shows loops of anti-parallel -sheets inserted into the DNA minor groove (Section 10.6.2, Figure 10.16b)
in non-sequence specific binding. Second, a large nucleoprotein complex in bacteria is involved in inte-
gration of phage DNA into the host chromosome and is called an intasome. This has the phage DNA
wrapped as a left-handed supercoil around a complex of proteins including several copies of two DNA-
binding proteins, the phase-coded integrase and the IHP protein (integration host factor). The IHP binds to
a specific DNA sequence. These developments suggest that structural analysis of the bacterial chromosome
may well overtake that of eukaryotic systems.
Tremendous progress has been made in the characterisation of nucleic acid structure during the past
three decades. The ability to chemically synthesise oligodeoxynucleotides paved the way to a character-
isation of DNA structure in atomic detail. Following the focus of early studies on (a) the conformations of
the double helical families, (b) the sequence dependence of their structures, and (c) interactions between
DNA and small molecule drugs, attention has progressively shifted to new tertiary structural motifs, such
as junctions and four-stranded motifs, some of which were discussed in this chapter, and the interactions
between DNA and proteins. Considerable numbers of DNA structures are now deposited in public data bases
every year, many of them revealing surprises and shedding light on familiar but hitherto relatively poorly
characterised phenomena such as conformational transitions.^78 ‘Is there anything then that we still do not
know about the structure of DNA?’ the reader may ask. Of course, new exploitations of DNA’s chemical
and conformational versatility warrant structural characterisations. Supramolecular assemblies and nanos-
tructures constructed from DNA are one example.79,80Many questions regarding the interactions between
proteins and DNA and the important role that DNA plays in them remain to be answered. Suffice it to men-
tion replication and the need for understanding the nature of nucleotide incorporation by high-fidelity and
trans-lesion polymerases opposite native and lesioned DNA templates.^81 Also studies directed at a chemical
etiology of nucleic acid structure based on the creation and characterisation of dozens of artificial pairing
systems have created a further need for structural data.^82 With regard to RNA, the last decade has wit-
nessed an explosion in the analysis of its structure and function. In 1994, the only RNA molecule whose
70 Chapter 2
Figure 2.45 Schematic drawing to illustrate the gradual organisation of DNA into highly condensed chromatin.
(1) DNA fixed to the protein scaffold; (2) DNA complexed with all histones except H1; (3) aggregation
into a 100 Å fibre; (4) formation of ‘superbeads’and (5) contraction into a 600 Å knob
(Adapted from K.-P. Rindt and L. Nover, Biol. Zentralblat., 1980, 99 , 641–673. © (1980), with per-
mission from Elsevier)