2. Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure / Benzer (1959) Finally found a mentor! Is there anything that we should physically or electronically be turning in as proof?

3. DNA Structure ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG... A class discussion on the tetranucleotide hypothesis might help.

4. DNA Structure ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG... TAGGCCACTGCCCAACCCTCCAT CATAAAACTTGGGCTTGGGAGG CAGAGCCTAACCTCTCTCACTCT AGACAGGTCTAAGATGATTGGG AACGAAATGAGCCGTCTCGACTT TTTCGCGAAGTGGCTAA... #1: Hello! #2: Complete description of our civilization

5. DNA Structure

6. SQ7. What would you expect to happen to the diffraction pattern if the helix shown in Fig. 8B-D were squashed, i.e. the helix were more tightly wound, more like a solenoid?

7. DNA Directionality & Palindromes …would like to go into deeper discussion about palindromic sequences

8. Palindromic Sequences What is it? What about with DNA? AGTTGA Backwards = forwards ROTATOR TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded SQ16. … why is AGTTGA not a DNA palindrome?

9. What is it? What about with DNA? AGTTGA Backwards = forwards ROTATOR DNA is redundant TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded Palindromic Sequences

10. What is it? What about with DNA? AGTTGA Backwards = forwards ROTATOR DNA is redundant TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA DNA is double stranded TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA DNA has direction (read 5’->3’) 5’- -3’ 3’- -5’ Palindromic Sequences

11. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ TA T G GC AT GC TA GC TTAAT TCATT AATTA AGTAA CG TA CG AT CG G T AT DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA The full biological roles of palindromic sequences is still a bit unclear to me SQ18. What is the relationship between a palindromic sequence and a potential hairpin structure?

12. TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ tRNA UA U G GC AU GC UA GC UUAAU UCAUU DNA: cruciform RNA: stem/loop Palindromic Sequences Palindromic sequences as structural RNA

13. recognizes GTGAGTT NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

14. NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA Palindromic Sequences Palindromic sequences as protein binding sites

15. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

16. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

17. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

18. recognizes GTGAGTT Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNNNNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

19. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

20. Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

21. Palindromes: Serve as binding sites for dimeric protein Palindromic Sequences Palindromic sequences as protein binding sites NNNNNNNNNNNNNNN NNNNNNNNNNNNN TTAATGTGAGTTAGCTCACTCATT AATGAGTGAGCTAACTCACATTAA

22. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites

23. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene Transcription factor RNA Polymerase Palindromic Sequences Palindromic sequences as protein binding sites RNA TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?

25. Probability How often A-A-A-A-A-A?

26. Probability How often 1-1-1-1-1-1?

27. Probability How often A-A-A-A-A-A?

28. Probability How often 1-1-1-1-1-1?

29. Probability How often 1-2-1-1-1-1?

30. Probability How often 1-1-1-1-1-1?

31. Probability How often 1-1-1-1-1-1?

32. Probability How often A-A-A-A-A-A?

33. Probability How often A-T-G-G-T-A?

34. Probability How often A-T-G-G-T-A? Counting

35. GTA..(8).. TAC 5’-GTA..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CAT..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN gene Transcription factor Palindromic Sequences Palindromic sequences as protein binding sites RNA TTAATGTGAGTTAGCTCACTCATT AATTACACTCAATCGAGTGAGTAA 5’- -3’ 3’- -5’ How many 12-nt palindromes would you expect at random in the genome of Anabaena variabilis?

36. Welcome to Molecular Biology Through Discovery Tuesday, 17 September 2013 DNA Structure / Benzer (1959)

37. Fermi Problems What is the question?

38. Fermi Problems Focus on what is being asked Estimate what can be estimated Set limits on what can't How many piano tuners are there in Chicago?

39. Fermi Problems Focus on what is being asked Estimate what can be estimated Set limits on what can't What fraction of the cells in your body are bacterial?

40. Fermi Problems What is the question? What do you need?

41. Benzer (1959) Hoping you will go over the experiment. It is so hard to visualize what goes down in a lab without actually laying on hands.

42. Wrinch (1936) – What is a Gene? Morgan T (1934) Nobel Lecture Drosophila chromosome What are genes?... There is no consensus of opinion amongst geneticists as to what the genes are – whether they are real or purely fictitious...

43. Benzer (1959)

45. Complementation Test

46. Benzer (1959) Complementation Test Phage E. coli

47. Benzer (1959)

48. Recomination Test Phage E. coli (Cis-Trans Test) Measure distance

49. Benzer (1959) Recomination Test Phage E. coli (Cis-Trans Test) Measure distance

50. Benzer (1959) Complementation Test? Phage E. coli Recombination Test?

51. Benzer (1959) What is a Gene? SQ2. Is there any reason to believe from classical genetics that genes have internal structure?

52. Benzer (1959) rII region of bacteriophage T4 What do you need for the experiment?

53. Benzer (1959) rII region of bacteriophage T4 mutation

54. Benzer (1959) experiment

60. Problem Set 5

62. Benzer (1959) rII region of bacteriophage T4

63. Benzer (1959) Determine distances between markers by Recombination

64. Benzer (1959) I still have trouble connecting recombination with the distance b/w genetic markers.

65. Benzer (1959) I still have trouble connecting recombination with the distance b/w genetic markers. Richard Twyman, University of Warwick

66. Benzer (1959) I still have trouble connecting recombination with the distance b/w genetic markers. Elizabeth Ellis University of Strathclyde

67. Goodbye from Molecular Biology Through Discovery Thursday, 19 September 2013 ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG ACTG... G-O-O-D-B-Y-E