logic in this case is slightly more convoluted. Because cytosine is disturbingly readily deaminated to form uracil, the methyl group added to thymine allows repair enzymes to discriminate between pyrimidines that were intended to have two keto groups (i.e., thymine) and those that are the products of cytosine deamination and need to be removed (i.e., uracil).

The chemical repertoire of nucleic acids can be greatly expanded by modifications introduced after replication or transcription. Particularly for functional RNAs, species from all kingdoms of life have evolved a vast number of enzymes, comprising up to approximately 10% of coding genomes, that modify nucleobases after transcription (Chapter 14). At last count, about 100 different modified nucleosides have been identified in RNA. It is becoming clear that base modifications, in particular, are functionally significant: they are required for pre-mRNA splicing, they improve translational fidelity, and they increase RNA stability.

1.2.3 Canonical A- and B-form Helices

Despite the great variety of folds that RNA can adopt and the variation observed in DNA structure, the double helix remains the most common element of nucleic acid structure. The base pairing scheme first suggested by Watson and Crick is special in that the distances and angles between glycosidic bonds are constant, creating a regular structure that is independent of sequence, to a first approximation (Figure 1.3). Thus, nucleic acids with Watson– Crick base pairs adopt a deceptively simple structure: the double helix. When viewed in more detail however, the double helix is really a family of related conformations, by far the most common of which are the two forms termed A and B. Detailed descriptions of their anatomy can be found in many texts;1 only a basic reminder is included here.

The backbone conformations of A- and B-form helices differ primarily in the puckers of their sugar rings: C2'-endo for B-form, and C3'-endo for A-form (Figure 1.4). The pucker makes relatively little difference to the placement of the atoms within the sugar ring itself. However, the pucker determines the relative placement of the substituents, namely the base and the flanking phosphates, which are critical to the overall conformation of the duplex.

Duplex RNA is largely limited to the A-form, for two reasons: canonical B-form helices are sterically incompatible with the protruding 2'-hydroxyl groups of RNA, and the intrinsic sugar pucker preferences are affected by the 2'-substituent. Both A- and B-forms are readily accessible to DNA, although the B-form predominates...