10.7 Polymerases 409
10.7.1 DNA-Directed DNA Polymerases 409
10.7.2 DNA-Directed RNA Polymerases 410- 8Machines that Manipulate Duplex DNA 413
10.8.1 Helicases 413
10.8.2 DNA Pumps 413
10.8.3 DNA Topoisomerases 416
10.9 RNA–Protein Interactions and RNA-Mediated Assemblies 416
10.9.1 Single-Stranded RNA Recognition 417
10.9.2 Duplex RNA Recognition 417
10.9.3 Transfer RNA Synthetases 417
10.9.4 Small Interfering RNA Recognition 421
Web Resources 421
References 422
384 Chapter 10
In this chapter, we will review the known principles of protein–nucleic acid interactions and explain how
these molecules recognize and distinguish specific binding sites from all other potential binding sites in
the cell. We will also discuss how nucleic acids are manipulated by macromolecular machines when they
are packaged, copied, transcribed, translated, modified chemically, or transformed topologically.
10.1 Features of DNA Recognized by Proteins
DNA structures may be classified (Section 2.2) according to idealized representations. For instance, in the
B-form of duplex DNA (Figure 10.1 centre, see also Figure 2.17), the two polynucleotide strands wind
around each other in anti-parallel directions, with the bases pairing within planes that lie at roughly right
angles to the helical axis and the sugar–phosphate units forming repetitive linkages. To a first approxima-
tion, the striking helical character of the duplex results from the propensity of the bases to stack one on top
of the other while accommodating the inextensible but flexible sugar–phosphate backbone.^1 Both the
propensity for base stacking and Watson–Crick hydrogen bonding guide the successive pairing of bases in
a highly co-operative manner, so that DNA strands that are several thousand base pairs in length can self-
assemble spontaneously into stable duplexes. However, most other aspects of DNA assembly and recog-
nition in living systems require the orchestrated actions of proteins.
The most conspicuous features of DNA that can be recognized by proteins and other ligands, such as drugs
(see Chapter 9), are the major and minor grooves(Figure 10.1). These grooves arise from the helical
geometry of the strands. In the B-form, the major groove is wide and accessible, whilst the minor groove is
comparatively narrow. The grooves are hydrated canyons that can accommodate secondary structural elem-
ents of proteins. For instance, the major groove of the B-form is sufficiently wide (11.7 Å) and deep (8.8 Å)
to accommodate an -helixor two strands of a -ribbon. In contrast, the minor groove of relaxed, undis-
torted B-form DNA is narrower (5.7Å in width and 7.5Å in depth on average) and is thus less accessible
to secondary protein structures, although it is well suited to the insertion of a single peptide chain. The pro-
teins that recognize DNA bury parts of their surfaces within these exposed grooves, sometimes through
forces that deform the DNA shape, so as to optimise the complementarity of the molecular shapes.
Accessible within the major and minor grooves of the DNA are the hydrogen-bond donorsand
acceptorson the edges of the base pairs. A protein can contact these features directly or indirectly through
one or more water molecules. It is also apparent that the negatively charged phosphate backbone may be
a target for electrostatic recognition, and in stable complexes it is often matched by a positively charged
surface of the protein. Associated with these phosphate groups is a highly mobile layer of counter-ions that