Figure 12.1 The factory approach to large

scale DNA sequencing.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.2 Strategies for assembly of a

contiguous genome sequence: (a) the

shotgun approach; (b) the clone contig

approach.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.3 A schematic of the key steps in

the H. influenzae genome sequencing project.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.4 Using oligonucleotide

hybridization to close gaps in the H.

influenzae genome sequence.

Oligonucleotides 2 and 5 both hybridize to the

same l clone, indicating that contigs I and III

are adjacent. The gap between them can be

closed by sequencing the appropriate part of

the l clone.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.5 One problem with the shotgun

approach. An incorrect overlap is made

between two sequences that both terminate

within a repeated element. The result is that

a segment of the DNA molecule is absent

from the DNA sequence.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.6 Chromosome walking.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.7 Building up a clone contig by a

clone fingerprinting technique.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.8 Interspersed repeat element

PCR (IRE–PCR).

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.9 The basis to STS content

mapping.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.10 Typing a restriction site

polymorphism by PCR. In the middle lane the

PCR product gives two bands because it is cut

by treatment with the restriction enzyme. In

the right-hand lane there is just one band

because the template DNA lacks the

restriction site.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.11 Typing an STR by PCR. The PCR

product in the right-hand lane is slightly

longer than that in the middle lane, because

the template DNA from which it is generated

contains an additional CA unit.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.12 Two versions of an SNP.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.13 The principle behind the use of

a mapping reagent. It can be deduced that

markers 1 and 2 are relatively close because

they are present together on four DNA

fragments. In contrast, markers 3 and 4 must

be relatively far apart because they occur

together on just one fragment.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.14 Searching for open reading

frames. (a) Every DNA sequence has six open

reading frames, any one of which could

contain a gene. (b) The typical result of a

search for ORFs in a bacterial genome. The

arrows indicate the directions in which the

genes and spurious ORFs run.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.15 The consensus sequences for

the upstream and downstream exon–intron

boundaries of vertebrate introns. Py =

pyrimidine nucleotide (C or T), N = any

nucleotide. The arrows indicate the boundary

positions.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.16 Homology between two

sequences that share a common ancestor.

The two sequences have acquired mutations

during their evolutionary histories but their

sequence similarities indicate that they are

homologues.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.17 Gene knockout by

recombination between a chromosomal copy

of a gene and a deleted version carried by a

plasmid cloning vector.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.18 Microarray analysis. The

microarray shown here has been hybridized

to two different cDNA preparations, each

labelled with a fluorescent marker. The clones

which hybridize with the cDNAs are identified

by confocal microscopy.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.19 A DNA chip. A real chip would

carry many more oligonucleotides than those

shown here, and each oligonucleotide would

be 20–30 nucleotides in length.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.20 A single gene can give rise to

two proteins, with distinct functions, if the

initial translation product is modified in two

different ways by post-translational

processing.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.

Figure 12.21 Identification of a protein by

two-dimensional electrophoresis followed by

MALDI-TOF mass spectrometry.

Gene Cloning and DNA Analysis by T.A. Brown. © 2006 T.A.
Brown.