Palindromes

Palindromes - words or phrases that can be read the same forwards or backwards.

Oh, no, Don Ho

• 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

• 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?

ATAT ?

NO

yes

C GA TT A

Make a sequence that is palidromic:

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 GTACGG 3’3’ GGCATG 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 GTACGGATACGTACC 3’3’ TATTTGGCAGCTGGCATG CC TATGCATGG 5’

Bacterial DNA:

5’ GCC GTACGGTATAAGCGC CC GTACGGATGAGGG 3’3’ CGGCATG CC ATATTCGCG GGCATG CCTACTCCC 5’

5’ ATAAACCGTCGACC GTACGGTATAAGCGC CC GTACGGATACGTACC 3’3’ TATTTGGCAGCTGGCATG CC ATATTCGCG GGCATG CC TATGCATGG 5’

Recombinant DNA:

Naming Restriction EnzymesHundreds 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 Haemophilusin: from the species influenzaeD: from strain D of this speciesIII: the 3rd enzyme from this organism that was isolated

BamHIB: from the genus Bacillusam: from the species amyloliquefaciensH; from strain H of this speciesI: 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