1. Figure : The reactions catalysed by the two different kinds of nuclease. (a) An exonuclease, which removes nucleotides from the end of a DNA molecule. (b) An endonuclease, which breaks internal phosphodiester bonds.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

2. Figure The reactions catalysed by different types of exonuclease
Figure  The reactions catalysed by different types of exonuclease. (a) Bal31, which removes nucleotides from both strands of a double-stranded molecule. (b) Exonuclease III, which removes nucleotides only from the 3¢ terminus (see p. •• for a description of the differences between the 3¢ and 5¢ termini of a polynucleotide).
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

3. Figure The reactions catalysed by different types of endonuclease
Figure  The reactions catalysed by different types of endonuclease. (a) S1 nuclease, which cleaves only single-stranded DNA, including single-stranded nicks in mainly double-stranded molecules. (b) DNase I, which cleaves both single- and double-stranded DNA. (c) A restriction endonuclease, which cleaves double-stranded DNA, but only at a limited number of sites.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

4. Figure The two reactions catalysed by DNA ligase
Figure  The two reactions catalysed by DNA ligase. (a) Repair of a discontinuity – a missing phosphodiester bond in one strand of a double-stranded molecule. (b) Joining two molecules together.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

5. Figure The reactions catalysed by DNA polymerases
Figure  The reactions catalysed by DNA polymerases. (a) The basic reaction: a new DNA strand is synthesized in the 5¢ to 3¢ direction. (b) DNA polymerase I, which initially fills in nicks but then continues to synthesize a new strand, degrading the existing one as it proceeds. (c) The Klenow fragment, which only fills in nicks. (d) Reverse transcriptase, which uses a template of RNA.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

6. Figure The reactions catalysed by DNA modifying enzymes
Figure The reactions catalysed by DNA modifying enzymes. (a) Alkaline phosphatase, which removes 5¢-phosphate groups. (b) Polynucleotide kinase, which attaches 5¢-phosphate groups. (c) Terminal deoxynucleotidyl transferase, which attaches deoxyribonucleotides to the 3¢ termini of polynucleotides in either (i) single-stranded or (ii) double-stranded molecules.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

7. Figure  The need for very precise cutting manipulations in a gene cloning experiment.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

8. Figure  The function of a restriction endonuclease in a bacterial cell: (a) phage DNA is cleaved, but (b) bacterial DNA is not.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

9. Figure  The ends produced by cleavage of DNA with different restriction endonucleases. (a) A blunt end produced by AluI. (b) A sticky end produced by EcoRI. (c) The same sticky ends produced by BamHI, BglII and Sau3A.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

10. Figure Restriction of the l DNA molecule
Figure  Restriction of the l DNA molecule. (a) The positions of the recognition sequences for BglII, BamHI and SalI. (b) The fragments produced by cleavage with each of these restriction endonucleases. The numbers are the fragment sizes in base pairs.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

11. Figure  Performing a restriction digest in the laboratory (see text for details).
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

12. Figure  (a) Standard electrophoresis does not separate DNA fragments of different sizes, whereas (b) gel electrophoresis does.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

13. Figure  Visualizing DNA bands in an agarose gel by EtBr staining and ultraviolet (UV) irradiation.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

14. Figure  The use of autoradiography to visualize radioactively labelled DNA in an agarose gel.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

15. Figure  Radioactive labelling: (a) the structure of a-32P-deoxyadenosine triphosphate ([a-32P]dATP); (b) labelling DNA by nick translation; (c) labelling DNA by end filling.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

16. Figure Estimation of the sizes of DNA fragments in an agarose gel
Figure  Estimation of the sizes of DNA fragments in an agarose gel. (a) A rough estimate of fragment size can be obtained by eye. (b) A more accurate measurement of fragment size is gained by using the mobilities of the HindIII–l fragments to construct a calibration curve; the sizes of the unknown fragments can then be determined from the distances they have migrated.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

17. Figure  Using a restriction map to work out which restriction endonucleases should be used to obtain DNA fragments containing individual genes.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

18. Figure Restriction mapping
Figure  Restriction mapping. This example shows how the positions of the XbaI, XhoI and KpnI sites on the l DNA molecule can be determined.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

19. Figure  Ligation: the final step in construction of a recombinant DNA molecule.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

20. Figure  The different joining reactions catalysed by DNA ligase: (a) ligation of blunt-ended molecules; (b) ligation of sticky-ended molecules.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

21. Figure  Linkers and their use: (a) the structure of a typical linker; (b) the attachment of linkers to a blunt-ended molecule.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

22. Figure A possible problem with the use of linkers
Figure  A possible problem with the use of linkers. Compare this situation with the desired result of BamHI restriction, as shown in Figure 4.21(b).
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

23. Figure Adaptors and the potential problem with their use
Figure  Adaptors and the potential problem with their use. (a) A typical adaptor. (b) Two adaptors could ligate to one another to produce a molecule similar to a linker, so that (c) after ligation of adaptors a blunt-ended molecule is still blunt-ended and the restriction step is still needed.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

24. Figure  The distinction between the 5¢ and 3¢ termini of a polynucleotide.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

25. Figure  The use of adaptors: (a) the actual structure of an adaptor, showing the modified 5¢-OH terminus; (b) conversion of blunt ends to sticky ends through the attachment of adaptors.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.

26. Figure  Homopolymer tailing: (a) synthesis of a homopolymer tail; (b) construction of a recombinant DNA molecule from a tailed vector plus tailed insert DNA; (c) repair of the recombinant DNA molecule. dCTP = 2¢-deoxycytidine 5¢-triphosphate.
Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A. Brown.