Palindromes

1. Palindromes

2. Palindromes - words or phrases that can be read the same forwards or backwards. Oh, no, Don Ho

3. 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.

4. 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

5. 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!

6. Palindromes In Molecular Biology a DNA sequence can be read the same in the 5’ -> 3’ direction on COMPLEMENTARY strands: 5’GCAATTGC3’ 3’CGTTAACG5’

7. 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

8. 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

9. Can you find the six-base palindromic sequence in this DNA fragment? 5’TATACGGTACCGATCGACAGTTGGTGCCGTTAATT3’ 5’TATACGGTACCGATCGACAGTTGGTGCCGTTAATT3’ 3’ATATGCCATGGCTAGCTGTGAACCACGGCAATTAA5’

10. 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.

11. A Transgenic organism is one that has received foreign DNA (usually a plasmid). How do we do this?

12. We can Cut DNA using Restriction Endonucleases (Restriction Enzymes) Restriction enzymes cut at specific recognition sites These sites are palindromic sequences!

13. How do Restriction Enzymes cut? 5’ CCGTACGG 3’ 5’ CCGTACGG 3’ 3’ GGCATGCC 5’ 5’ CC GTACGG 3’ 3’ GGCATG CC 5’ Sticky ends There are 4-base cutters, 6-base cutters, 8-base cutters, and others.

14. 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

15. 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’ Recombinant DNA: 5’ ATAAACCGTCGACC GTACGGTATAAGCGC CC GTACGGATACGTACC 3’ 3’ TATTTGGCAGCTGGCATG CC ATATTCGCG GGCATG CC TATGCATGG 5’

17. 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

18. EcoR1 (rasmol image) • From E. Coli Click here and open the rasmol folder Teachers shared-> Science -> Biotech -> Rasmol folder Select EcoR1