Repetitive DNA

Sequence
By,
Dr.M.Rajamehala, AP/BT
Vivekanandha College of Engineering for Women
 Analysis of DNA Sequences in Eukaryotic
Genomes
• The technique that is used to determine the sequence complexity of any
genome involves the denaturation and renaturation of DNA.
• DNA is denatured by heating which melts the H-bonds and renders the
DNA single-stranded.
• If the DNA is rapidly cooled, the DNA remains single-stranded.
• But if the DNA is allowed to cool slowly, sequences that are
complementary will find each other and eventually base pair again.
• The rate at which the DNA reanneals is a function of the species from
which the DNA was isolated.
• The Y-axis is the percent of the DNA that remains single
stranded.
• This is expressed as a ratio of the concentration of single-
stranded DNA (C) to the total concentration of the starting
DNA (Co).
• The X-axis is a log-scale of the product of the initial
concentration of DNA (in moles/liter) multiplied by length
of time the reaction proceeded (in seconds).
• The designation for this value is Cot and is called the "Cot"
value.
• The curve itself is called a "Cot" curve.
• As can be seen the curve is rather smooth which indicates
that reannealing occurs slowing but gradually over a period of
time.

• One particular value that is useful is Cot½ , the Cot value

where half of the DNA has reannealed.

• The shape of a "Cot" curve for a given species is a function of

two factors:
• the size or complexity of the genome; and

• the amount of repetitive DNA within the genome

• Genomes that contain these different
classes of sequences reanneal in a different
manner than genomes with only single copy
sequences.
• Instead of having a single smooth "Cot"
curve, three distinct curves can be seen,
each representing a different repetition
class.
• The first sequences to reanneal are the
highly repetitive sequences because so
many copies of them exist in the genome,
and because they have a low sequence
complexity.
• The second portion of the genome to
reanneal is the middle repetitive DNA, and
the final portion to reanneal is the single
copy DNA or unique DNA sequence.
EUKARYOTIC DNA SEQUENCES
APPLICATIONS
INTERSPERSED DNA REPEATS
 TRANSPOSONS
“a DNA sequence that is able to move or insert itself
at a new location in the genome.” The phenomenon of
movement of a transposon to a new site in the genome is
referred to as transposition.
Transposons in Humans:
Transposons in humans are in the form of repetitive
DNA which consists of sequences that are interspersed
within the entire human genome. These sequences are
transposable and can move to different locations within
the genome.
LTR Transposons
 LINES - Long Interspersed Nuclear Elements

sequences in the families are

about 1,000–7,000bp long
 SINES - Short Interspersed Nuclear Elements

the sequences in the families are 100–400 bp long

The SINEs are also transposons, but they do not

encode the enzymes they need for movement. They
can move, however, if those enzymes are supplied by
an active LINE transposon.
SINEs can be best described as non-autonomous
LINEs, because they have the structural features of
LINEs but do not encode their own reverse
transcriptase