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This form of DNA was first synthesised in the laboratory and is thought not to exist

in vivo. The various forms of DNA serve to show that it is not a static molecule but

dynamic and constantly in flux, and may be coiled, bent or distorted at certain times.

Although RNA almost always exists as a single strand, it often contains sequences

within the same strand that are self-complementary, and which can therefore base-pair

if brought together by suitable folding of the molecule. A notable example is transfer

RNA (tRNA) which folds up to give a clover-leaf secondary structure (Fig. 5.6).

5.2.3 Separation of double-stranded DNA

The two antiparallel strands of DNA are held together only by the weak forces of

hydrogen bonding between complementary bases, and partly by hydrophobic inter-

actions between adjacent, stacked base pairs, termedbase-stacking. Little energy is

needed to separate a few base pairs, and so, at any instant, a few short stretches of

DNA will be opened up to the single-stranded conformation. However, such stretches

immediately pair up again at room temperature, so the molecule as a whole remains

predominantly double-stranded.

If, however, a DNA solution is heated to approximately 90C or above there will be

enough kinetic energy to denature the DNA completely, causing it to separate into

single strands. This is termeddenaturationand can be followed spectrophotometrically

by monitoring the absorbance of light at 260 nm. The stacked bases of double-stranded

DNA are less able to absorb light than the less constrained bases of single-stranded

molecules, and so the absorbance of DNA at 260 nm increases as the DNA becomes

denatured, a phenomenon known as thehyperchromic effect.

3  5 

C G

A T

T A

CG

A T

G C

C G

A T

AT

CG

TA

GC

A T

CG

3  5 

Sugar–phosphate

backbone

Base-pairs at centre

of double helix

Strands run in opposite

directions (antiparallel)

10 base-pairs per turn

Fig. 5.5The DNA double helix.

143 5.2 Structure of nucleic acids