254 Chapter 7
RNA sequences also contain sufficient information to fold themselves into specific shapes with distinct
chemical properties. Thus, RNA is unique amongst biopolymers in that it encodes genetic information,
provides structural scaffolding, recognizes and transports other molecules, and carries out many forms of
chemical catalysis in the cell.
7.1.1 Basic Structural Features of RNA
It is remarkable that the diverse capabilities of RNA, and many of its distinctions from DNA, stem from a
few simple chemical differences (Section 2.4). The most important distinction in RNA is the ribose sugar,
which bears a 2 -hydroxyl group (Figure 2.2). This simple modification confers unique conformational
features, specific hydration and electrostatic properties in the RNA polymer, and provides a set of hydrogen-
bond donors and acceptors along the RNA backbone. A second difference is the uracilnucleobase in RNA,
which lacks the major groove 5-methyl group of thymidine in DNA.
Primarily as a consequence of the ribose sugar conformation, RNA duplexes are more compact and have
geometrical features that differ from B-DNA. This is because ribose nucleotides tend to adopt the C3-endo
sugar pucker (Figure 2.11), which draws the flanking phosphates close together (5.9 Å), resulting in compact
A-form duplexesthat contain 11 base pairs per turn. The two grooves in A-form duplexes differ from those in
B-form DNA. The “major” groove of A-form helices is very narrow and deep, while the “minor” groove is wide
and flat (Figure 2.40). As a result, ligands employ a different set of strategies for recognizing RNA and DNA.
The major groove of RNA has a markedly negative electrostaticpotential (Figure 7.1), which tends to
draw small, positively charged ions and side-chains into the major groove.^1 In DNA, the minor groove
Figure 7.1 The electrostatic surface potential of an RNA helix. Red color indicates the region of greatest negative
potential, seen particularly in the RNA major groove. Blue color indicates region of most positive
electrostatic potential, and white approximates neutrality
(Reprinted from Ref. 1. © (1999), with permission from Macmillan Publications Ltd)