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chapter 23
Structure and Properties of DNA
23.5 Repetitive DNA Sequences
Cot
curves from various eukaryotic organisms show
the presence of repetitive sequences to varying de-
grees. Unique sequences represent genes, approximately
1 0 0 , 0 0 0
in the human genome, but constitute only
1
-
2
%
of the total genetic information in the human genome.
Some genes may be slightly repetitive if they are related
to
pseudogenes,
sequences of DNA that resemble genes
but that are no longer expressed.
About one-third of the human genome consists of se-
quences of bases that are repeated at least
2 0
times or
more.
Moderately repetitive
refers to sequences that usu-
ally contain between
1 0
and several hundred copies;
highly
repetitive
refers to sequences that are repeated thousands
or millions of times throughout the genome. The distinc-
tion among various classes of repetitive sequences is fre-
quently blurred and additional categories are sometimes
defined.
Repetitive sequences are also defined by the number of
base pairs in each repeated segment. Sequences that have
from 100 to 500 bp are referred to as SINES (short in-
terspersed repeated sequences) and sequences that have
several thousand base pairs are referred to as LINES (long
interspersed repeated sequences.) Thus, repetitive DNA
sequences can be described both by the length of the seg-
ment and the degree to which it is repeated.
Some examples of moderately repetitive sequences
are transposable elements including retroviruses, his-
tone genes that are repeated 30-40 times in the hu-
man genome, and genes coding for ribosomal RNAs
and transfer RNAs. Most of the moderately repetitive
genes do not code for proteins but serve other func-
tions in the cell.
Histones are involved in conden-
sation of DNA in chromosomes and both ribosomal
RNAs and transfer RNA are involved in protein synthe-
sis.
One special class of a highly repetitive sequence is
satellite DNA
which
consists
of
6 - 8
bp
(such
as
ATAAACT) and may account for 10-20% of the total
DNA. The term
satellite DNA
derives from the observation
that if fragmented DNA is centrifuged in a density gradi-
ent solution that separates DNA by weight, a small band
of DNA is observed that is separate from the bulk of the
DNA. The base composition of satellite DNA is AT-rich,
which explains why it separates from the rest of the DNA.
Satellite DNA is thought to play a structural role in
chromosomes. Certain satellite DNA sequences are con-
centrated near the centromeres of chromosomes, the site
where spindle fibers attach when sister chromatids are
separated. Other satellite DNA sequences are located in
telomeres, structures at the ends of chromosomes that play
a critical role in DNA replication (Chapter 24).
Another class of highly repetitive sequences is the
Alu
family,
which consist of about 300 bp that are repeated
millions of times throughout the genome. Any Alu se-
quence is at least 85% homologous in base sequence to
any other Alu sequence; hence, the family of genes has
been highly conserved. Each Alu sequence contains a re-
striction site that is recognized by the Alul restriction en-
zyme, from which the name of the family of sequences is
derived.
23.6 Degradation of DNA
Nucleases
A variety of enzymes break phosphodiester bonds in nu-
cleic acids;
deoxyribonucleases (DNases)
cleave DNA
and
ribonucleases (RNases)
cleave RNA. DNases usually
are specific for single- or double-stranded DNA although
some DNases can cleave both. DNases can act as
exonu-
cleases
in which they remove one nucleotide at a time from
either the 3' or 5' end of the strand. Other DNases function
as
endonucleases
and are specific for cleaving between
particular pairs of bases.
Restriction Enzymes
An important class of DNA endonucleases are
restric-
tion enzymes
(restriction endonucleases) that recognize
specific sequences of bases in DNA (a restriction site)
and make two cuts, one in each strand that generates
fragments of double-stranded DNA. Microorganisms use
their restriction enzymes to degrade any foreign DNA that
may enter the cell in the form of viruses, plasmids, or
naked DNA. Hundreds of different restriction enzymes
have been isolated from microorganisms; these enzymes
generally recognize sequences of four, six, eight, or rarely
more bases that have an axis of symmetry (Table 23-1).
Restriction sites that have an axis of symmetry are called
palindromes,
which means that the restriction site can be
rotated 180 degrees and the sequence of bases will remain
the same.
Restriction enzymes can cut DNA in either of two ways.
Each strand can be cleaved along the axis of symmetry
generating fragments of double-stranded DNA that have
blunt (flush) ends. Symmetrical cuts that are staggered
around the axis of symmetry generate fragments of double-
stranded DNA that have single-stranded cohesive ends
(Figure 23-11). Fragments of DNA with cohesive ends
