Answer 1:
HindIII and HaeII are proteins known as
restriction enzymes. Restriction enzymes are
found naturally in bacterial cells and their
function is to cut up foreign DNA (such as viral
DNA) at a specific target sequence. These
target sequences are usually (although not
always) what is referred to as “palindromic”. A
palindrome is something that can be read the
same way both forwards and backwards. You may
have heard of palindromic words, such as
racecar, mom, or civic. These words can be
spelled the same way both forwards and
backwards. A genetic palindrome, however, is
slightly different. A molecule of DNA has a
specific orientation based on the chemical
structure of the molecules that make up DNA. A
molecule of DNA is composed of two strands, each
strand complementary to each other and running
in the opposite orientation. We refer to the
direction of the strand as either being 5’ 3’
or 3’ 5’ (this is determined by the direction
the sugar backbone of DNA is facing).
Complementation in DNA refers to what bases
are paired together in each of the two strands.
The four bases of DNA are A, T, G, and C, where
A and T pair together and G and C pair
together. Now that we know a bit about the
structure of DNA, we can discuss a genetic
palindrome. When we “read” DNA, we always read
in the 5’ 3’ direction, just like you would
always read left to right on a page. Let’s look
at the HindIII recognition sequence as an
example:
5’ AAGCTT 3’
3’ TTCGAA 5’
You may notice if you read the top strand in
the 5’ 3’ direction and the bottom strand in
the 5’  3’ direction that the sequences are
both AAGCTT. This is what is meant by a genetic
palindrome. A sequence that may be considered
palindromic as a word, such as AAGGAA, would not
be considered a genetic palindrome. If you look
at this sequence and its complement:
5’ AAGGAA 3’
3’ TTCCTT 5’
You can see that the 5’ 3’ sequence AAGGAA
is not the same as the 5’ 3’ sequence TTCCTT.
Therefore this is not a genetic palindrome. To
answer you second question, if you want to pick
a restriction enzyme that will cut your DNA into
to small pieces, you would pick a restriction
enzyme with a shorter recognition sequence (4
base pairs instead of 8 base pairs). The reason
for this is that the probability of a 4 base
pair sequence randomly showing up in DNA is much
more likely than an 8 base pair sequence
randomly showing up. For each position in the
DNA, there are 4 possible base pairs (because
there are 4 different DNA bases, A,T,G,C). If
we think about the possible permutations for a 4
base pair sequence it would be 4 possibilities
for the first base, 4 possibilities for the
second base, 4 possibilities for the third base,
and 4 possibilities for the fourth base.
Mathematically this would be:
4 X 4 X 4 X 4 = 44= 256 possible sequences
Only 1 of those sequences is the correct
recognition sequence, so there is a 1/256 chance
of finding our specific sequence in the
genome.
Now, if we were looking for a specific 8 base
pair sequence, the possible permutations for 8
bases would be:
4 x 4 x 4 x 4 x 4 x 4 x 4 x 4 = 48 = 65,536
possible sequences
Therefore there is a 1/65,536 chance of
finding that specific sequence. This is much
less probable so we will find many fewer
specific 8 base pair sequences than 4 base pair
sequences, which means the DNA will be cut less
if your recognition sequence is 8 base pairs
instead of 4 base pairs.
Hope that helped you!
