cases, the shape of the melting curve can be analysed to identify several components of defined compos-
ition melting in series.
Because of end-effects, short homo-oligomers melt at lower temperatures and with broader transitions
than longer homo-polymers. For example for poly(rA)npoly(rU)m, the octamer melts at 9°C, the unde-
camer at 20°C, and long oligomers at 49°C in the same sodium cacodylate buffer at pH 6.9. Consequently,
in the design of synthetic, self-complementary duplexes for crystallisation and X-ray structure determina-
tion, CG pairs are often places at the ends of hexamers and octamers to stop them ‘fraying’. Lastly, the
marked dependence of Tmon salt concentration is seen for DNA from Diplococcus pneumoniaewhose Tm
rises from 70°C at 0.01 M KCl to 87°C for 0.1 M KCl and to 98°C at 1.0 M KCl.
Data from many melting profiles have been analysed to give a stability matrixfor nearest neighbour
stacking (Table 2.9). This can be used to predict Tmfor a B-DNA polymer of known sequence with a gen-
eral accuracy of 2–3°C.^65
The converse of melting is the renaturationof two separated complementary strands to form a correctly
paired duplex. In practice, the melting curve for denaturation of DNA is reversible only for relatively short
oligomers, where the rate-determining process is the formation of a nucleation site of about 3 bp followed
by rapid zipping-up of the strands and where there is no competition from other impeding processes.
When solutions of unpaired, complementary large nucleic acids are incubated at 10–20°C below their
Tm, renaturation takes place over a period of time. For short DNAs of up to several hundred base pairs,
DNA and RNA Structure 65
Figure 2.43 Scheme illustrating the melting of AT-rich regions (colour) followed by mixed regions, then by
CG-rich regions (black) with rise in temperature (left→right)
Figure 2.42 Thermal denaturation of DNAs as a function of base composition (per cent GC) for three species of
bacteria: (a) Pneumococcus (38% GC). (b) E. coli (52% GC). (c) M. phlei (66% GC)
(Adapted from J. Marmur and P. Doty,Nature, 1959, 183 , 1427–1429.© (1959), with permission from
Macmillan publishers Ltd)