Palindromes
Palindromes - words or
phrases that can be read the same
forwards or backwards.
Oh, no, Don Ho
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Pupils slip up
Rats live on no evil star
Do Geese see God?
Flee to me, remote elf
Dennis and Edna sinned
Go deliver a dare, vile dog
Wonton? Not now.
• A man, a plan, a cat, a canal: Panama
• A dog, a plan, a canal: Pagoda
• A man, a plan, a cat, a ham, a yak, a
yam, a hat, a canal: Panama
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Never odd or even
Tips spill, lips spit
Devil never even lived
Go hang a Salami, I’m a lasagna hog
So many dynamos
Sit on a potato pan, Otis
Mr. Owl ate my metal worm
• So, Ida, adios!
Palindromes In Molecular Biology
a DNA sequence can be read the
same in the 5’ -> 3’ direction on
COMPLEMENTARY strands:
5’GCAATTGC3’
3’CGTTAACG5’
How do you know if a sequence is
a palindrome?
ATTA?
NO
ATAT ?
yes
Make a sequence that is palidromic:
T
A C G T
A
Any 6 base sequence will occur once in every 46
bases of a genome. These sites exist randomly.
46 = 4096
A bacterial genome is 106 bases. A six-base
sequence will occur how many times?
10 6 / 4096 = 244 times
Can you find the six-base palindromic
sequence in this DNA fragment?
5’TATACGGTACCGATCGACAGTTGGTGCCGTTAATT3’
5’TATACGGTACCGATCGACAGTTGGTGCCGTTAATT3’
3’ATATGCCATGGCTAGCTGTGAACCACGGCAATTAA5’
Genetic Engineering involves Transferring
DNA from one organism to another.
Recombinant DNA is a piece of DNA that is
combined from 2 or more different organisms.
Example: a plasmid.
PLASMID - a circular piece of DNA found in bacteria
that is used as a vehicle (vector) for transferring genes
from one organism to another.
Example: Agrobacterium transfers a plasmid to plants. Humans
have engineered this plasmid to contain Bt toxin so the plant can
fight insects.
A Transgenic organism is one that has
received foreign DNA (usually a plasmid).
How do we do this?
We can Cut DNA using
Restriction Endonucleases (Restriction Enzymes)
Restriction enzymes cut at specific
recognition sites
These sites are
palindromic sequences!
How do Restriction Enzymes cut?
There are 4-base cutters, 6-base cutters, 8-base cutters, and
others.
5’ CCGTACGG 3’
5’ CCGTACGG 3’
3’ GGCATGCC 5’
5’ CC
3’ GGCATG
GTACGG 3’
CC 5’
Sticky ends
DNA from one organism can be cut so it has
sticky ends
DNA from another organism can be cut so it has
THE SAME sticky ends
The sticky ends can be pasted back together
because of base complementarity
Plant DNA:
5’ ATAAACCGTCGACC
3’ TATTTGGCAGCTGGCATG
GTACGGATACGTACC 3’
CC TATGCATGG 5’
Bacterial DNA:
5’ GCC
3’ CGGCATG
GTACGGTATAAGCGC CC
CC ATATTCGCG GGCATG
GTACGGATGAGGG 3’
CCTACTCCC 5’
Recombinant DNA:
5’ ATAAACCGTCGACC GTACGGTATAAGCGC CC GTACGGATACGTACC 3’
3’ TATTTGGCAGCTGGCATG CC ATATTCGCG GGCATG CC TATGCATGG 5’
Naming Restriction Enzymes
Hundreds of restriction enzymes have been isolated
from bacteria – each with its own specific
recognition sequence (these enzymes serve as a
crude immune system for bacteria)
HinDIII
H : from the genus Haemophilus
in: from the species influenzae
D: from strain D of this species
III: the 3rd enzyme from this organism that was isolated
BamHI
B: from the genus Bacillus
am: from the species amyloliquefaciens
H; from strain H of this species
I: the first enzyme from this organism that was isolated
EcoR1 (rasmol image)
• From E. Coli
Click here and open the rasmol
folder
Teachers shared-> Science ->
Biotech -> Rasmol folder
Select EcoR1